Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Vibrational force constant and electron relaxation in H2 and Li2

The force constants of H2 and Li2 are evaluated employing their extended Hartree-Fock wavefunctions by a polynomial fit of their force curves. It is suggested that, based on incomplete multiconfiguration Hartree-Fock wavefunctions, force constants calculated from the energy derivatives are numerically more accurate than those obtained from the derivatives of the Hellmann-Feynman forces. It is observed that electrons relax during the nuclear vibrations in such a fashion as to facilitate the nuclear motions.

Excited-state structures of molecules with nearby electronic states

Vibronic coupling among the nearby excited electronic states via the in-plane and the out-of-plane nuclear motions is examined in benzene, pyrazine, formaldehyde and thioformaldehyde. Results reveal that in benzene the structure distorts via the most active nuclear bending (planar) motion while in the other molecules the structures distort through an out-of-plane bending motion in their respective lowest excited states.

Inelastic Torsional Response of a Single-Story Framed Structure

In this paper, a single-story, bilinear-hysteretic structure, square in plan and supported on four columns, subjected to two horizontal ground motions is studied. The model is assumed to possess three degrees of freedom, viz., translational displacements along the two horizontal orthogonal directions and a rotation about the vertical axis. Interaction of the bending moments in the two perpendicular directions has been considered.

Temperature- and pressure-dependent study of Cl-35 NQR frequency and spin lattice relaxation time in 2,3-dichloroanisole

The temperature and pressure dependence of Cl-35 NQR frequency and spin lattice relaxation time (T-1) were investigated in 2,3-dichloroanisole. Two NQR signals were observed throughout the temperature and pressure range studied. T-1 were measured in the temperature range from 77 to 300 K and from atmospheric pressure to 5 kbar. Relaxation was found to be due to the torsional motion of the molecule and also reorientation f motion of the CH3 group. T-1 versus temperature data were analyzed on the basis of Woessner and Gutowsky model, and the activation energy for the reorientation of the CH3 group was estimated. The temperature dependence of the average torsional lifetimes of the molecules and the transition probabilities were also obtained. NQR frequency shows a nonlinear behavior with pressure, indicating both dynamic and static effects of pressure. The pressure coefficients were observed to be positive for both the lines. A thermodynamic analysis of the data was carried out to determine the constant volume temperature coefficients of the NQR frequency. The variation of spin lattice time with pressure was very small, showing that the relaxation is mainly due to the torsional motions of the molecules. Copyright (C) 2010 John Wiley & Sons, Ltd.

Critical age-dependent branching Markov processes and their scaling limits

This paper studies:(i)the long-time behaviour of the empirical distribution of age and normalized position of an age-dependent critical branching Markov process conditioned on non-extinction;and (ii) the super-process limit of a sequence of age-dependent critical branching Brownian motions.

Coupled ocean-atmosphere inter-decadal modes in the tropics

Homogencous upper air data for 50 years (1949-1998) from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis project, sea surface temperatures and sea level pressure are used to bring out the three dimensional structure of two dominant decadal/multi-decadal variations in the tropics. The global three dimensional modes represent generalized forms of inter-decadal modes studied earlier only with surface data. In the vertical, both modes show approximate first baroclinic structures over the tropics. The Walker circulation associated with the multidecadal mode has a wavenumber two structure in the zonal direction. It is shown that the magnitude of major ascending and descending motions associated with the multi-decadal Hadley and Walker circulations, are comparable to those associated with the dominant inter-annual mode. Implications of these large scale global circulations associated with the low frequency oscillations in modulating regional climate on a inter-annual time scale are discussed.

Total risk rating and stability analysis of embankment dams in the Kachchh Region, Gujarat, India

A method for total risk analysis of embankment dams under earthquake conditions is discussed and applied to the selected embankment dams, i.e., Chang, Tapar, Rudramata, and Kaswati located in the Kachchh region of Gujarat, India, to obtain the seismic hazard rating of the dam site and the risk rating of the structures. Based on the results of the total risk analysis of the dams, coupled non-linear dynamic numerical analyses of the dam sections are performed using acceleration time history record of the Bhuj (India) earthquake as well as five other major earthquakes recorded worldwide. The objective of doing so is to perform the numerical analysis of the dams for the range of amplitude, frequency content and time duration of input motions. The deformations calculated from the numerical analyses are also compared with other approaches available in literature, viz, Makdisi and Seed (1978) approach, Jansen's approach (1990), Swaisgood's method (1995), Bureau's method (1997). Singh et al. approach (2007), and Saygili and Rathje approach (2008) and the results are utilized to foresee the stability of dams in future earthquake scenario. (C) 2010 Elsevier B.V. All rights reserved.

Complexation of siRNA with Dendrimer: A Molecular Modeling Approach

This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2 x G3 or 2xG4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA-dendrimer complex over nanosecond time scale. With the increase in dendrimcr generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the den-rimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water. counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA back hone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na-1) and dendrimer (Cl-) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of IG3 and IG4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer.

A theory on the migration of an extraneous electron across hydrogen bonds in polypeptides

The migrating electrons in biological systems normally are extraneous and taking this into account the electron delocalisation across the hydrogen bonds in proteins is re-examined. It is seen that an extraneous electron can travel rapidly via the low-lying virtual orbitals of the hydrogen-bonded π-electronic structure of peptide units in proteins. The frequency of electron transfer decreases slowly with an increase in the path length. However, the coupling of electron and protonic motions enhances this frequency. Transfer of electrons across the hydrogen bonds in accordance with the double-exchange mechanism does not appear to be possible. This theory offers a possibility for an extraneous electron to transfer within protein structures.

Miniature Compliant Grippers With Vision-Based Force Sensing

This paper is concerned with grasping biological cells in aqueous medium with miniature grippers that can also help estimate forces using vision-based displacement measurement and computation. We present the design, fabrication, and testing of three single-piece, compliant miniature grippers with parallel and angular jaw motions. Two grippers were designed using experience and intuition, while the third one was designed using topology optimization with implicit manufacturing constraints. These grippers were fabricated using different manufacturing techniques using spring steel and polydimethylsiloxane ( PDMS). The grippers also serve the purpose of a force sensor. Toward this, we present a vision-based force-sensing technique by solving Cauchy's problem in elasticity using an improved algorithm. We validated this technique at the macroscale, where there was an independent method to estimate the force. In this study, the gripper was used to hold a yeast ball and a zebrafish egg cell of less than 1 mm in diameter. The forces involved were estimated to be about 30 and 10 mN for the yeast ball and the zebrafish egg cell, respectively.

Seismic response of a long span cable

The dynamic response of a single span cable due to a travelling seismic excitation is studied in this paper. The influence of propagation time between the supports is investigated in detail. The importance of considering both vertical and longitudinal equations of motion in the analysis is highlighted. The results indicate the considerable influence of the time-lagged support motions on the cable dynamic tension. A modal combination rule based on the response spectrum method is developed to arrive at the peak estimates of the cable response. Some significant aspects of cable behaviour, especially under horizontal support motion, are discussed.

Temperature and pressure dependence of 35Cl NQR in NaClO3 and Ba(ClO3)2·H2O

Pressure and temperature dependence of 35Cl nuclear quadrupole resonance (NQR) has been investigated in NaClO3 and Ba(ClO3)2·H2O. NQR frequencies are measured in the temperature range 77–300 K and up to 5 kbar pressure. The torsional frequency of the ClO3 pyramid and its variation with both pressure and temperature are evaluated from the NQR frequencies under the harmonic approximation. In general, the pressure effect on the internal motions is found to be less in Ba (ClO3)2·H2O compared to NaClO3. When the samples are cooled to 77 K the pressure coeffecient of NQR frequency becomes nearly zero in sodium chlorate, whereas it retains a value of 6 kHz kbar−1 in barium chlorate. This behaviour follows from the fact that at 77K, the torsional frequency in NaClO3 is unaffected by the application of pressure while it increases at the rate 12 cm−1 kbar−1 in Ba(ClO3)2·H2O.

Two-Fermi liquid model for high Tc superconductivity involving suppression of tunnelling by decoherence

We consider a model system of two interacting Fermi-liquids, one of which is light and the other much heavier. In the normal state the lighter component provides a quantum mechanical bath coupled 'ohmically' to the heavier component in the sense of Caldeira and Leggett, suppressing thereby the band (tunnelling) matrix elements of the heavier component. Thus we lose the energy of delocalization. On the other hand, a superconducting ordering stiffens the bath spectral function at low energies and so restores the tunnelling. The resulting regain of the delocalization energy bootstraps so as to stabilize the superconducting order that caused it. It is conceivable that the motions parallel to the easy ab-plane and along the hard c-axis may also effectively correspond to the light and the heavy Fermi-liquids, respectively.

Dense granular flow down an inclined plane A comparison between the hard particle model and soft particle simulations

The granular flow down an inclined plane is simulated using the discrete element (DE) technique to examine the extent to which the dynamics of an unconfined dense granular flow can be well described by a hard particle model First, we examine the average coordination number for the particles in the flow down an inclined plane using the DE technique using the linear contact model with and without friction, and the Hertzian contact model with friction The simulations show that the average coordination number decreases below 1 for values of the spring stiffness corresponding to real materials, such as sand and glass, even when the angle of inclination is only 10 larger than the angle of repose Additional measures of correlations in the system, such as the fraction of particles with multibody contact, the force ratio (average ratio of the magnitudes of the largest and the second largest force on a particle), and the angle between the two largest forces on the particle, show no evidence of force chains or other correlated motions in the system An analysis of the bond-orientational order parameter indicates that the flow is in the random state, as in event-driven (ED) simulations V Kumaran, J Fluid Mech 632, 107 (2009), J Fluid Mech 632, 145 (2009)] The results of the two simulation techniques for the Bagnold coefficients (ratio of stress and square of the strain rate) and the granular temperature (mean square of the fluctuating velocity) are compared with the theory V Kumaran, J Fluid Mech 632, 107 (2009), J Fluid Mech 632, 145 (2009)] and are found to be in quantitative agreement In addition, we also conduct a comparison of the collision frequency and the distribution of the precollisional relative velocities of particles in contact The strong correlation effects exhibited by these two quantities in event-driven simulations V Kumaran, J Fluid Mech 632, 145 (2009)] are also found in the DE simulations (C) 2010 American Institute of Physics doi 10 1063/1 3504660]