Allostery and Conformational Dynamics in cAMP-binding Acyltransferases

Mycobacteria harbor unique proteins that regulate protein lysine acylation in a cAMP-regulated manner. These lysine acyltransferases from Mycobacterium smegmatis (KATms) and Mycobacterium tuberculosis (KATmt) show distinctive biochemical properties in terms of cAMP binding affinity to the N-terminal cyclic nucleotide binding domain and allosteric activation of the C-terminal acyltransferase domain. Here we provide evidence for structural features in KATms that account for high affinity cAMP binding and elevated acyltransferase activity in the absence of cAMP. Structure-guided mutational analysis converted KATms from a cAMP-regulated to a cAMP-dependent acyltransferase and identified a unique asparagine residue in the acyltransferase domain of KATms that assists in the enzymatic reaction in the absence of a highly conserved glutamate residue seen in Gcn5-related N-acetyltransferase-like acyltransferases. Thus, we have identified mechanisms by which properties of similar proteins have diverged in two species of mycobacteria by modifications in amino acid sequence, which can dramatically alter the abundance of conformational states adopted by a protein.

Topological blocking in quantum quench dynamics

We study the nonequilibrium dynamics of quenching through a quantum critical point in topological systems, focusing on one of their defining features: ground-state degeneracies and associated topological sectors. We present the notion of ``topological blocking,'' experienced by the dynamics due to a mismatch in degeneracies between two phases, and we argue that the dynamic evolution of the quench depends strongly on the topological sector being probed. We demonstrate this interplay between quench and topology in models stemming from two extensively studied systems, the transverse Ising chain and the Kitaev honeycomb model. Through nonlocal maps of each of these systems, we effectively study spinless fermionic p-wave paired topological superconductors. Confining the systems to ring and toroidal geometries, respectively, enables us to cleanly address degeneracies, subtle issues of fermion occupation and parity, and mismatches between topological sectors. We show that various features of the quench, which are related to Kibble-Zurek physics, are sensitive to the topological sector being probed, in particular, the overlap between the time-evolved initial ground state and an appropriate low-energy state of the final Hamiltonian. While most of our study is confined to translationally invariant systems, where momentum is a convenient quantum number, we briefly consider the effect of disorder and illustrate how this can influence the quench in a qualitatively different way depending on the topological sector considered.

Fish distribution dynamics in the Aghanashini estuary of Uttara Kannada, west coast of India

Fish diversity (77 species) in the Aghanashini River estuary of the Indian west coast is linked to variable salinity conditions and zones I, II and III for high, medium and low salinity respectively. Zone I, the junction between Arabian Sea and the estuary, had all species in yearly succession due to freshwater conditions in monsoon to high salinity in pre-monsoon. The medium (zone II) and low (zone III) salinity mid and upstream portions had maximum of 67 and 39 fish species respectively. Maintenance of natural salinity regimes in estuary, among other ecological factors, is critical for its fish diversity.

Conducting polymer-carbon black nanocomposite sensor for volatile organic compounds and correlating sensor response by molecular dynamics

Volatile organic compounds (VOCs) are present in our every day used products such as plastics, cosmetics, air fresheners, paint, etc. The determination of amount of VOC present in atmosphere can be carried out via various sensors. In this work a nanocomposite of a novel thiophene based conducting polymer and carbon black is used as a volatile organic compound sensor. The fabricated 2 lead chemiresistor sensor was tested for vapours of toluene, acetone, cylcohexane, and carbon tetrachloride. The sensor responds to all the vapours, however, exhibit maximum response to toluene vapours. The sensor was evaluated for various concentrations of toluene. The lower limit of detection of the sensor is 15 +/- 10 ppm. The study of the effect of humidity on senor response to toluene showed that the response decreases at higher humidity conditions. The surface morphology of the nanocomposite was characterized by scanning electron microscopy. Diffuse reflectance spectroscopy was used to investigate the absorption of vapours by the nanocomposite film. Contact angle measurements were used to present the effect of water vapour on the toluene response of nanocomposite film. Solubility parameter of the conducting polymer is predicted by molecular dynamics. The sensing behaviour of the conducting polymer is correlated with solubility parameter of the polymer. Dispersion interaction of conducting polymer with toluene is believed to be the reason for the selective response towards toluene. (C) 2014 Elsevier B.V. All rights reserved.

Molecular Dynamics Study of Phonon Screening in Graphene

Phonon interaction with electrons or phonons or with structural defects result in a phonon mode conversion. The mode conversion is governed by the frequency wave-vector dispersion relation. The control over phonon mode or the screening of phonon in graphene is studied using the propagation of amplitude modulated phonon wave-packet. Control over phonon properties like frequency and velocity opens up several wave guiding, energy transport and thermo-electric applications of graphene. One way to achieve this control is with the introduction of nano-structured scattering in the phonon path. Atomistic model of thermal energy transport is developed which is applicable to devices consisting of source, channel and drain parts. Longitudinal acoustic phonon mode is excited from one end of the device. Molecular dynamics based time integration is adopted for the propagation of excited phonon to the other end of the device. The amount of energy transfer is estimated from the relative change of kinetic energy. Increase in the phonon frequency decreases the kinetic energy transmission linearly in the frequency band of interest. Further reduction in transmission is observed with the tuning of channel height of the device by increasing the boundary scattering. Phonon mode selective transmission control have potential application in thermal insulation or thermo-electric application or photo-thermal amplification.

Diffusing-wave spectroscopy in an inhomogeneous object: Local viscoelastic spectra from ultrasound-assisted measurement of correlation decay arising from the ultrasound focal volume

We demonstrate diffusing-wave spectroscopy (DWS) in a localized region of a viscoelastically inhomogeneous object by measurement of the intensity autocorrelation g(2)(tau)] that captures only the decay introduced by the temperature-induced Brownian motion in the region. The region is roughly specified by the focal volume of an ultrasound transducer which introduces region specific mechanical vibration owing to insonification. Essential characteristics of the localized non-Markovian dynamics are contained in the decay of the modulation depth M(tau)], introduced by the ultrasound forcing in the focal volume selected, on g(2)(tau). The modulation depth M(tau(i)) at any delay time tau(i) can be measured by short-time Fourier transform of g(2)(tau) and measurement of the magnitude of the spectrum at the ultrasound drive frequency. By following the established theoretical framework of DWS, we are able to connect the decay in M(tau) to the mean-squared displacement (MSD) of scattering centers and the MSD to G*(omega), the complex viscoelastic spectrum. A two-region composite polyvinyl alcohol phantom with different viscoelastic properties is selected for demonstrating local DWS-based recovery of G*(omega) corresponding to these regions from the measured region specific M(tau(i))vs tau(i). The ultrasound-assisted measurement of MSD is verified by simulating, using a generalized Langevin equation (GLE), the dynamics of the particles in the region selected as well as by the usual DWS experiment without the ultrasound. It is shown that whereas the MSD obtained by solving the GLE without the ultrasound forcing agreed with its experimental counterpart covering small and large values of tau, the match was good only in the initial transients in regard to experimental measurements with ultrasound.

A molecular dynamics study of ambient and high pressure phases of silica: Structure and enthalpy variation with molar volume

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, alpha-PbO2-type, and pyrite-type for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase. (C) 2014 AIP Publishing LLC.

Kinetics of phase separation in polymer mixtures: A molecular dynamics study

We present detailed results from a molecular dynamics (MD) simulation of phase-separation kinetics in polymer mixtures. Our MD simulations naturally incorporate hydrodynamic effects. We find that polymeric phase separation (with dynamically symmetric components) is in the same universality class as segregation of simple fluids: the degree of polymerization only slows down the segregation kinetics. For d = 2 polymeric fluids, the domain growth law is L(t) similar to t(phi) with phi showing a crossover from 1/3 -> 1/2 -> 2/3. For d = 3 polymeric fluids, we see the crossover phi = 1/3 -> 1. Our MD simulations do not yet access the inertial hydrodynamic regime (with L similar to t(2/3)) of phase separation in 3-d fluids. (C) 2014 AIP Publishing LLC.

Current kinematics and dynamics of Africa and the East African Rift System

Although the East African Rift System (EARS) is an archetype continental rift, the forces driving its evolution remain debated. Some contend buoyancy forces arising from gravitational potential energy (GPE) gradients within the lithosphere drive rifting. Others argue for a major role of the diverging mantle flow associated with the African Superplume. Here we quantify the forces driving present-day continental rifting in East Africa by (1) solving the depth averaged 3-D force balance equations for 3-D deviatoric stress associated with GPE, (2) inverting for a stress field boundary condition that we interpret as originating from large-scale mantle tractions, (3) calculating dynamic velocities due to lithospheric buoyancy forces, lateral viscosity variations, and velocity boundary conditions, and (4) calculating dynamic velocities that result from the stress response of horizontal mantle tractions acting on a viscous lithosphere in Africa and surroundings. We find deviatoric stress associated with lithospheric GPE gradients are similar to 8-20 MPa in EARS, and the minimum deviatoric stress resulting from basal shear is similar to 1.6 MPa along the EARS. Our dynamic velocity calculations confirm that a force contribution from GPE gradients alone is sufficient to drive Nubia-Somalia divergence and that additional forcing from horizontal mantle tractions overestimates surface kinematics. Stresses from GPE gradients appear sufficient to sustain present-day rifting in East Africa; however, they are lower than the vertically integrated strength of the lithosphere along most of the EARS. This indicates additional processes are required to initiate rupture of continental lithosphere, but once it is initiated, lithospheric buoyancy forces are enough to maintain rifting.

Orientation, Size, and Temperature Dependent Ductile Brittle Transition in NiAl Nanowire under Tensile Loading - A Molecular Dynamics Study

In the present paper, thermo-mechanical response of B2-NiAl nanowire along the < 100 >, < 110 >, and < 111 > orientations has been studied using molecular dynamics simulations. Nanowire with cross-sectional dimensions of similar to 20x20 angstrom(2), similar to 25x25 angstrom(2), and similar to 30x30 angstrom(2) and temperature range of 10 K-900 K has been considered. A Combined effect of size, orientation, and temperature on the stress-strain behavior under uniaxial tensile loading has been presented. It has been observed that < 111 > oriented NiAl nanowire that is energetically most stable gives highest yield stress which further reduces with < 110 > and < 100 > orientations. A remarkable ductile brittle transition (DBT) with an increase in temperature has also been reported for all the orientations considered in the present study. The DBT observed for the nanowire has also been compared with the reported DBT of bulk B2-NiAl obtained from experiments. Alternate technique has also been proposed to increase the toughness of a given material especially at lower temperature regions, i.e. below DBT.

Memory-induced anomalous dynamics in a minimal random walk model

A discrete-time dynamics of a non-Markovian random walker is analyzed using a minimal model where memory of the past drives the present dynamics. In recent work N. Kumar et al., Phys. Rev. E 82, 021101 (2010)] we proposed a model that exhibits asymptotic superdiffusion, normal diffusion, and subdiffusion with the sweep of a single parameter. Here we propose an even simpler model, with minimal options for the walker: either move forward or stay at rest. We show that this model can also give rise to diffusive, subdiffusive, and superdiffusive dynamics at long times as a single parameter is varied. We show that in order to have subdiffusive dynamics, the memory of the rest states must be perfectly correlated with the present dynamics. We show explicitly that if this condition is not satisfied in a unidirectional walk, the dynamics is only either diffusive or superdiffusive (but not subdiffusive) at long times.

Oscillation dynamics of sessile droplets subjected to substrate vibration

Sessile droplets on a vibrating substrate are investigated focusing on axisymmetric oscillations with pinned contact line. Proper orthogonal decomposition is employed to identify the different modes of droplet shape oscillation and quantitatively assess the droplet oscillation and spectral response. We offer the first experimental evidence for the analogy of an oscillating sessile droplet with a non-linear spring mass damper system. The qualitative and quantitative agreement of amplitude response and phase response curves and limit cycles of the model dynamical system with that observed experimentally suggest that the bulk oscillations in the fundamental mode of a sessile droplet can be very well modeled by a Duffing oscillator with a hard spring, especially near the resonance. The red shift of the resonance peak with an increase in the glycerol concentration is clearly evidenced by both the experimental and predicted amplitude response curves. The influence of various operational parameters such as excitation frequency and amplitude and fluid properties on the droplet oscillation characteristics is adequately captured by the model. (C) 2014 Elsevier Ltd. All rights reserved.

Impact dynamics of high Weber number drops on chemically modified metallic surfaces

Hydrophobic/superhydrophobic metallic surfaces prepared via chemical treatment are encountered in many industrial scenarios involving the impingement of spray droplets. The effectiveness of such surfaces is understood through the analysis of droplet impact experiments. In the present study, three target surfaces with aluminum (Al-6061) as base material-acid-etched, Octadecyl Trichloro Silane (OTS) coated, and acid-etched plus OTS-coated-were prepared. Experiments on the impact of inertia dominated water drops on these chemically modified aluminum surfaces were carried out with the objective to highlight the effect of chemical treatment on the target surfaces on key sub-processes occurring in drop impact phenomenon. High speed videos of the entire drop impact dynamics were captured at three Weber number (We) conditions representative of high We (We > 200) regime. During the early stages of drop spreading, the drop impact resulted in ejection of secondary droplets from spreading drop front on the etched surfaces resembling prompt splash on rough surfaces whereas no such splashing was observable on untreated aluminum surface. Prominent development of undulations (fingers) were observed at the rim of drop spreading on the etched surfaces; between the etched surfaces the OTS-coated surface showed a subdued development of fingers than the uncoated surface. The impacted drops showed intense receding on OTS-coated surfaces whereas on the etched surface a highly irregular receding, with drop liquid sticking to the surface, was observed. Quantitative analyses were performed to reveal the effect of target surface characteristics on drop impact parameters such as temporal variation of spread factor of drop lamella, temporal variation of average finger length during spreading phase, maximum drop spreading, time taken to attain maximum spreading, sensitivity of maximum spreading to We, number of fingers at maximum spreading, and average receding velocity of drop lamella. Existing models for maximum drop spreading showed reasonably good agreement with the experimental measurements on the target surfaces except the acid-etched surface. (C) 2014 Elsevier B.V. All rights reserved.

Study Of Lattice Dynamics In Yttrium Doped NdMnO3 Using Raman Spectroscopy

A systematic study of Raman spectra on Yttrium doped NdMnO3 polycrystalline samples was undertaken to understand the lattice dynamics in this compound. Raman active phonons were analyzed and the observed peak were assigned to elucidate various phonon modes in the range (200 - 800) cm(-1). It was observed that at 325 cm(-1) phonon frequency shifts upward as much as upto 4 % with increase in Yttrium content. Lattice distortions manifest themselves by frequency shifts in both bending and tilt modes of MnO6 octahedra, resulting in increase of Raman band line-widths.

De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.