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Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain
No full textgp120 is key to the human immunodeficiency virus type 1 viral cell entry. Knowledge of the detailed conformational states of gp120 is crucial to intervention, yet the unbound form is still resistant to structural characterization probably because of its flexibility. Toward this goal, we performed molecular dynamics simulations on the wild type gp120 core domain extracted from its ternary crystal structure and on a modeled mutant, S375W, that experimentally has a significantly different phenotype from the wild type. Although the mutant retained a bound-like conformation, the wild type drifted to a different conformational state. The wild type beta strands 2 and 3 of the bridging sheet were very mobile and partially unfolded, and the organization among the inner and outer domains and beta strands 20 and 21 of the bridging sheet, near the mutation site, was more open than in the bound form, although the overall structure was maintained. These differences were apparently a result of the strengthening of the hydrophobic core in the mutant. This stabilization further explains the experimentally significantly different thermodynamic properties between the wild type and the mutant. Taken together, our results suggest that the free form, although different from the bound state, shares many of the bound structural features. The observed loss of freedom near the binding site, rather than the previously hypothesized more dramatic conformational transition from the unbound to the bound state, appears to be the major contributor to the large entropy cost for the CD4 binding to the wild type
Solvation of carbonaceous molecules by para-H2 and ortho-D2clusters. II. Fullerenes
No full textThe coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D-2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C-60(+) and C-70(+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments
Origins of solidification when a simple molecular fluid is confined between two plates
No full textA simple globular-shaped liquid (octamethylcyclotetrasiloxane, OMCTS) was placed between two rigid mica plates at variable spacings comparable to the size of this molecule and the linear shear viscoelasticity of the confined interfacial film was measured. Strong monotonic increase of the shear relaxation time, elastic modulus, and effective viscosity were observed as the spacing was decreased below about 10 molecular dimensions. The frequency dependence of the viscoelastic spectra measured at different film thicknesses appeared to scale with reduced variables. The data are inconsistent with the abrupt first-order transition, from bulk fluid to solid with decreasing film thickness, whose possibility has been hypothesized, and suggest a glasslike transition instead
Correcting for electrostatic cutoffs in free energy simulations: toward consistency between simulations with different cutoffs
No full textThe use of electrostatic cutoffs in calculations of free energy differences by molecular simulations introduces errors. Even though both solute-solvent and solvent-solvent cutoffs are known to create discrepancies, past efforts have mostly been directed toward correcting for the solute-solvent cutoffs. In this work, an approach based on the generalized reaction field formalism is developed to correct for the solvent-solvent cutoff errors as well. It is shown using a series of simulations that when the cutoff lengths are significantly smaller than the half unit cell size, and the solute-solvent cutoff is not much larger than the solvent-solvent cutoff, the new algorithm is able to yield better agreement among simulations employing different truncation lengths
Cluster observations of whistler mode ducts and banded chorus
No full textBell et al. (2009) proposed that the source region for banded chorus consists of whistler mode ducts of depleted electron density (N-e) for upper band (UB) chorus for all wave normal angles (theta) and ducts of either enhanced or depleted N-e for lower band (LB) chorus for small theta and theta near or greater than the Gendrin angle, respectively. This paper provides support for this model using new high resolution (17 km) N-e observations from the Cluster WHISPER and EFW instruments. Data is examined from January 20, 2004, when strong banded chorus was observed over 3000 km of the Cluster 2 orbit, ending at the magnetic equator. Previous analysis of LB chorus on this day indicated the wave normal angles were larger than the Gendrin angle. Using the N-e data, we show that the LB chorus is generated within depletion ducts in the source region and that the half-width of these ducts (similar to 70 km) is comparable to the transverse scale (similar to 100 km) of the chorus source region. Making use of the fact that the group velocity of the LB chorus waves has a significant cross-L component, we show that the source region extends over 500 km near the magnetic equator
Vibrational cooling of spin-stretched dimer states by He buffer gas: quantum calculations for Li(2)(a (3)Sigma(+)(u)) at ultralow energies
No full textThe interaction between the triplet state of the lithium dimer, (7)Li(2), with (4)He is obtained from accurate ab initio calculations where the vibrational dependence of the potential is newly computed. Vibrational quenching dynamics within a coupled-channel quantum treatment is carried out at ultralow energies, and large differences in efficiency as a function of the initial vibrational state of the targets are found as one compares the triplet results with those of the singlet state of the same target
Figurine of goddess depicted as a mother breastfeeding child, Horoztepe
No full textFrontal view of the figurine of goddess depicted as a mother breastfeeding child, Horoztepe, from the province of Tokat. This sculpture is currently at the Museum of Anatolian Civilizations in Ankara.Black & white photograph
Old sun disc as burial finding - Pre-Hittite Hattic religious standard, Alacahöyük
No full textImage of one of the burial findings, cult object found in the royal tombs of pre-Hittite (Hatti) times from 3rd millenium BC, represented to gods. It is currently housed in Anatolian Civilization Museum in Ankara.Black & white photograph
Tunable integrated optical filters based on sapphire microspheres and liquid crystals
No full textWe present an integrated optical narrowband electrically tunable filter based on the whispering gallery modes of sapphire microspheres and double ion-exchanged channel BK7 glass waveguides. Tuning is provided by a liquid crystal infiltrated between the spheres and the glass substrate. By suitably choosing the radii of the spheres and of the circular apertures, upon which the spheres are positioned, arrays of different filters can be realized on the same substrate with a low cost industrial process. We evaluate the performance in terms of quality factor, mode spacing, and tuning range by comparing the numerical results obtained by the numerical finite element modeling approach and with the analytical approach of the Generalized Lorenz-Mie Theory for various design parameters. By reorienting the LC in an external electrical field, we demonstrate the tuning of the spectral response of the sapphire microsphere based filter. We find that the value of the mode spacing remains nearly unchanged for the different values of the applied electric field. An increase of the applied electric field strength, changes the refractive index of the liquid crystal, so that for a fixed geometry the mode spacing remains unchanged
Temperature-induced tuning of emission spectra of liquid-crystal optical microcavities
No full textEmulsion droplets of liquid crystals (LC) suspended in water and labeled with a suitable fluorescent dye can serve as active optofluidic microcavities, since the contrast of refractive index between the LC droplets and the surrounding aqueous medium allows excitation of whispering gallery modes (WGMs) in the droplets. In addition, such emulsion droplets can be also stably trapped in three-dimensions using optical tweezers which stabilizes the droplets while investigating their spectral characteristics. We explore various combinations of fluorescently dyed LC droplets and host liquid-surfactant systems and show that the WGM emission spectrum of an optically trapped LC droplet-based cavity can be largely and (almost) reversibly tuned by controlled changes of the ambient temperature that induce phase transitions in the LC droplets. Our results indicate feasibility of this approach for creating miniature tunable sources of coherent light