Self-consistent microscopic treatment of the effects of self-motion of the probe on ionic and dipolar solvation dynamics

A simple but self-consistent microscopic theory for the time dependent solvation energy of both ions and dipoles is presented which includes, for the first time, the details of the self-motion of the probe on its own solvation dynamics. The theory leads to several interesting predictions. The most important of them is that, for dipolar solvation, both the rotational and the translational motions of the dipolar solute probe can significantly accelerate the rate of solvation. In addition, the rotational self-motion of the solute can also give rise to an additional mechanism of nonexponentiality in solvation time correlation functions in otherwise slow liquids. A comparison between the present theoretical predictions and the recent experimental studies of Maroncelli et al. on solvation dynamics of aniline in l-propanol seems to indicate that the said experiments have missed the initial solvent response up to about 45 ps. After mapping the experimental results on the redefined time scale, the theoretical results can explain the experimental results for solvation of aniline in 1-propanol very well. For ionic solvation, the translational motion is significant for light solutes only. For example, for Li+ in water, translational motion speeds up the solvation by about 20%. The present theory demonstrates that in dipolar solvation the partial quenching of the self-motion due to the presence of specific solute-solvent interactions (such as H-bonding) may lead to a much slower solvation than that when the self-motion is present. This point has been discussed. In addition, we present the theoretical results for solvation of aniline in propylene carbonate, Here, the solvation is predicted to be complete within 15-20 ps.

Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Reactivation kinetics of acceptors in hydrogenated InP during unbiased annealing

The reactivation kinetics of passivated Mg acceptors in hydrogenated InP during unbiased annealing of a Schottky diode is reported. The reactivation is found to slow down gradually with annealing time and this phenomenon is attributed to substantial retrapping of H at the acceptor sites. It is found from the concentration profiles and the kinetics data that the reactivation is most likely limited by H2 molecule formation processes for longer annealing times; for shorter annealing times, contributions from in-diffusion of H also become significant. The diffusion of H during the initial period follows an Arrhenius relation with an activation energy for the effective diffusion coefficient of 1.13±0.10 eV. In the H2 formation regime, the reactivation is thermally activated with an activation energy for the annealing parameter of 1.71±0.10 eV. The H2 formation-limited regime of reactivation occurs sooner as the annealing temperature is increased.

The Folding Mechanism of Barstar: Evidence for Multiple Pathways and Multiple Intermediates

The mechanism of folding of the small protein barstar in the pre-transition zone at pH 7, 25 degrees C has been characterized using rapid mixing techniques. Earlier studies had established the validity of the three-state U-S reversible arrow U-F reversible arrow N mechanism for folding and unfolding in the presence of guanidine hydrochloride (GdnHCl) at concentrations greater than 2.0 M, where U-S and U-F are the slow-refolding and fast-refolding unfolded forms, respectively, and N is the fully folded form. It is now shown that early intermediates, I-S1 and I-S2 as well as a late native-like intermediate, I-N, are present on the folding pathways of U-S, and an early intermediate I-F1 on the folding pathway of U-F, when bars tar is refolded in concentrations of GdnHCl below 2.0 M. The rates of formation and disappearance of I-N, and the rates of formation of N at three different concentrations of GdnHCl in the pre-transition zone have been measured. The data indicate that in 1.5 M GdnHCl, I-N is not fully populated on the U-S --> I-S1 --> I-N --> N pathway because the rate of its formation is so slow that the U-S reversible arrow U-F reversible arrow N pathway can effectively compete with that pathway. In 1.0 M GdnHCl, the U-S --> I-S1 --> I-N transition is so fast that I-N is fully populated. In 0.6 M GdnHCl, I-N appears not to be fully populated because an alternative folding pathway, U-S --> I-S2 --> N, becomes available for the folding of U-S, in addition to the U-S --> I-S1 --> I-N --> N pathway Measurement of the binding of the hydrophobic dye 1-anilino-8-naphthalenesulphonate (ANS) during folding indicates that ANS binds to two distinct intermediates, I-M1 and I-M2, that form within 2 ms on the U-S --> I-M1 --> I-S1 --> I-N --> N and U-S --> I-M2 --> I-S2 --> N pathways. There is no evidence for the accumulation of intermediates that can bind ANS on the folding pathway of U-F.

Improving the convergence rate of the inverse iteration method

Solution of generalized eigenproblem, K phi = lambda M phi, by the classical inverse iteration method exhibits slow convergence for some eigenproblems. In this paper, a modified inverse iteration algorithm is presented for improving the convergence rate. At every iteration, an optimal linear combination of the latest and the preceding iteration vectors is used as the input vector for the next iteration. The effectiveness of the proposed algorithm is demonstrated for three typical eigenproblems, i.e. eigenproblems with distinct, close and repeated eigenvalues. The algorithm yields 29, 96 and 23% savings in computational time, respectively, for these problems. The algorithm is simple and easy to implement, and this renders the algorithm even more attractive.

Low temperature H-1 NMR relaxation studies of phase transitions in dicalcium barium propionate

The two low-temperature phase transitions in dicalcium barium propionate have been investigated by H-1 NMR relaxation (T-1,T-2,T-1 rho) studies carried out at a Larmor frequency of 300 MHz. The T-1 and T-1 rho results indicate the presence of C2H5 dynamics near these two transitions. We infer from the T-1 rho results that the slow motions of the C2H5 groups are responsible for the II-III transition.

Interannual variations of Indian summer monsoon in a GCM: External conditions versus internal feedbacks

The potential predictability of the Indian summer monsoon due to slowly varying sea surface temperature (SST) forcing is examined. Factors responsible for limiting the predictability are also investigated. Three multiyear simulations with the R30 version of the Geophysical Fluid Dynamics Laboratory's climate model are carried out for this purpose, The mean monsoon simulated by this model is realistic including the mean summer precipitation over the Indian continent. The interannual variability of the large-scale component of the monsoon such as the "monsoon shear index" and its teleconnection with Pacific SST is well simulated by the model in a 15-yr integration with observed SST as boundary condition. On regional scales, the skill in simulating the interannual variability of precipitation over the Indian continent by the model is rather modest and its simultaneous correlation with eastern Pacific SST is negative but poor as observed. The poor predictability of precipitation over the Indian region in the model is related to the fact that contribution to the interannual variability over this region due to slow SST variations [El Nino-Southern Oscillation (ENSO) related] is comparable to those due to regional-scale fluctuations unrelated to ENSO SST. The physical mechanism through which ENSO SST tend to produce reduction in precipitation over the Indian continent is also elucidated. A measure of internal variability of the model summer monsoon is obtained from a 20-yr integration of the same model with fixed annual cycle SST as boundary conditions but with predicted soil moisture and snow cover. A comparison of summer monsoon indexes between this run and the observed SST run shows that the internal oscillations can account for a large fraction of the simulated monsoon variability. The regional-scale oscillations in the observed SST run seems to arise from these internal oscillations. It is discovered that most of the interannual internal variability is due to an internal quasi-biennial oscillation (QBO) of the model atmosphere. Such a QBO is also found in the author's third 18-yr simulation in which fixed annual cycle of SST as well as soil moisture and snow cover are prescribed. This shows that the model QBO is not due to land-surface-atmosphere interaction. It is proposed that the model QBO arises due to an interaction between nonlinear intraseasonal oscillations and the annual cycle. Spatial structure of the QBO and its role in limiting the predictability of the Indian summer monsoon is discussed.

MIMO Precoding With X- and Y- Codes

We consider a slow fading multiple-input multiple-output (MIMO) system with channel state information at both the transmitter and receiver. A well-known precoding scheme is based upon the singular value decomposition (SVD) of the channel matrix, which transforms the MIMO channel into parallel subchannels. Despite having low maximum likelihood decoding (MLD) complexity, this SVD precoding scheme provides a diversity gain which is limited by the diversity gain of the weakest subchannel. We therefore propose X- and Y-Codes, which improve the diversity gain of the SVD precoding scheme but maintain the low MLD complexity, by jointly coding information across a pair of subchannels. In particular, subchannels with high diversity gain are paired with those having low diversity gain. A pair of subchannels is jointly encoded using a 2 2 real matrix, which is fixed a priori and does not change with each channel realization. For X-Codes, these rotation matrices are parameterized by a single angle, while for Y-Codes, these matrices are left triangular matrices. Moreover, we propose X-, Y-Precoders with the same structure as X-, Y-Codes, but with encoding matrices adapted to each channel realization. We observed that X-Codes/Precoders are good for well-conditioned channels, while Y-Codes/Precoders are good for ill-conditioned channels.

NMR in liquid crystals spinning at and near magic angle

NMR spectra of liquid crystalline phases and the molecules dissolved therein, spinning at and near the magic angle provide information on the director dynamics and the order parameter. The studies on the dynamics of the liquid crystal director for sample spinning near magic angle in mesophases with positive and negative diamagnetic susceptibility anisotropies (Delta chi) and their mixtures with near-zero macroscopic diamagnetic susceptibility anisotropies have been reported. In systems with weakly positive Delta chi, the director has been observed to switch from an orientation parallel to the spinning axis at low rotational speeds to one perpendicular to the spinning axis at high rotational speeds, when the angle theta, the axis of rotation makes with the magnetic field is smaller than the magic angle theta(m). For systems with a small negative Delta chi, similar director behaviour has been observed for theta greater than theta(m). At magic angle, the spectra under slow spinning speeds exhibit a centre band and side bands at integral values of the spinning speeds. The intensities of the spinning side bands have been shown to contain information on the sign and the magnitude of the order parameter(s). The results are discussed with illustrative examples. Results on the orientation of the chemical shielding tensor obtained from a combination of the NMR studies in the solid and the liquid crystalline states, have been described.

Relaxation behavior of twin nonlinear optical chromophores: Effect of the spacer length

A new series of twin nonlinear optical (NLO) molecules, having two 4-nitrophenol chromophores that are linked via a flexible polymethylene spacer of varying length [(CH2)(n), n = 1-12], were synthesized. Powder second harmonic generation measurements of these twin samples indicated a pronounced odd-even oscillation, with the odd twins exhibiting a high SHG value while the even ones gave no measurable SH signal. This behavior reflects the crystal packing preferences in such twin NLO systems that have odd and even numbers of atoms linking them - the even ones appear to prefer a centrosymmetric packing arrangement. The orientational/disordering dynamics of these twin NLO molecules, doped in a polymer (poly(methyl methacrylate)) matrix, has also been studied using SHG in electric field poled samples. Interestingly, the maximum attainable SH signal, chi((2)), in, the poled samples also showed an odd-even oscillation; the odd ones again having a higher value of chi((2)) This unprecedented odd-even oscillation in such molecularly doped systems is rationalized as being due to the intrinsically greater ease of a parallel alignment of the two chromophores in the twins with an odd spacer than in those with an even one. Further, the temporal stability of the SHG intensity at 70 degrees C, after the removal of the applied corona, was also studied. The relaxation of all the twin chromophores followed a biexponential decay; the characteristic relaxation time (tau(2)) for the slow decay component suggests that while the twin with a single methylene unit relaxes relatively slowly, the relaxation is significantly faster in cases where n = 2 and 3. In the twins with even longer spacer segments, the relaxation again becomes slower and reaches a saturation value. The observed minimum appears to reflect the interplay of two competing factors that affect the chromophore alignment in such twin systems, namely, the electrostatic repulsion between neighboring oriented dipoles and the intrinsic flexibility of the spacer.

The genetics of Mycobacterium tuberculosis

Gene manipulation in Mycobacterium tuberculosis has been slow in coming of age owing to the inherent difficulties associated with working on this aerosol-transmitted pathogen, in addition to the paucity of molecular tools such as plasmids and transposons. One of the early approaches to overcome these difficulties was the development of phasmids, which combined the properties of phages and plasmids and allowed introduction of recombinant genes into mycobacteria. The lone plasmid pAL5000 of mycobacteria has been exploited to its fullest potential in the construction of a plethora of vectors. Above all, the single most important achievement has been the development of elegant and innovative approaches to overcome the problem of illegitimate recombination which threatened the success of allelic-exchange mutagenesis in the slow-growing pathogenic mycobacterial species. In this review I discuss the current status of conditionally replicating plasmid and transposon vectors and their application in generating targeted mutations in mycobacteria.

Structural phase transitions in Bi2V1-xGexO5.5-x/2 (x=0.2, 0.4, and 0.6) single crystals: X-ray crystallographic study

Single crystals of Bi2V1-xGexO5.5-x/2 (x = 0.2, 0.4, and 0.6) were grown by slow cooling of melts. Bismuth vanadate transforms from an orthorhombic to a tetragonal structure and subsequently to an orthorhombic system when the Ge4+ concentration was varied from x = 0.2 to x = 0.6. All of these compositions crystallized in polar space groups (Aba2, F4mm, and Fmm2 for x = 0.2, 0.4, and 0.6, respectively). The structures were fully determined by single crystal X-ray diffraction studies, (C) 1999 Elsevier Science Ltd.

Non-resonant perturbation formula for interaction impedance measurement for a folded-waveguide SWS

The non-resonant perturbation formula for the measurement of interaction impedance of a folded-waveguide slow-wave structure was derived for the relevant electromagnetic field configuration at the axis of the beam-hole of the structure. Efficacy of the theory was benchmarked through virtual measurement using 3D electromagnetic modeling in CST-studio.

Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.

Polarization switching studies in ferroelectric glycine phosphite single crystals

Glycine Phosphite [NH3CH2COOH3PO3], abbreviated as GPI, undergoes a para-ferroelectric phase transition from the monoclinic symmetry P2(1)/a to P2(1) at 224.7 K. We report here a systematic study of the polarization switching process in this crystal. Growth of these crystals from aqueous solution has been undertaken employing both solvent evaporation and slow cooling methods. Hysteresis loop measurements along the polar b-axis yielded a spontaneous polarization value of 0.5 muC/cm(2) and a coercive field of 2.5 kV/cm. Conventional Merz technique was employed for polarization switching studies, wherein bipolar square pulses were applied to the sample to induce domain reversal. The transient switching pulse that flows through the sample on application of the field was recorded. The maximum switching time required for domain switching was measured both as a function of electric field and temperature. The experimentally observed switching curves were fitted with the model based on the Pulvari-Kuebler theory of nucleation and growth of domains. From the experimental data, the values of mobility and activation field were obtained. It was observed that switching process in this crystal is predominantly governed by the forward growth of domain walls in the high field region. However, switching process in GPI crystal was found to be slower than that found in other glycine based ferroelectric crystals.