Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Effective Q Criterion for Disk Stability in an External Potential

The standard Q criterion (with Q > 1) describes the stability against local, axisymmetric perturbations in a disk supported by rotation and random motion. Most astrophysical disks, however, are under the influence of an external gravitational potential, which can significantly affect their stability. A typical example is a galactic disk embedded in a dark matter halo. Here, we do a linear perturbation analysis for a disk in an external potential and obtain a generalized dispersion relation and the effective stability criterion. An external potential, such as that due to the dark matter halo concentric with the disk, contributes to the unperturbed rotational field and significantly increases its stability. We obtain the values for the effective Q parameter for the Milky Way and for a low surface brightness galaxy, UGC 7321. We find that in each case the stellar disk by itself is barely stable and it is the dark matter halo that stabilizes the disk against local, axisymmetric gravitational instabilities. Thus, the dark matter halo is necessary to ensure local disk stability. This result has been largely missed so far because in practice the Q parameter for a galactic disk is obtained using the observed rotational field that already includes the effect of the halo

EFFECTIVE Q CRITERION FOR DISK STABILITY IN AN EXTERNAL POTENTIAL

standard Q criterion (with Q > 1) describes the stability against local, axisymmetric perturbations in a disk supported by rotation and random motion. Most astrophysical disks, however, are under the influence of an external gravitational potential, which can significantly affect their stability. A typical example is a galactic disk embedded in a dark matter halo. Here, we do a linear perturbation analysis for a disk in an external potential and obtain a generalized dispersion relation and the effective stability criterion. An external potential, such as that due to the dark matter halo concentric with the disk, contributes to the unperturbed rotational field and significantly increases its stability. We obtain the values for the effective Q parameter for the Milky Way and for a low surface brightness galaxy, UGC 7321. We find that in each case the stellar disk by itself is barely stable and it is the dark matter halo that stabilizes the disk against local, axisymmetric gravitational instabilities. Thus, the dark matter halo is necessary to ensure local disk stability. This result has been largely missed so far because in practice the Q parameter for a galactic disk is obtained using the observed rotational field that already includes the effect of the halo.

Transition in vortex breakdown modes in a coaxial isothermal unconfined swirling jet

This paper reports first observations of transition in recirculation pattern from an open-bubble type axisymmetric vortex breakdown to partially open bubble mode through an intermediate, critical regime of conical sheet formation in an unconfined, co-axial isothermal swirling flow. This time-mean transition is studied for two distinct flow modes which are characterized based on the modified Rossby number (Ro(m)), i.e., Ro(m) <= 1 and Ro(m) > 1. Flow modes with Ro(m) <= 1 are observed to first undergo cone-type breakdown and then to partially open bubble state as the geometric swirl number (S-G) is increased by similar to 20% and similar to 40%, respectively, from the baseline open-bubble state. However, the flow modes with Ro(m) > 1 fail to undergo such sequential transition. This distinct behavior is explained based on the physical significance associated with Ro(m) and the swirl momentum factor (xi). In essence, xi represents the ratio of angular momentum distributed across the flow structure to that distributed from central axis to the edge of the vortex core. It is observed that xi increases by similar to 100% in the critical swirl number band where conical breakdown occurs as compared to its magnitude in the S-G regime where open bubble state is seen. This results from the fact that flow modes with Ro(m) <= 1 are dominated by radial pressure gradient due to swirl/rotational effect when compared to radial pressure deficit arising from entrainment (due to the presence of co-stream). Consequently, the imparted swirl tends to penetrate easily towards the central axis causing it to spread laterally and finally undergo conical sheet breakdown. However, the flow modes with Ro(m) > 1 are dominated by pressure deficit due to entrainment effect. This blocks the radial inward penetration of imparted angular momentum thus preventing the lateral spread of these flow modes. As such these structures fail to undergo cone mode of vortex breakdown which is substantiated by a mere 30%-40% rise in xi in the critical swirl number range. (C) 2014 AIP Publishing LLC.

Isotropic finite volume discretization

Finite volume methods traditionally employ dimension by dimension extension of the one-dimensional reconstruction and averaging procedures to achieve spatial discretization of the governing partial differential equations on a structured Cartesian mesh in multiple dimensions. This simple approach based on tensor product stencils introduces an undesirable grid orientation dependence in the computed solution. The resulting anisotropic errors lead to a disparity in the calculations that is most prominent between directions parallel and diagonal to the grid lines. In this work we develop isotropic finite volume discretization schemes which minimize such grid orientation effects in multidimensional calculations by eliminating the directional bias in the lowest order term in the truncation error. Explicit isotropic expressions that relate the cell face averaged line and surface integrals of a function and its derivatives to the given cell area and volume averages are derived in two and three dimensions, respectively. It is found that a family of isotropic approximations with a free parameter can be derived by combining isotropic schemes based on next-nearest and next-next-nearest neighbors in three dimensions. Use of these isotropic expressions alone in a standard finite volume framework, however, is found to be insufficient in enforcing rotational invariance when the flux vector is nonlinear and/or spatially non-uniform. The rotationally invariant terms which lead to a loss of isotropy in such cases are explicitly identified and recast in a differential form. Various forms of flux correction terms which allow for a full recovery of rotational invariance in the lowest order truncation error terms, while preserving the formal order of accuracy and discrete conservation of the original finite volume method, are developed. Numerical tests in two and three dimensions attest the superior directional attributes of the proposed isotropic finite volume method. Prominent anisotropic errors, such as spurious asymmetric distortions on a circular reaction-diffusion wave that feature in the conventional finite volume implementation are effectively suppressed through isotropic finite volume discretization. Furthermore, for a given spatial resolution, a striking improvement in the prediction of kinetic energy decay rate corresponding to a general two-dimensional incompressible flow field is observed with the use of an isotropic finite volume method instead of the conventional discretization. (C) 2014 Elsevier Inc. All rights reserved.

Molecular topology of three ring nematogens from C-13-H-1 dipolar couplings

Molecules in their liquid crystalline phase undergo rotational motion about the long axis of the molecule and the shape adopted by the rotating molecule plays an important role in influencing the mesophase morphology. In this context, obtaining the topology and the relative orientation of the different sub-units are important steps. For studying the liquid crystalline phase, C-13 NMR spectroscopy is a convenient method and for certain specifically designed nematogens, 2-dimensional separated local field (2D-SLF) NMR spectroscopy provides a particularly simple and straightforward means of arriving at the molecular topology. We demonstrate this approach on two three ring based nematogens designed with a phenyl or a thiophene ring at one of the termini. From the C-13-H-1 dipolar couplings of the terminal carbon obtained using the 2D-SLF NMR technique, the order parameter of the local symmetry axis of the terminal phenyl ring as well as of the long molecular axis could be easily estimated. For the thiophene nematogen, the lack of symmetry of the thiophene moiety necessitates some additional computational steps. The results indicate that the thiophene unit has its local ordering axis oriented away from the long molecular axis by a small angle, consistent with a bent structure expected in view of the thiophene geometry. The experiment also demonstrates the ability of 2D-SLF NMR to provide high resolution spectra by separation of several overlapped resonances in terms of their C-13-H-1 dipolar couplings. The results are consistent with a rod-like topology of the core of the investigated mesogens. The investigation demonstrates the potential of 2D-SLF NMR C-13 spectroscopy for obtaining atomistic level information and its utility for topological studies of different mesogens.

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.

Dynamical facilitation governs glassy dynamics in suspensions of colloidal ellipsoids

One of the greatest challenges in contemporary condensed matter physics is to ascertain whether the formation of glasses from liquids is fundamentally thermodynamic or dynamic in origin. Although the thermodynamic paradigm has dominated theoretical research for decades, the purely kinetic perspective of the dynamical facilitation (DF) theory has attained prominence in recent times. In particular, recent experiments and simulations have highlighted the importance of facilitation using simple model systems composed of spherical particles. However, an overwhelming majority of liquids possess anisotropy in particle shape and interactions, and it is therefore imperative to examine facilitation in complex glass formers. Here, we apply the DF theory to systems with orientational degrees of freedom as well as anisotropic attractive interactions. By analyzing data from experiments on colloidal ellipsoids, we show that facilitation plays a pivotal role in translational as well as orientational relaxation. Furthermore, we demonstrate that the introduction of attractive interactions leads to spatial decoupling of translational and rotational facilitation, which subsequently results in the decoupling of dynamical heterogeneities. Most strikingly, the DF theory can predict the existence of reentrant glass transitions based on the statistics of localized dynamical events, called excitations, whose duration is substantially smaller than the structural relaxation time. Our findings pave the way for systematically testing the DF approach in complex glass formers and also establish the significance of facilitation in governing structural relaxation in supercooled liquids.

The role of buoyancy in polarity reversals of the geodynamo

We investigate polarity reversals in the geodynamo using a rotating, convection-driven dynamo model. As the flow in rapidly rotating convection is dominated by columns aligned with the axis of rotation, the focus is on the dynamics of columnar vortices. By studying the growth of a seed magnetic field to a stable axial dipole field, we show that the magnetic field acts in ways that significantly enhance the relative helicity between cyclonic and anticyclonic vortices. This flow asymmetry is the hallmark of a dipolar dynamo. Strong buoyancy, on the other hand, offsets the effect of the magnetic field, establishing parity between positive and negative vortices. As the dipole field is deprived of the helicity required to support itself, the dynamo is pushed into a reversing state. This is a likely regime for polarity reversals in the Earth's core. The integral lengthscale at which buoyancy injects energy is not significantly different from the convective flow lengthscale, which implies that buoyancy does not feed vortices at the small scales where non-linear inertia is present. The lengthscale at which the Lorentz force acts in the reversing dynamo is small, which may allow the passive presence of non-linear inertia in the small scales.

Structure, dynamics and thermodynamics of single-file water under confinement: effects of polarizability of water molecules

Various structural, dynamic and thermodynamic properties of water molecules confined in single-wall carbon nanotubes (CNTs) are investigated using both polarizable and non-polarizable water models. The inclusion of polarizability quantitatively affects the nature of hydrogen bonding, which governs many properties of confined water molecules. Polarizable water leads to tighter hydrogen bonding and makes the distance between neighboring water molecules shorter than that for non-polarizable water. Stronger hydrogen bonding also decreases the rotational entropy and makes the diffusion constant smaller than in TIP3P and TIP3PM water models. The reorientational dynamics of the water molecules is governed by a jump mechanism, the barrier for the jump being highest for the polarizable water model. Our results highlight the role of polarizability in governing the dynamics of confined water and demonstrate that the inclusion of polarizability is necessary to obtain agreement with the results of ab initio simulations for the distributions of waiting and jump times. The SPC/E water model is found to predict various water properties in close agreement with the results of polarizable water models with much lower computational costs.

Formation Flying with Nonlinear Partial Integrated Guidance and Control

Using the dynamic inversion philosophy, a nonlinear partial integrated guidance and control approach is presented in this paper for formation flying. It is based on the evolving philosophy of integrated guidance and control. However, it also retains the advantages of the conventional guidance then control philosophy by retaining the timescale separation between translational and rotational dynamics explicitly. Simulation studies demonstrate that the proposed technique is effective in bringing the vehicles into formation quickly and maintaining the formation.

Antioxidant activity and electrochemical elucidation of the enigmatic redox behavior of curcumin and its structurally modified analogues

Here, we report studies on the antioxidant activity and redox behavior of curcumin and its structurally modified synthetic analogues. We have synthesized a number of analogues of curcumin which abrogate its keto-enol tautomerism or substitute the methylene group at the centre of its heptadione moiety implicated in the hydride transfer and studied their redox property. From cyclic voltammetric studies, it is demonstrated that H-atom transfer from CH2 group at the center of the heptadione link also plays an important role in the antioxidant properties of curcumin along with that of its phenolic -OH group. In addition, we also show that the conversion of 1, 3-dicarbonyl moiety of curcumin to an isosteric heterocycle as in pyrazole curcumin, which decreases its rotational freedom, leads to an improvement of its redox properties as well as its antioxidant activity. (C) 2014 Elsevier Ltd. All rights reserved.

A strongly coupled anisotropic fluid from dilaton driven holography

We consider a system consisting of 5 dimensional gravity with a negative cosmological constant coupled to a massless scalar, the dilaton. We construct a black brane solution which arises when the dilaton satisfies linearly varying boundary conditions in the asymptotically AdS(5) region. The geometry of this black brane breaks rotational symmetry while preserving translational invariance and corresponds to an anisotropic phase of the system. Close to extremality, where the anisotropy is big compared to the temperature, some components of the viscosity tensor become parametrically small compared to the entropy density. We study the quasi normal modes in considerable detail and find no instability close to extremality. We also obtain the equations for fluid mechanics for an anisotropic driven system in general, working upto first order in the derivative expansion for the stress tensor, and identify additional transport coefficients which appear in the constitutive relation. For the fluid of interest we find that the parametrically small viscosity can result in a very small force of friction, when the fluid is enclosed between appropriately oriented parallel plates moving with a relative velocity.

A micropolar peridynamic theory in linear elasticity

A state-based micropolar peridynamic theory for linear elastic solids is proposed. The main motivation is to introduce additional micro-rotational degrees of freedom to each material point and thus naturally bring in the physically relevant material length scale parameters into peridynamics. Non-ordinary type modeling via constitutive correspondence is adopted here to define the micropolar peridynamic material. Along with a general three dimensional model, homogenized one dimensional Timoshenko type beam models for both the proposed micropolar and the standard non-polar peridynamic variants are derived. The efficacy of the proposed models in analyzing continua with length scale effects is established via numerical simulations of a few beam and plane-stress problems. (C) 2015 Elsevier Ltd. All rights reserved.

Acoustic response of vortex breakdown modes in a coaxial isothermal unconfined swirling jet

The present experimental work is concerned with the study of amplitude dependent acoustic response of an isothermal coaxial swirling jet. The excitation amplitude is increased in five distinct steps at the burner's Helmholtz resonator mode (i.e., 100 Hz). Two flow states are compared, namely, sub-critical and super-critical vortex breakdown (VB) that occur before and after the critical conical sheet breakdown, respectively. The geometric swirl number is varied in the range 2.14-4.03. Under the influence of external pulsing, global response characteristics are studied based on the topological changes observed in time-averaged 2D flow field. These are obtained from high resolution 2D PIV (particle image velocimetry) in the longitudinal-mid plane. PIV results also illustrate the changes in the normalized vortex core coordinates (r(vcc)/(r(vcc))(0) (Hz), y(vcc)/(y(vcc))(0) (Hz)) of internal recirculation zone (IRZ). A strong forced response is observed at 100 Hz (excitation frequency) in the convectively unstable region which get amplified based on the magnitude of external forcing. The radial extent of this forced response region at a given excitation amplitude is represented by the acoustic response region (b). The topological placement of the responsive convectively unstable region is a function of both the intensity of imparted swirl (characterized by swirl number) and forcing amplitude. It is observed that for sub-critical VB mode, an increase in the excitation amplitude till a critical value shifts the vortex core centre (particularly, the vortex core moves downstream and radially outwards) leading to drastic fanning-out/widening of the IRZ. This is accompanied by similar to 30% reduction in the recirculation velocity of the IRZ. It is also observed that b < R (R: radial distance from central axis to outer shear layer-OSL). At super-critical amplitudes, the sub-critical IRZ topology transits back (the vortex core retracts upstream and radially inwards) and finally undergoes a transverse shrinkage ((r(vcc))/(r(vcc))(0 Hz) decreases by similar to 20%) when b >= R. In contrast, the vortex core of super-critical breakdown mode consistently spreads radially outwards and is displaced further downstream. Finally, the IRZ fans-out at the threshold excitation amplitude. However, the acoustic response region b is still less than R. This is explained based on the characteristic geometric swirl number (S-G) of the flow regimes. The super-critical flow mode with higher S-G (hence, higher radial pressure drop due to rotational effect which scales as Delta P similar to rho u theta(2) and acts inwards towards the center line) compared to sub-critical state imposes a greater resistance to the radial outward spread of b. As a result, the acoustic energy supplied to the super-critical flow mode increases the degree of acoustic response at the pulsing frequency and energizes its harmonics (evident from power spectra). As a disturbance amplifier, the stronger convective instability mode within the flow structure of super-critical VB causes the topology to widen/fan-out severely at threshold excitation amplitude. (C) 2015 AIP Publishing LLC.