DMT of Multihop Networks: End Points and Computational Tools

In this paper, the diversity-multiplexing gain tradeoff (DMT) of single-source, single-sink (ss-ss), multihop relay networks having slow-fading links is studied. In particular, the two end-points of the DMT of ss-ss full-duplex networks are determined, by showing that the maximum achievable diversity gain is equal to the min-cut and that the maximum multiplexing gain is equal to the min-cut rank, the latter by using an operational connection to a deterministic network. Also included in the paper, are several results that aid in the computation of the DMT of networks operating under amplify-and-forward (AF) protocols. In particular, it is shown that the colored noise encountered in amplify-and-forward protocols can be treated as white for the purpose of DMT computation, lower bounds on the DMT of lower-triangular channel matrices are derived and the DMT of parallel MIMO channels is computed. All protocols appearing in the paper are explicit and rely only upon AF relaying. Half-duplex networks and explicit coding schemes are studied in a companion paper.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Molecular interactions in bis(2-aminopyridinium) malonate: A crystal isostructural to bis(2-aminopyridinium) maleate crystal

Crystals of a new salt in 2:1 ratio of 2-aminopyridine and malonic acid are grown by slow evaporation. These crystals of bis(2-aminopyridinium) malonate are orthorhombic and belong to the non-centrosymmetric space group, Fdd2 with parameters a = 22.0786(6), b = 23.0218(6), c = 5.5595(1)angstrom and Z=8 at 300 K. The crystals are isostructural to those of bis(2-aminopyridinium) maleate, which is a NLO material. The isostructurality index between bis(2-aminopyridinium) maleate and bis(2-aminopyridinium) malonate was also calculated. The hyperpolarizability calculated using semi empirical method MOPAC2009 showed that bis(2-aminopyridinium) malonate has slightly higher beta value compared to that of bis(2-aminopyridinium) maleate. (C) 2011 Elsevier B.V. All rights reserved.

Oscillatory settling in wormlike-micelle solutions: bursts and a long time scale

We study the dynamics of a spherical steel ball falling freely through a solution of entangled wormlike-micelles. If the sphere diameter is larger than a threshold value, the settling velocity shows repeated short oscillatory bursts separated by long periods of relative quiescence. We propose a model incorporating the interplay of settling-induced flow, viscoelastic stress and, as in M. E. Cates, D. A. Head and A. Ajdari, Phys. Rev. E, 2002, 66, 025202(R) and A. Aradian and M. E. Cates, Phys. Rev. E, 2006, 73, 041508, a slow structural variable for which our experiments offer independent evidence.

Two-dimensional moist stratified turbulence and the emergence of vertically sheared horizontal flows

Moist stratified turbulence is studied in a two-dimensional Boussinesq system influenced by condensation and evaporation. The problem is set in a periodic domain and employs simple evaporation and condensation schemes, wherein both the processes push parcels towards saturation. Numerical simulations demonstrate the emergence of a moist turbulent state consisting of ordered structures with a clear power-law type spectral scaling from initially spatially uncorrelated conditions. An asymptotic analysis in the limit of rapid condensation and strong stratification shows that, for initial conditions with enough water substance to saturate the domain, the equations support a straightforward state of moist balance characterized by a hydrostatic, saturated, vertically sheared horizontal flow (VSHF). For such initial conditions, by means of long time numerical simulations, the emergence of moist balance is verified. Specifically, starting from uncorrelated data, subsequent to the development of a moist turbulent state, the system experiences a rather abrupt transition to a regime which is close to saturation and dominated by a strong VSHF. On the other hand, initial conditions which do not have enough water substance to saturate the domain, do not attain moist balance. Rather, the system is observed to remain in a turbulent state and oscillates about moist balance. Even though balance is not achieved with these general initial conditions, the time scale of oscillation about moist balance is much larger than the imposed time scale of condensation and evaporation, thus indicating a distinct dominant slow component in the moist stratified two-dimensional turbulent system. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694805]

Structural, vibrational and thermal studies of a new nonlinear optical material: L-Asparagine-L-tartaric acid

Crystals of a new nonlinear optical (NLO) material, viz., L-asparagine-L-tartaric acid (LALT)(1) were grown by slow evaporation of an aqueous solution containing equimolar concentrations of L-asparagine and t-tartaric acid. The structure of the title compound which crystallizes in the non-centrosymmetric monoclinic space group P2(1) consists of a molecule of L-asparagine and a molecule of free L-tartaric acid both of which are interlinked by three varieties of H-bonding interactions namely O-H center dot center dot center dot O, N-H center dot center dot center dot O and C-H center dot center dot center dot O. The UV-Vis-NIR spectrum of 1 reveals its transparent nature while the vibrational spectra confirm the presence of the functional groups in 1. The thermal stability and second harmonic generation (SHG) conversion efficiency of 1 were investigated. (C) 2012 Elsevier B.V. All rights reserved.

Statistical properties of entropy-consuming fluctuations in jammed states of laponite suspensions: Fluctuation relations and generalized Gumbel distribution

We report a universal large deviation behavior of spatially averaged global injected power just before the rejuvenation of the jammed state formed by an aging suspension of laponite clay under an applied stress. The probability distribution function (PDF) of these entropy consuming strongly non-Gaussian fluctuations follow an universal large deviation functional form described by the generalized Gumbel (GG) distribution like many other equilibrium and nonequilibrium systems with high degree of correlations but do not obey the Gallavotti-Cohen steady-state fluctuation relation (SSFR). However, far from the unjamming transition (for smaller applied stresses) SSFR is satisfied for both Gaussian as well as non-Gaussian PDF. The observed slow variation of the mean shear rate with system size supports a recent theoretical prediction for observing GG distribution.

Electrical Treeing and the Associated PD Characteristics in LDPE Nanocomposites

Treeing in low density polyethylene (LDPE) filled with alumina nanocomposite as well as unfilled LDPE samples stressed with 50 Hz ac voltage has been studied. The tree inception voltage was monitored for various samples with different nano-filler loadings and it is seen that there is an increase in tree inception voltage with filler loading in LDPE. Treeing pattern and tree growth duration for unfilled and nano-filled LDPE samples have also been studied. Different tree growth patterns as well as a slower tree growth with increase in filler loading in LDPE nanocomposites were observed. The observed slow propagation of tree growth with filler loading is attributed to the changes in the polymer crystalline morphology induced by the presence of nano-particles and the greater ability of the nanoparticles to resist discharge growth. SEM studies carried out to determine the morphology of unfilled and nano-filled LDPE showed an increase in lamellae packing in LDPE nanocomposites and this increased lamellar density leads to a reduction in the tree propagation rate. Partial discharge activities were also monitored during the electrical tree growth in both the unfilled and the nano-filled LDPE samples and were found to be significantly different. PD magnitude and the number of PD pulses per cycle were found to be lower with electrical tree growth duration in LDPE nanocomposites as compared to unfilled LDPE. The same trend was seen with increased filler loading also.

Study of Low Temperature Magnetic Properties of a Single Chain Magnet with Alternate Isotropic and Non-collinear Anisotropic Units

Here we study thermodynamic properties of an important class of single-chain magnets (SCMs), where alternate units are isotropic and anisotropic with anisotropy axes being non-collinear. This class of SCMs shows slow relaxation at low temperatures which results from the interplay of two different relaxation mechanisms, namely dynamical and thermal. Here anisotropy is assumed to be large and negative, as a result, anisotropic units behave like canted spins at low temperatures; but even then simple Ising-type model does not capture the essential physics of the system due to quantum mechanical nature of the isotropic units. We here show how statistical behavior of this class of SCMs can be studied using a transfer matrix (TM) method. We also, for the first time, discuss in detail how weak inter-chain interactions can be treated by a TM method. The finite size effect is also discussed which becomes important for low temperature dynamics. At the end of this paper, we apply this technique to study a real helical chain magnet.

Autophosphorylation of Ser(428) of EhC2PK Plays a Critical Role in Regulating Erythrophagocytosis in the Parasite Entamoeba histolytica

The protozoan parasite Entamoeba histolytica can invade both intestinal and extra intestinal tissues resulting in amoebiasis. During the process of invasion E. histolytica ingests red blood and host cells using phagocytic processes. Though phagocytosis is considered to be a key virulence determinant, the mechanism is not very well understood in E. histolytica. We have recently demonstrated that a novel C2 domain-containing protein kinase, EhC2PK is involved in the initiation of erythrophagocytosis. Because cells overexpressing the kinase-dead mutant of EhC2PK displayed a reduction in erythrophagocytosis, it appears that kinase activity is necessary for initiation. Biochemical analysis showed that EhC2PK is an unusual Mn2+-dependent serine kinase. It has a trans-autophosphorylated site at Ser(428) as revealed by mass spectrometric and biochemical analysis. The autophosphorylation defective mutants (S428A, KD Delta C) showed a reduction in auto and substrate phosphorylation. Time kinetics of in vitro kinase activity suggested two phases, an initial short slow phase followed by a rapid phase for wild type protein, whereas mutations in the autophosphorylation sites that cause defect (S428A) or conferred phosphomimetic property (S428E) displayed no distinct phases, suggesting that autophosphorylation may be controlling kinase activity through an autocatalytic mechanism. A reduction and delay in erythrophagocytosis was observed in E. histolytica cells overexpressing S428A and KD Delta C proteins. These results indicate that enrichment of EhC2PK at the site of phagocytosis enhances the rate of trans-autophosphorylation, thereby increasing kinase activity and regulating the initiation of erythrophagocytosis in E. histolytica.

Synthesis and Electrochemical Characterization of LiNi0.8Co0.2O2 as Cathode Material for Aqueous Rechargeable Lithium Batteries

LiNi0.8Co0.2O2 cathode material for lithium ion batteries is synthesized by reaction under autogenic pressure at elevated temperature (RAPET) method. The simple synthesis procedure is time and energy saving, and thus is promising for commercial application. The structure and stability of the material have been characterized by means of XRD and TG-DTA. The electrochemical properties of the LiNi0.8Co0.2O2 cathode are investigated in 2 M Li2SO4 aqueous electrolyte and they are compared to that in an organic electrolyte. A battery cell consisting of LiNi0.8Co0.2O2 as cathode in 2 M Li2SO4 solution is constructed in combination with LiTi2 (PO4)(3) as anode. The cell retained almost constant discharge capacity over hundred cycles. The electrochemical impedance spectral ( EIS) studies in aqueous and nonaqueous electrolytes revealed that the mechanism of lithium ion intercalation and deintercalation processes in LiNi0.8Co0.2O2 electrode follow almost similar mechanism in both aqueous and nonaqueous electrolytes. The chemical diffusion coefficient was calculated from slow scan rate cyclic voltammetry and EIS. (C) 2012 The Electrochemical Society. DOI: 10.1149/2.075205jes] All rights reserved.

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

Anaerobic retting of banana and arecanut wastes in a plug flow digester for recovery of fiber, biogas and compost

Leaves and leaf sheath of banana and areca husk (Areca catechu) constitute an important component of urban solid waste (USW) in India which are difficult to degrade under normal windrow composting conditions. A successful method of anaerobic digestion built around the fermentation properties of these feedstock has been evolved which uses no moving parts, pretreatment or energy input while enabling recovery of four products: fiber, biogas, compost and pest repellent. An SRT of 27 d and 35 d was found to be optimum for fiber recovery for banana leaf and areca husk, respectively. Banana leaf showed a degradation pattern different from other leaves with slow pectin-1 degradation (80%) and 40% lignin removal in 27 d SRT. Areca husk however, showed a degradation pattern similar to other plant biomass. Mass recovery levels for banana leaf were fiber-20%, biogas-70% (400 ml/g TS) and compost-10%. For areca husk recovery was fiber-50%, biogas-45% (250 ml/g TS) and compost-5%. (C) 2012 Elsevier Inc. All rights reserved.

Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

Background: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C). However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA) of the predominant HIV-1C strains. Methodology/Principal Findings: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10%) of unique recombinant forms (BC and A1C) was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively). The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag) to 1974 (env). Pol-gene analysis was considered to provide the most reliable estimate 1971, (95% CI: 1965-1976)]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. Conclusions/Significance: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular surveillance to guide efficient disease intervention strategies.

Non-monotonic, distance-dependent relaxation of water in reverse micelles: Propagation of surface induced frustration along hydrogen bond networks

Layer-wise, distance-dependent orientational relaxation of water confined in reverse micelles (RM) is studied using theoretical and computational tools. We use both a newly constructed ``spins on a ring'' (SOR) Ising-type model (with Shore-Zwanzig rotational dynamics) and atomistic simulations with explicit water. Our study explores the effect of reverse micelle size and role of intermolecular correlations, compromised by the presence of a highly polar surface, on the distance (from the interface) dependence of water relaxation. The ``spins on a ring'' model can capture some aspects of distance dependence of relaxation, such as acceleration of orientational relaxation at intermediate layers. In atomistic simulations, layer-wise decomposition of hydrogen bond formation pattern clearly reveals that hydrogen bond arrangement of water at a certain distance away from the surface can remain frustrated due to the interaction with the polar surface head groups. This layer-wise analysis also reveals the presence of a non-monotonic slow relaxation component which can be attributed to this frustration effect and which is accentuated in small to intermediate size RMs. For large size RMs, the long time component decreases monotonically from the interface to the interior of the RMs with slowest relaxation observed at the interface. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4732095]