Entropy and dynamics of water in hydration layers of a bilayer

We compute the entropy and transport properties of water in the hydration layer of dipalmitoylphosphatidylcholine bilayer by using a recently developed theoretical scheme two-phase thermodynamic model, termed as 2PT method; S.-T. Lin et al., J. Chem. Phys. 119, 11792 (2003)] based on the translational and rotational velocity autocorrelation functions and their power spectra. The weights of translational and rotational power spectra shift from higher to lower frequency as one goes from the bilayer interface to the bulk. Water molecules near the bilayer head groups have substantially lower entropy (48.36 J/mol/K) than water molecules in the intermediate region (51.36 J/mol/K), which have again lower entropy than the molecules (60.52 J/mol/K) in bulk. Thus, the entropic contribution to the free energy change (T Delta S) of transferring an interface water molecule to the bulk is 3.65 kJ/mol and of transferring intermediate water to the bulk is 2.75 kJ/mol at 300 K, which is to be compared with 6.03 kJ/mol for melting of ice at 273 K. The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface. This behavior is supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water. The ratio of reorientational relaxation time for Legendre polynomials of order 1 and 2 is approximately 2 for interface, intermediate, and bulk water, indicating the presence of jump dynamics in these water molecules. (C) 2010 American Institute of Physics. doi:10.1063/1.3494115]

Discriminative learning of Bayesian networks via factorized conditional log-likelihood

We propose an efficient and parameter-free scoring criterion, the factorized conditional log-likelihood (ˆfCLL), for learning Bayesian network classifiers. The proposed score is an approximation of the conditional log-likelihood criterion. The approximation is devised in order to guarantee decomposability over the network structure, as well as efficient estimation of the optimal parameters, achieving the same time and space complexity as the traditional log-likelihood scoring criterion. The resulting criterion has an information-theoretic interpretation based on interaction information, which exhibits its discriminative nature. To evaluate the performance of the proposed criterion, we present an empirical comparison with state-of-the-art classifiers. Results on a large suite of benchmark data sets from the UCI repository show that ˆfCLL-trained classifiers achieve at least as good accuracy as the best compared classifiers, using significantly less computational resources.

Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage

A 4 A electron-density map of Pf1 filamentous bacterial virus has been calculated from x-ray fiber diffraction data by using the maximum-entropy method. This method produces a map that is free of features due to noise in the data and enables incomplete isomorphous-derivative phase information to be supplemented by information about the nature of the solution. The map shows gently curved (banana-shaped) rods of density about 70 A long, oriented roughly parallel to the virion axis but slewing by about 1/6th turn while running from a radius of 28 A to one of 13 A. Within these rods, there is a helical periodicity with a pitch of 5 to 6 A. We interpret these rods to be the helical subunits of the virion. The position of strongly diffracted intensity on the x-ray fiber pattern shows that the basic helix of the virion is right handed and that neighboring nearly parallel protein helices cross one another in an unusual negative sense.

Conditional linearization in nonlinear random vibration

In this paper, an improved probabilistic linearization approach is developed to study the response of nonlinear single degree of freedom (SDOF) systems under narrow-band inputs. An integral equation for the probability density function (PDF) of the envelope is derived. This equation is solved using an iterative scheme. The technique is applied to study the hardening type Duffing's oscillator under narrow-band excitation. The results compare favorably with those obtained using numerical simulation. In particular, the bimodal nature of the PDF for the response envelope for certain parameter ranges is brought out.

Molecular interpretation of the linear relationship between the entropy and the enthalpy of activation of charge transfer reactions in polar liquids

The well-known linear relationship (T?S# =??H# +?, where 1 >? > 0,? > 0) between the entropy (?S#) and the enthalpy (?H#) of activation for reactions in polar liquids is investigated by using a molecular theory. An explicit derivation of this linear relation from first principles is presented for an outersphere charge transfer reaction. The derivation offers microscopic interpretation for the quantities? and?. It has also been possible to make connection with and justify the arguments of Bell put forward many years ago.

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

Zero-point entropy in 'spin ice'

Common water ice (ice I-h) is an unusual solid-the oxygen atoms form a periodic structure but the hydrogen atoms are highly disordered due to there being two inequivalent O-H bond lengths'. Pauling showed that the presence of these two bond lengths leads to a macroscopic degeneracy of possible ground states(2,3), such that the system has finite entropy as the temperature tends towards zero. The dynamics associated with this degeneracy are experimentally inaccessible, however, as ice melts and the hydrogen dynamics cannot be studied independently of oxygen motion(4). An analogous system(5) in which this degeneracy can be studied is a magnet with the pyrochlore structure-termed 'spin ice'-where spin orientation plays a similar role to that of the hydrogen position in ice I-h. Here we present specific-heat data for one such system, Dy2Ti2O7, from which we infer a total spin entropy of 0.67Rln2. This is similar to the value, 0.71Rln2, determined for ice I-h, SO confirming the validity of the correspondence. We also find, through application of a magnetic field, behaviour not accessible in water ice-restoration of much of the ground-state entropy and new transitions involving transverse spin degrees of freedom.

Assessment of conditional moment closure models of turbulent autoignition using DNS data

A systematic assessment of the submodels of conditional moment closure (CMC) formalism for the autoignition problem is carried out using direct numerical simulation (DNS) data. An initially non-premixed, n-heptane/air system, subjected to a three-dimensional, homogeneous, isotropic, and decaying turbulence, is considered. Two kinetic schemes, (1) a one-step and (2) a reduced four-step reaction mechanism, are considered for chemistry An alternative formulation is developed for closure of the mean chemical source term , based on the condition that the instantaneous fluctuation of excess temperature is small. With this model, it is shown that the CMC equations describe the autoignition process all the way up to near the equilibrium limit. The effect of second-order terms (namely, conditional variance of temperature excess sigma(2) and conditional correlations of species q(ij)) in modeling is examined. Comparison with DNS data shows that sigma(2) has little effect on the predicted conditional mean temperature evolution, if the average conditional scalar dissipation rate is properly modeled. Using DNS data, a correction factor is introduced in the modeling of nonlinear terms to include the effect of species fluctuations. Computations including such a correction factor show that the species conditional correlations q(ij) have little effect on model predictions with a one-step reaction, but those q(ij) involving intermediate species are found to be crucial when four-step reduced kinetics is considered. The "most reactive mixture fraction" is found to vary with time when a four-step kinetics is considered. First-order CMC results are found to be qualitatively wrong if the conditional mean scalar dissipation rate is not modeled properly. The autoignition delay time predicted by the CMC model compares excellently with DNS results and shows a trend similar to experimental data over a range of initial temperatures.

Implementation of conditional phase-shift gate for quantum information processing by NMR, using transition-selective pulses

Experimental realization of quantum information processing in the field of nuclear magnetic resonance (NMR) has been well established. Implementation of conditional phase-shift gate has been a significant step, which has lead to realization of important algorithms such as Grover's search algorithm and quantum Fourier transform. This gate has so far been implemented in NMR by using coupling evolution method. We demonstrate here the implementation of the conditional phase-shift gate using transition selective pulses. As an application of the gate, we demonstrate Grover's search algorithm and quantum Fourier transform by simulations and experiments using transition selective pulses. (C) 2002 Elsevier Science (USA). All rights reserved.

Evidence of residual entropy in the cubic spinel Zn2TiO4

The standard free energies of formation of Zn2Ti04 and ZnTi03 have been determined in the temperature range 930° to i ioo'x from electromotive force measurements on reversible solid oxide galvanic cells;Ag-5at%znll I Pt, + CaO-Zr02 ZnO I II Ag-5at%Zn Y20r Th02 CaO-Zr02 + ,Pt Zn2Ti04+ ZnTi03 and II Ag-5at%Zn CaO-Zr02 + ,Pt ZnTi03+ Ti02 The values may be expressed by the equations,2ZnO (wurtz) + Ti02(rut) -> Zn2Ti04(sp), f:!:.Go = -750-2-46T (±75)cal;ZnO(wurtz) +Ti02(rut) -> ZnTi03(ilmen) ,f:!:.Co = -]600-0·]99T(±50)cal.Combination of the free energy values with the calorimetric heat of formation, and low-temperature and high-temperature heat capacity of Zn2Ti04 reported in literature, suggests a residual entropy of ],9 (±0·6) cal K-1 mol ? for the cubic spinel. Ideal mixing of Zn2+ and Ti4+ ions on the octahedral sites would result in a configurational contribution to the entropy of 2· 75 cal K-1 rnol ".The difference is indicative of short-range ordering of cations on octahedral sites.

An entropy meter based on the thermoelectric potential of a nonisothermal solid electrolyte cell

The theory, design, and performance of a solid electrolyte twin thermocell for the direct determination of the partial molar entropy of oxygen in a single-phase or multiphase mixture are described. The difference between the Seebeck coefficients of the concentric thermocells is directly related to the difference in the partial molar entropy of oxygen in the electrodes of each thermocell. The measured potentials are sensitive to small deviations from equilibrium at the electrodes. Small electric disturbances caused by simultaneous potential measurements or oxygen fluxes caused by large oxygen potential gradients between the electrodes also disturb the thermoelectric potential. An accuracy of ±0.5 calth K−1 mol−1 has been obtained by this method for the entropies of formation of NiO and NiAl2O4. This “entropy meter” may be used for the measurement of the entropies of formation of simple or complex oxides with significant residual contributions which cannot be detected by heat-capacity measurements.

The standard enthalpy and entropy of formation of Rh2O3 - A third-law optimization

The standard Gibbs energy of formation of Rh203 at high temperature has been determined recently with high precision. The new data are significantly different from those given in thermodynamic compilations.Accurate values for enthalpy and entropy of formation at 298.15 K could not be evaluated from the new data,because reliable values for heat capacity of Rh2O3 were not available. In this article, a new measurement of the high temperature heat capacity of Rh2O3 using differential scanning calorimetry (DSC) is presented.The new values for heat capacity also differ significantly from those given in compilations. The information on heat capacity is coupled with standard Gibbs energy of formation to evaluate values for standard enthalpy and entropy of formation at 289.15 K using a multivariate analysis. The results suggest a major revision in thermodynamic data for Rh2O3. For example, it is recommended that the standard entropy of Rh203 at 298.15 K be changed from 106.27 J mol-' K-'given in the compilations of Barin and Knacke et al. to 75.69 J mol-' K". The recommended revision in the standard enthalpy of formation is from -355.64 kJ mol-'to -405.53 kJ mol".

Magnetic Field Dependence of Entropy And Specific Heat of YBa2Cu3O7-delta Superconductors

The change in thermodynamic quantities (e. g., entropy, specific heat etc.) by the application of magnetic field in the case of the high-T-c superconductor YBCO system is examined phenomenological by the Ginzburg-Landau theory of anisotropic type-II superconductors. An expression for the change in the entropy (Delta S) and change in specific heat (Delta C) in a magnetic field for any general orientation of an applied magnetic field B-a with respect to the crystallographic c-axis is obtained. The observed large reduction of specific heat anomaly just below the superconducting transition and the observed variation of entropy with magnetic field are explained quantitatively.