NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

Nonlinear preconditioning for efficient and accurate interface capturing in simulation of multicomponent compressible flows

Single fluid schemes that rely on an interface function for phase identification in multicomponent compressible flows are widely used to study hydrodynamic flow phenomena in several diverse applications. Simulations based on standard numerical implementation of these schemes suffer from an artificial increase in the width of the interface function owing to the numerical dissipation introduced by an upwind discretization of the governing equations. In addition, monotonicity requirements which ensure that the sharp interface function remains bounded at all times necessitate use of low-order accurate discretization strategies. This results in a significant reduction in accuracy along with a loss of intricate flow features. In this paper we develop a nonlinear transformation based interface capturing method which achieves superior accuracy without compromising the simplicity, computational efficiency and robustness of the original flow solver. A nonlinear map from the signed distance function to the sigmoid type interface function is used to effectively couple a standard single fluid shock and interface capturing scheme with a high-order accurate constrained level set reinitialization method in a way that allows for oscillation-free transport of the sharp material interface. Imposition of a maximum principle, which ensures that the multidimensional preconditioned interface capturing method does not produce new maxima or minima even in the extreme events of interface merger or breakup, allows for an explicit determination of the interface thickness in terms of the grid spacing. A narrow band method is formulated in order to localize computations pertinent to the preconditioned interface capturing method. Numerical tests in one dimension reveal a significant improvement in accuracy and convergence; in stark contrast to the conventional scheme, the proposed method retains its accuracy and convergence characteristics in a shifted reference frame. Results from the test cases in two dimensions show that the nonlinear transformation based interface capturing method outperforms both the conventional method and an interface capturing method without nonlinear transformation in resolving intricate flow features such as sheet jetting in the shock-induced cavity collapse. The ability of the proposed method in accounting for the gravitational and surface tension forces besides compressibility is demonstrated through a model fully three-dimensional problem concerning droplet splash and formation of a crownlike feature. (C) 2014 Elsevier Inc. All rights reserved.

Flexibility in flapping foil suppresses meandering of induced jet in absence of free stream

Thrust-generating flapping foils are known to produce jets inclined to the free stream at high Strouhal numbers St = fA/U-infinity, where f is the frequency and A is the amplitude of flapping and U-infinity is the free-stream velocity. Our experiments, in the limiting case of St —> infinity (zero free-stream speed), show that a purely oscillatory pitching motion of a chordwise flexible foil produces a coherent jet composed of a reverse Benard-Karman vortex street along the centreline, albeit over a specific range of effective flap stiffnesses. We obtain flexibility by attaching a thin flap to the trailing edge of a rigid NACA0015 foil; length of flap is 0.79 c where c is rigid foil chord length. It is the time-varying deflections of the flexible flap that suppress the meandering found in the jets produced by a pitching rigid foil for zero free-stream condition. Recent experiments (Marais et al., J. Fluid Mech., vol. 710, 2012, p. 659) have also shown that the flexibility increases the St at which non-deflected jets are obtained. Analysing the near-wake vortex dynamics from flow visualization and particle image velocimetry (PIV) measurements, we identify the mechanisms by which flexibility suppresses jet deflection and meandering. A convenient characterization of flap deformation, caused by fluid-flap interaction, is through a non-dimensional effective stiffness', EI* = 8 EI/(rho V-TEmax(2) s(f) c(f)(3)/2), representing the inverse of the flap deflection due to the fluid-dynamic loading; here, EI is the bending stiffness of flap, rho is fluid density, V-TEmax is the maximum velocity of rigid foil trailing edge, s(f) is span and c(f) is chord length of the flexible flap. By varying the amplitude and frequency of pitching, we obtain a variation in EI* over nearly two orders of magnitude and show that only moderate EI*. (0.1 less than or similar to EI * less than or similar to 1 generates a sustained, coherent, orderly jet. Relatively `stiff' flaps (EI* greater than or similar to 1), including the extreme case of no flap, produce meandering jets, whereas highly `flexible' flaps (EI* less than or similar to 0.1) produce spread-out jets. Obtained from the measured mean velocity fields, we present values of thrust coefficients for the cases for which orderly jets are observed.

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

Using a molecular model for octamethylcydotetrasiloxane (OMCTS), molecular dynamics simulations are carried out to probe the phase state of OMCTS confined between two mica surfaces in equilibrium With a reservoir. Molecular dynamics simulations are carried out for elevations ranging from 5 to 35 K above the melting point for the OMCTS model used in this study. The Helmholtz free energy is, computed for a specific confinement using the :two-phase thermodynamic (2PT) method. Analysis of the in-plane pair correlation functions did not reveal signatures of freezing even under an extreme confinement of two layers. OMCTS is found to orient with a wide distribution of orientations with respect to the mica surface, with a distinct preference for the surface parallel configuration in the contact layers. The self-intermediate scattering function is found to decay with increasing relaxation times as the surface separation is decreased, and the two-step relaxation in the scattering function, a signature of glassy dynamics, distinctly evolves as the temperature is lowered. However, even at 5 K above the melting point, we did not observe a freezing transition and the self-intermediate scattering functions relax within 200 ps for the seven-layered confined system. The self diffusivity and relaxation times obtained from the Kohlrausch-Williams-Watts stretched exponential fits to the late alpha-relaxation exhibit power law scalings with the packing fraction as predicted by mode coupling theory. A distinct discontinuity in the Helmholtz free energy, potential energy, and a sharp change in the local bond order parameter, Q(4), was observed at 230 K for a five-layered system upon cooling, indicative of a first-order transition. A freezing point depression of about 30 K was observed for this five-layered confined system, and at the lower temperatures, contact layers were found to be disordered with long-range order present only in the inner layers. These dynamical signatures indicate that confined OMCTS undergoes a slowdown akin to a fluid approaching a glass transition upon increasing confinement, and freezing under confinement would require substantial subcooling below the bulk melting point of OMCTS.