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Prediction and validation of HIV-1 gp41 ecto-transmembrane domain post-fusion trimeric structure using molecular modeling
No full textThe glycoproteins on the surface of human immunodeficiency virus (HIV) undergoes cascade of conformational transitions to evade the human immune system. The virus replicates inside the host and infects the T-cells instigating acquired immunodeficiency syndrome (AIDS). The glycoprotein 41 (gp41) of HIV helps to mediate the fusion of virus and host membranes. The detailed mechanism of host cell invasion by virus remains obscure due to the unavailability of experimental structure of complete gp41. In the current study, the post-fusion (PoF) trimeric structure of ecto-domain including transmembrane domain of gp41 was modeled using multiple homologous templates of Simian immunodeficiency virus (SIV) and HIV-1. In order to validate the gp41 model, interactions of three peptide inhibitors: T20, C37 and C34; were studied using all-atom molecular dynamics (MD) simulations, binding free-energy calculation and per-residue energy decomposition analysis. The binding free energy calculated using MM-PBSA (Molecular Mechanics Poisson-Boltzmann surface area) method predicts maximum affinity for C34 and minimum by T20 for gp41, which is in good agreement with the available computational and experimental studies. The van der Waals interaction is a dominant contributor for the peptide-gp41 complexes. The per-residue decomposition of energy confirmed the role of Trp117, Trp120 and Ile124, present in C34 and C37, for the strong hydrophobic interactions with the deep pocket localized around the N-terminal of gp41, which is lacking in T20. The HIV-1 gp41 structure developed in this work can be used in future study to gain insight into the mechanism of virus invasion and probing potent inhibitor to eliminate AIDS
Tracing groundwater salinization using geochemical and isotopic signature in Southeastern coastal Tamilnadu, India
No full textAttempt has been made to discriminate groundwater salinity causes along the east coast of India. A total of 122 groundwater samples (61/season) were collected for two diverse seasons (Pre Monsoon and Post Monsoon) and analyzed for physical and chemical components along with stable isotopes. The Piper diagram proposes samples along the coast predisposed by saltwater incursion. Ionic ratio plots recommend groundwater discriminatory by changing geochemical signatures. The statistical correlation suggests impact of saltwater incursion, anthropogenic and rock water interaction as sources for dissolved constituents in groundwater. The thermodynamic stability plot suggests higher silicate dissolution, weathering and ion exchange prompting water chemistry nevertheless of seasons. The delta O-18 and delta H-2 increases towards the sea suggesting enrichment attributed to the sea water influence and rainfall influences along the southwestern parts of the study area
Tailoring fields of one-sheet and two-sheet planar ion trap mass analyzers
No full textIn this paper, a simulation study on tailoring the fields in planar ion trap geometries for making them suitable for mass analysis is presented. Two different planar trap geometries were considered: the first is a One-Sheet Ion Trap Geometry in which the ions are trapped off-plane and the second is a Two-Sheet Ion Trap Geometry in which the ions are trapped in between the two sheets. Both DC and RF potentials were used to trap ions. The fields were tailored to obtain linear trapping fields in these two geometries. This was done by splitting the central electrode into segments and applying suitable DC potentials to them. The potentials were computed using a least square method. The simulations were carried out considering a printed circuit board (PCB) with a Teflon base. The One-Sheet Ion Trap Geometry consists of five electrodes, of which the central electrode is segmented. In Two-Sheet Ion Trap Geometry, each sheet consists of three electrodes, of which the central electrode is segmented. The method outlined in the study is able to tailor fields to be linear as well as mildly superlinear
Experimental Insights into the Electronic Nature, Spectral Features, and Role of Entropy in Short CH3 center dot center dot center dot CH3 Hydrophobic Interactions
No full textHydrophobic interactions are often explored in solution-state aggregation of molecules. However, an experimental electron density description about these interactions is still lacking. Here, we report a systematic study on the electronic nature of methyl center dot center dot center dot methyl hydrophobic interactions in a series of multicomponent crystals of biologically active molecules. Charge density models based on high-resolution X-ray diffraction allow the visualization of subtle details of electron density features in the interaction region. Our study classifies these interactions as atypical group center dot center dot center dot group interactions in contrast to sigma-hole interactions, which are stabilized by the minimized electrostatic repulsion and maximized dispersion forces. For the first time, we quantified the solid-state entropic contribution from the torsional mode of the methyl groups in stabilizing these interactions by thermal motion analysis based on neutron diffraction as well as variable-temperature crystallography. The carbon atoms in methyl center dot center dot center dot methyl interactions show a unique upfield chemical shift in the C-13 solid-state NMR signal
The Effect of Bulge Mass on Bar Pattern Speed in Disk Galaxies
No full textWe present a study of the effect of bulge mass on the evolution of bar pattern speed in isolated disk galaxies using N-body simulations. Earlier studies have shown that disk stars at the inner resonances can transfer a significant amount of angular momentum to the dark matter halo and this results in the slowdown of the bar pattern speed. In this paper we investigate how the mass of the other spheroidal component, the bulge, affects bar pattern speeds. In our galaxy models the initial bars are all rotating fast as the <CDATA<i parameter. The ratio of the corotation radius to bar radius is less than 1.4, which is typical of fast bars. However, as the galaxies evolve with time, the bar pattern speed (?(p)) slows down, leading to <CDATA<i for all the models except for the model with the most massive bulge, in which the bar formed late and did not have time to evolve. The rapid slowdown of ?(p) is due to the larger angular momentum transfer from the disk to the bulge and to interactions between stars at the inner resonances and those in the bar. Hence we conclude that the decrease in ?(p) clearly depends on bulge mass in barred galaxies and decreases faster for galaxies with more massive bulges. We discuss the implications of our results for observations of bar pattern speeds in galaxies
Dynamics of Phenotypic Heterogeneity Associated with EMT and Stemness during Cancer Progression
No full textGenetic and phenotypic heterogeneity contribute to the generation of diverse tumor cell populations, thus enhancing cancer aggressiveness and therapy resistance. Compared to genetic heterogeneity, a consequence of mutational events, phenotypic heterogeneity arises from dynamic, reversible cell state transitions in response to varying intracellular/extracellular signals. Such phenotypic plasticity enables rapid adaptive responses to various stressful conditions and can have a strong impact on cancer progression. Herein, we have reviewed relevant literature on mechanisms associated with dynamic phenotypic changes and cellular plasticity, such as epithelial-mesenchymal transition (EMT) and cancer stemness, which have been reported to facilitate cancer metastasis. We also discuss how non-cell-autonomous mechanisms such as cell-cell communication can lead to an emergent population-level response in tumors. The molecular mechanisms underlying the complexity of tumor systems are crucial for comprehending cancer progression, and may provide new avenues for designing therapeutic strategies
Gate-Induced Metal-Insulator Transition in 2D van der Waals Layers of Copper Indium Selenide Based Field-Effect Transistors
No full textThe existence of an exquisite phenomenon such as a metal-insulator transition (MIT) in two-dimensional (2D) systems, where completely different electronic functionalities in the same system can emerge simply by regulating parameters such as charge carrier density in them, is noteworthy. Such tunability in material properties can lead to several applications where precise tuning of function specific properties are desirable. Here, we report on our observation on the occurrence of MIT in the 2D material system of copper indium selenide (CuIn7Se11). Clear evidence of the metallic nature of conductivity (sigma) under the influence of electrostatic doping via the gate, which crosses over to an insulating phase upon lowering the temperature, was observed by investigating the temperature and gate dependence of a in CuIn7Se11 field-effect transistor devices. At higher charge carrier densities (n > 10(12) cm(-1)), we found that sigma similar to (n)(alpha) with a similar to 2, which suggests the presence of bare Coulomb impurity scattering within the studied range of temperature (280 K > T > 20 K). Our analysis of the conductivity data following the principles of percolation theory of transition where sigma similar to (n - n(C))(delta) show that the critical percolation exponent delta(T) has average values similar to 1.57 +/- 0.27 and 1.02 +/- 0.35 within the measured temperature range for the two devices and it is close to the 2D percolation exponent value of 1.33. We believe that the 2D MIT seen in our system is due to the charge density inhomogeneity caused by electrostatic doping and unscreened charge impurity scattering that leads to a percolation driven transition. The findings reported here for CuIn7Se11 system provide a different material platform to investigate MIT in 2D and are crucial in order to understand the fundamental basis of electronic interactions and charge-transport phenomenon in other unexplored 2D electron systems
Activated carbon-carbon dioxide based two stage adsorption compression Brayton cycle power generation
No full textEnhancement of energy delivery of a carbon dioxide (CO2) Brayton cycle without compression work liability is achievable using low grade heat for thermal compression. The limitation of the expansion ratios of a single stage adsorption thermal compression is obviated by opting for pressure build up in two stages. Despite the use of a large number of adsorbers, it is shown that, specific work output can be augmented substantially with no undue penalty on the overall cycle efficiency albeit with a marginal shortfall in work output per unit mass of adsorbent. These features are elucidated through an activated carbon based thermal compression of CO2 yet limiting high side pressures to 80 bar and the principal heat source at a temperature equal to or less than 300 degrees C in tandem with another low grade source at 100 degrees C for thermal compression. The net outcome is a substantial reduction in the size of the power block and heat exchangers resulting from enhancement of the expansion ratio and reduction in the mass flow rate in the circuit
Nonuniform Isospectrals of Uniform Timoshenko Beams
No full textSpectrally equivalent systems are those that have the same free vibration natural frequencies for a given boundary condition. In this paper, we establish isospectrality between certain classes of nonuniform Timoshenko beams with a given uniform Timoshenko beam. We apply a transformation to convert the nondimensional coupled nonuniform Timoshenko beam equations from the (x,W) frame of reference to a hypothetical (z,U) frame of reference. The transformed equations are then combined by eliminating one of the variables. Specific material and geometric properties are chosen, and a few auxiliary variables are introduced to convert the transformed equation into the required form. If the coefficients of the transformed equation match with the required uniform equation, then the nonuniform beam is said to be isospectral to the uniform beam. The boundary configurations also change during this transformation. We present the constraints under which they are preserved. Frequency equivalence of the beams is confirmed by the finite element method. For the considered cases, examples of beams having a rectangular cross-section are also presented
Coupled Ocean-Atmosphere Summer Intraseasonal Oscillation over the Bay of Bengal
No full textThis study shows the active role of subsurface ocean temperature in the evolution of coupled intra-seasonal oscillation (ISO) in the Bay of Bengal (BoB) using multi-satellite observations and ocean analysis product. Satellite-derived humidity profiles obtained from the atmospheric infrared sounder (AIRS) show that intense rains over the BoB are associated with the moistening (drying) in the lower and mid-troposphere during the active (break) phase of summer intraseasonal oscillation (ISO). Anomalous moistening in the mid-troposphere up to 500 hPa ahead of the maximum precipitation band over north BoB gives a precursor signal for the northward movement of the rain band. During the active (break) phase, the upper-tropospheric positive (negative) temperature anomaly ahead of the maximum rain band also sets a precondition by heating the mid- to upper troposphere. Daily subsurface temperature from Global Ocean Data Assimilation System (GODAS) analysis show that during the active phase, tropospheric moistening (drying) coincides with the subsurface warm (cold) temperature up to 200-m depth. The upper ocean warms uniformly by \~ 1 degrees C during the active phase as compared to the break phase in the entire BoB. The presence of a thin warm layer below the maximum rain band creates an environment conducive to sustaining the active phase on the ISO time scale. A positive sea surface temperature (SST) anomaly along with upper ocean warming ahead of a rain band in the north BoB in association with lower and mid-tropospheric moistening sets a precondition for the northward movement of the rain band. The anomalous warming (cooling) in the thermocline is associated with deeper (shallower) thermocline depth 23 degrees isotherms (D23)] and coincides with the mixed-layer warmin