Conformation of the LL and LD hairpin bends with internal hydrogen bonds in proteins and peptides

The conformation of three linked peptide units having an internal 4 → 1 type of hydrogen bond has been studied in detail, and the low energy conformations are listed. These conformations all lead to the reversal of the chain direction, and may therefore be called as “hairpin bends” or “U-bends”. Since this bend can occur at the end of two chains hydrogen-bonded in the antiparallel β-conformation, it is also known as the “β-bend”. Two types of conformation are possible when the residues at the second and third Cα atoms are both of type L (the LL bend), while only one type is possible for the LD and the DL bend. The LL bend can also accommodate the sequences LG, GL, GG (G = glycine), while the LD bend can accommodate the sequences LG, GD and GG. The conformations for the sequences DD and DL are exact inverses (or mirror images) of those for the sequences LL and LD, respectively, and have dihedral angles (phi2, ψ2), (phi3, ψ3) of the same magnitudes, but of opposite signs as those for the former types, which are listed, along with the characteristics (length, angle and energy) of the hydrogen bonds. A comparison of the theoretical predictions with experimental data (from X-ray diffraction and NMR studies) on proteins and peptides, show reasonably good agreement. However, a systematic trend is observable in the experimental data, slightly deviating from theory, which indicates that some deformations occur in the shapes of the peptide units forming the bend, differing from that of the standard planar peptide unit.

Conformation of polypeptide-chains containing both l-residues and D-residues .2. Double-helical structures of poly-ld-peptides

Polypeptides with alternating L- and D-amino acid residues can take up stereochemically satisfactory coaxial double-helical structures, both antiparallel and parallel, which are stabilized by systematic interchain NH O hydrogen bonds. Semiempirical energy calculations over allowed regions of conformational space have yielded the characteristics of these double-helices. There are four possible types of antiparallel double-helices - A3, A4, A5 and A6, with n, the number of LD peptide units per turn, around 2.8, 3.6, 4.5 and 5.5 respectively, while for the parallel double-helices there are two types, P3 and P4, having similar helical parameters as in A3 and A4. The hydrogen-bonding scheme restricts the pitch in all the models to the narrow range of 10.0 to 11.5 Å. All these helices have large central cores whose radii increase proportionately with n. In this respect, A3 and A4 are suitable models for the structure of gramicidin A. In terms of their relative energies, antiparallel double-helices are marginally more stable than those with parallel strands. Our results indicate that the energy differences amongst the members in the antiparallel family are not significant and thus provide an explanation for the polymorphism reported for poly(γ-benzyl-LD-glutamate).

Responses of the Circadian Locomotor Activity Rhythm of Mus Booduga to Shifts in LD Schedules

The responses of the field mouse Mus booduga to shifts in schedules of LD cycles were monitored and the results were interpreted with the help of a PRC constructed for the same species. The results reveal that, M. booduga reentrained faster with a lesser number of transients after delay shifts than advance shifts, thus exhibiting “asymmetry effect.” A positive correlation was observed between the number of transients and the number of hours of shift. In most of the shifts, the sign of the transients (negative for delaying transients and positive for advancing transients) coincided with the direction of the shift. Interestingly, 11 and 12 h of advance shifting resulted in delaying transients. An 11-h advance shift can also be interpreted as a 13-h delay. Reentrainment through delaying transients is faster as compared to reentrainment through advancing transients. Thus, this animal might have taken a “shorter route,” as proved by the fact that an 11-h advance shift has evoked delaying transients. But a 13-h advance shift evoked only advancing transients. This prompts us to speculate that there may be a “phase jump” in M. booduga. Further, irrespective of whether L or D has been doubled in a 12-h shift, both evoked only delaying transients.

Charge transport in a Tomonaga-Luttinger liquid: Effects of pumping and bias

We study the current produced in a Tomonaga-Luttinger liquid by an applied bias and by weak, pointlike impurity potentials which are oscillating in time. We use bosonization to perturbatively calculate the current up to second order in the impurity potentials. In the regime of small bias and low pumping frequency, both the dc and ac components of the current have power-law dependences on the bias and pumping frequencies with an exponent 2K-1 for spinless electrons, where K is the interaction parameter. For K < 1/2, the current grows large for special values of the bias. For noninteracting electrons with K=1, our results agree with those obtained using Floquet scattering theory for Dirac fermions. We also discuss the cases of extended impurities and of spin-1/2 electrons.

Nonadiabatic charge pumping by oscillating potentials in one dimension: Results for infinite system and finite ring

We study charge pumping when a combination of static potentials and potentials oscillating with a time period T is applied in a one-dimensional system of noninteracting electrons. We consider both an infinite system using the Dirac equation in the continuum approximation and a periodic ring with a finite number of sites using the tight-binding model. The infinite system is taken to be coupled to reservoirs on the two sides which are at the same chemical potential and temperature. We consider a model in which oscillating potentials help the electrons to access a transmission resonance produced by the static potentials and show that nonadiabatic pumping violates the simple sin phi rule which is obeyed by adiabatic two-site pumping. For the ring, we do not introduce any reservoirs, and we present a method for calculating the current averaged over an infinite time using the time evolution operator U(T) assuming a purely Hamiltonian evolution. We analytically show that the averaged current is zero if the Hamiltonian is real and time-reversal invariant. Numerical studies indicate another interesting result, namely, that the integrated current is zero for any time dependence of the potential if it is applied to only one site. Finally we study the effects of pumping at two sites on a ring at resonant and nonresonant frequencies, and show that the pumped current has different dependences on the pumping amplitude in the two cases.

Peristaltic pumping in a circular tube in the presence of an eccentric catheter

The influence of an eccentrically inserted catheter on the peristaltic pumping in a tube is investigated under long wavelength, low Reynolds number assumptions. The radially asymmetric deformation of the wall arising through an eccentrically inserted catheter is taken into consideration by choosing an appropriate bipolar coordinate system. The effect of the position and size of the catheter on pumping characteristics is studied. The best performance of pumping is noticed at a certain position of the catheter. The size of the catheter, when placed eccentrically, alters the pressure signature significantly inside the bolus, unlike the concentric case discussed by Lykoudis and Roos (1971). Further, the maximum pressure rise in one period of the peristaltic wave is observed to decrease with an increase in the eccentricity.

Peristaltic pumping of a micropolar fluid in a tube

Peristaltic transport of a micropolar fluid in a circular tube is studied under low Reynolds number and long wavelength approximations. The closed form solutions are obtained. for velocity, microrotation components, as well as the stream function and they contain new additional parameters namely, N the coupling number and m the micropolar parameter. In the case of free pumping (pressure difference Deltap = 0) the difference in pumping flux is observed to be very small for Newtonian and micropolar fluids but in the case of pumping (Deltap > 0) the characteristics are significantly altered for different N and m. It is observed that the peristalsis in micropolar fluids works as a pump against a greater pressure rise compared with a Newtonian fluid. Streamline patterns which depict trapping phenomena are presented for different parameter ranges. The limit on the trapping of the center streamline is obtained. The effects of N and m on friction force for different Deltap are discussed.

TURBULENT PUMPING OF MAGNETIC FLUX REDUCES SOLAR CYCLE MEMORY AND THUS IMPACTS PREDICTABILITY OF THE SUN'S ACTIVITY

Prediction of the Sun's magnetic activity is important because of its effect on space environment and climate. However, recent efforts to predict the amplitude of the solar cycle have resulted in diverging forecasts with no consensus. Yeates et al. have shown that the dynamical memory of the solar dynamo mechanism governs predictability, and this memory is different for advection- and diffusion-dominated solar convection zones. By utilizing stochastically forced, kinematic dynamo simulations, we demonstrate that the inclusion of downward turbulent pumping of magnetic flux reduces the memory of both advection- and diffusion-dominated solar dynamos to only one cycle; stronger pumping degrades this memory further. Thus, our results reconcile the diverging dynamo-model-based forecasts for the amplitude of solar cycle 24. We conclude that reliable predictions for the maximum of solar activity can be made only at the preceding minimum-allowing about five years of advance planning for space weather. For more accurate predictions, sequential data assimilation would be necessary in forecasting models to account for the Sun's short memory.

Identification of parameters in unconfined aquifers

A method is presented for identification of parameters in unconfined aquifers from pumping tests, based on the optimisation of the objective function using the least squares approach. Four parameters are to be evaluated, namely: The hydraulic conductivity in the radial and the vertical directions, the storage coefficient and the specific yield. The sensitivity analysis technique is used for solving the optimisation problem. Besides eliminating the subjectivity involved in the graphical procedure, the method takes into account the field data at all time intervals without classifying them into small and large time intervals and does not use the approximation that the ratio of the storage coefficient to the specific yield tends to zero. Two illustrative examples are presented and it is found that the parameter estimates from the computational and graphical procedures differ fairly significantly.

X-ray Studies on Crystalline Complexes Involving Amino Acids and Peptides. XIII. Effect of Chirality on Molecular Aggregation: The Crystal Structures of L-Arginine D-Aspartate and L-Arginine D-Glutamate Trihydrate

The crystal structures of (1) L-arginine D-asparate, C6HIsN40~.C4H6NO4 [triclinic, P1, a=5.239(1), b=9.544(1), c=14.064(2)A, a=85"58(1), /3=88.73 (1), ~/=84.35 (1) °, Z=2] and (2) L-arginine D-glutamate trihydrate, C6H15N40~-.CsHsNO4.3H20 [monoclinic, P2~, a=9.968(2), b=4.652(1), c=19.930 (2) A, fl = 101.20 (1) °, Z = 2] have been determined using direct methods. They have been refined to R =0.042 and 0.048 for 2829 and 2035 unique reflections respectively [I>2cr(I)]. The conformations of the two arginine molecules in the aspartate complex are different from those observed so far in the crystal structures of arginine, its salts and complexes. In both complexes, the molecules are organized into double layers stacked along the longest axis. The core of each double layer consists of two parallel sheets made up of main-chain atoms, each involving both types of molecules. The hydrogen bonds within each sheet and those that interconnect the two sheets give rise to EL-, DD- and DE-type head-to-tail sequences. Adjacent double layers in (1) are held together by side-chain-side-chain interactions whereas those in (2) are interconnected through an extensive network of water molecules which interact with sidechain guanidyl and carboxylate groups. The aggregation pattern observed in the two LD complexes is fundamentally different from that found in the corresponding EL complexes.

Constant conductance fluctuations in disordered metals

We discuss the effect of fluctuations of the random potential in directions transverse to the current flow in a modified Migdal-Kadanoff approach to probabilistic scaling of conductance with size L, in d-dimensional metallic systems. The conductance cumulants are finite and vary as Ld−1−n for n greater-or-equal, slanted 2 i.e. conductance fluctuations are constant for d = 3. The mean conductance has a non-classical correction with Image Full-size image (<1K) for d greater-or-equal, slanted 2. The form of the higher cumulants is strongly influenced by the transverse potential fluctuations and may be compared with the results of perturbative diagrammatic approaches.

Estimating specific yield and transmissivity with magnetic resonance sounding in an unconfined sandstone aquifer (Niger)

The unconfined aquifer of the Continental Terminal in Niger was investigated by magnetic resonance sounding (MRS) and by 14 pumping tests in order to improve calibration of MRS outputs at field scale. The reliability of the standard relationship used for estimating aquifer transmissivity by MRS was checked; it was found that the parametric factor can be estimated with an uncertainty a parts per thousand currency sign150% by a single point of calibration. The MRS water content (theta (MRS)) was shown to be positively correlated with the specific yield (Sy), and theta (MRS) always displayed higher values than Sy. A conceptual model was subsequently developed, based on estimated changes of the total porosity, Sy, and the specific retention Sr as a function of the median grain size. The resulting relationship between theta (MRS) and Sy showed a reasonably good fit with the experimental dataset, considering the inherent heterogeneity of the aquifer matrix (residual error is similar to 60%). Interpreted in terms of aquifer parameters, MRS data suggest a log-normal distribution of the permeability and a one-sided Gaussian distribution of Sy. These results demonstrate the efficiency of the MRS method for fast and low-cost prospection of hydraulic parameters for large unconfined aquifers.

Coupled Solution for Forced Recharge in Confined Aquifers

Analytical solutions for forced well recharge currently in use were initially developed for pumping scenarios and applied for recharge cases assuming that radial flow in the recharge well replicates a mirror image of that in to a pumping well. Moreover these solutions were not extended to multiaquifer systems. Well bore numerical solutions were generally not considering the effect of well bore interaction, which has a significant effect in the case of a recharge well. In the present paper, improved analytical solutions are developed for a well fully penetrating either single or multiaquifers in respect.to of well storage, well loss, and interactions between the individual aquifers through well bore. The solution developed for constant and variable rates of injection and well loss is applied to the experimental data of the Hansol well injection project near the city of Ahmedabad in the Gujarat state in India. The paper also discusses the difference in well hydraulics of recharge and recovery wells.

CFD analysis of high frequency miniature pulse tube refrigerators for space applications with thermal non-equilibrium model

High frequency, miniature, pulse tube cryocoolers are extensively used in space applications because of their simplicity. Parametric studies of inertance type pulse tube cooler are performed with different length-to-diameter ratios of the pulse tube with the help of the FLUENT (R) package. The local thermal non-equilibrium of the gas and the matrix is taken into account for the modeling of porous zones, in addition to the wall thickness of the components. Dynamic characteristics and the actual mechanism of energy transfer in pulse are examined with the help of the pulse tube wall time constant. The heat interaction between pulse tube wall and the oscillating gas, leading to surface heat pumping, is quantified. The axial heat conduction is found to reduce the performance of the pulse tube refrigerator. The thermal non-equilibrium predicts a higher cold heat exchanger temperature compared to thermal equilibrium. The pressure drop through the porous medium has a strong non-linear effect due to the dominating influence of Forchheimer term over that of the linear Darcy term at high operating frequencies. The phase angle relationships among the pressure, temperature and the mass flow rate in the porous zones are also important in determining the performance of pulse tuberefrigerator.