Pairwise Interactions between Linear Alkanes in Water Measured by AFM Force Spectroscopy

Pairwise interactions between n-alkanes from decane to octadecane in water have been studied by single-molecule force spectroscopy. The interacting molecules are covalently tethered to the glass substrate and to the probe of an atomic force microscope by water-soluble linkers to facilitate single-molecule detection. However, the measured distribution of rupture forces deviates significantly from the distribution predicted by theoretical models for rupture of individual bonds. To describe the statistics of rupture forces, an analytical model that considers near-simultaneous rupture of two bonds loaded by tethers with different lengths is introduced. The common most probable force analysis approach is used for comparison. In both data analyses, the possible systematic errors due to nonlinear elasticity of polymeric tethers and variations in the shape of the potential of mean force were considered. Experimental distributions of rupture forces are well-fit by the two-bond rupture model using a single set of kinetic parameters for different experiments, while the most probable force approach yields parameters that vary significantly for different samples. The measured activation energies for dissociation of alkanes are close to the free energies predicted by cavity models of hydrophobic interactions. The surface free-energy density is estimated to be ∼21 kJ/(mol nm^2) and is close to the upper limit of free energies used in the computer simulations of hydrophobic interactions in proteins. In contrast to the predictions of the cavity models, the measured activation energy does not increase monotonically with increase in alkane chain size. To explain this discrepancy and the measured distance to the transition-state barrier (∼0.6 nm), it is suggested that alkanes undergo conformational transition to the collapsed state upon dimerization. Change in the alkane conformation from extended to helical has been observed previously for binding of alkanes in water to hydrophobic synthetic receptors. Here, however, conformational change is suggested without geometrical constraints imposed by small cavitands. The proposed collapsed state of the alkane dimers has implications for the kinetics of self-assembly of surfactant micelles

Effects of Multiple-Bond Ruptures in Force Spectroscopy Measurements of Interactions between Fullerene C_(60) Molecules in Water

Interactions between fullerene C_(60) molecules in water were measured by force spectroscopy. Fullerene molecules were covalently connected to bifunctional water-soluble poly(ethylene glycol) (PEG) linkers and subsequently tethered to the substrate and to the tip of the atomic force microscope to facilitate single molecule detection and avoid spurious surface effects. The distributions of rupture forces for substrates prepared with different incubation times of C_(60)-PEG-NH_2 exhibit high rupture forces that cannot be explained by the theoretical distribution of single molecule binding. Moreover, the relative amplitude of the high force peak in the histogram increases with incubation time. These observations are explained by attributing the measured high forces to the rupture of multiple bonds between fullerene molecules. Force spectroscopy data analysis based on the most probable forces gives significantly different dissociation rates for samples that exhibit different amplitudes of the high force peak. An approximate analytical model that considers ruptures of two bonds that are simultaneously loaded by tethers with different lengths is proposed. This model successfully fits the distributions of the rupture forces using the same set of kinetic parameters for samples prepared with different grafting densities. It is proposed that this model can be used as a common tool to analyze the probability distributions of rupture forces that contain peaks or shoulders on the high force side of the distribution

Anisotropy of Pairwise Interactions between Hexadecanes in Water Measured by AFM Force Spectroscopy

The pulling coordinate dependence of hexadecane dimer dissociation in water was studied using AFM-based single molecule force spectroscopy. Hexadecanes were covalently bound to both the AFM cantilever and to the glass substrates through hydrophilic poly-(ethylene glycol) tethers. The polymer tether was attached either to the end of hexadecane or in the middle of the molecule. Experimentally studied configurations of hexadecanes tethered to the AFM probe and to the glass substrate include a symmetric end-attached configuration (EE), an asymmetric end-attached vs middle-attached configuration (ME), and a symmetric middle-attached configuration (MM). Kinetic parameters of the distance to the transition state barrier (barrier width) and activation energy of dissociation were extracted from the statistical analysis of double tether rupture events. The rupture force analysis employs a recently introduced two-bond model that corrects for errors induced by potential multiple simultaneous rupture events and accounts for the tether stiffening effects. Effects of the shape of intermolecular potential were considered by using the Bell−Evans and Hummer−Szabo force spectroscopy models. The activation energies to dissociation were similar for all configurations while the barrier width was significantly shorter for the MM and ME configurations than for EE configurations. Primitive models that include touching or merging spherical or cylindrical shapes were considered. These models were inconsistent with the extracted kinetic parameters. It is suggested that the observed anisotropy may be a result of conformational transition of hexadecane from extended to collapsed state during dimerization. A flexible four-bead model of hexadecane was introduced to account for conformational flexibility. Using the length and solvent accessible surface area of hexadecane, the four-bead model gave molecular dissociation parameters consistent with the experimental data. This suggests that conformational flexibility is an important factor in hydrophobic interactions between alkane chains

A subsystems approach for parameter estimation of ODE models of hybrid systems

We present a new method for parameter identification of ODE system descriptions based on data measurements. Our method works by splitting the system into a number of subsystems and working on each of them separately, thereby being easily parallelisable, and can also deal with noise in the observations.Comment: In Proceedings HSB 2012, arXiv:1208.315

J-Band Infrared Spectroscopy of a Sample of Brown Dwarfs Using Nirspec on Keck II

Near-infrared spectroscopic observations of a sample of very cool, low-mass objects are presented with higher spectral resolution than in any previous studies. Six of the objects are L-dwarfs, ranging in spectral class from L2 to L8/9, and the seventh is a methane or T-dwarf. These new observations were obtained during commissioning of NIRSPEC, the first high-resolution near-infrared cryogenic spectrograph for the Keck II 10-meter telescope on Mauna Kea, Hawaii. Spectra with a resolving power of R=2500 from 1.135 to 1.360 microns (approximately J-band) are presented for each source. At this resolution, a rich spectral structure is revealed, much of which is due to blending of unresolved molecular transitions. Strong lines due to neutral potassium (K I), and bands due to iron hydride (FeH) and steam (H2O) change significantly throughout the L sequence. Iron hydride disappears between L5 and L8, the steam bands deepen and the K I lines gradually become weaker but wider due to pressure broadening. An unidentified feature occurs at 1.22 microns which has a temperature dependence like FeH but has no counterpart in the available FeH opacity data. Because these objects are 3-6 magnitudes brighter in the near-infrared compared to the I-band, spectral classification is efficient. One of the objects studied (2MASSW J1523+3014) is the coolest L-dwarf discovered so far by the 2-Micron All-Sky Survey (2MASS), but its spectrum is still significantly different from the methane-dominated objects such as Gl229B or SDSS 1624+0029.Comment: New paper, Latex format, 2 figures, accepted to ApJ Letter

AGN Populations in Large Volume X-ray Surveys: Photometric Redshifts and Population Types found in the Stripe 82X Survey

Multi-wavelength surveys covering large sky volumes are necessary to obtain an accurate census of rare objects such as high luminosity and/or high redshift active galactic nuclei (AGN). Stripe 82X is a 31.3 deg$^2$ X-ray survey with $Chandra$ and $XMM$-Newton observations overlapping the legacy Sloan Digital Sky Survey (SDSS) Stripe 82 field, which has a rich investment of multi-wavelength coverage from the ultraviolet to the radio. The wide-area nature of this survey presents new challenges for photometric redshifts for AGN compared to previous work on narrow-deep fields because it probes different populations of objects that need to be identified and represented in the library of templates. Here we present an updated X-ray plus multi-wavelength matched catalog, including $Spitzer$ counterparts, and estimated photometric redshifts for 5961 (96% of a total of 6181) X-ray sources, which have a normalized median absolute deviation, $\sigma_{\rm nmad}$ = 0.06 and an outlier fraction, $\eta$ = 13.7%. The populations found in this survey, and the template libraries used for photometric redshifts, provide important guiding principles for upcoming large-area surveys such as $eROSITA$ and 3$XMM$ (in X-ray) and the Large Synoptic Survey Telescope (LSST; optical).Comment: Accepted for publication by The Astrophysical Journal (33 pages, 20 figures, 13 tables). Final catalog of counterparts and photo-z supplementing the paper available here: http://stripe82x.com/docs/stripe82x-photometric-redshifts-and-multiwavelength-data-catalog

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility

Fasting ​glucose and ​insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association of a low-frequency nonsynonymous SNV in ​GLP1R (A316T; rs10305492; MAF=1.4%) with lower FG (β=−0.09±0.01 mmol l^(−1), P=3.4 × 10^(−12)), T2D risk (OR[95%CI]=0.86[0.76–0.96], P=0.010), early ​insulin secretion (β=−0.07±0.035 pmol_(insulin) mmol_(glucose)^(−1), P=0.048), but higher 2-h ​glucose (β=0.16±0.05 mmol l^(−1), P=4.3 × 10^(−4). We identify a gene-based association with FG at ​G6PC2 (pSKAT=6.8 × 10−6) driven by four rare protein-coding SNVs (H177Y, Y207S, R283X and S324P). We identify rs651007 (MAF=20%) in the first intron of ​ABO at the putative promoter of an antisense lncRNA, associating with higher FG (β=0.02±0.004 mmol l^(−1), P=1.3 × 10^(−8)). Our approach identifies novel coding variant associations and extends the allelic spectrum of variation underlying diabetes-related quantitative traits and T2D susceptibility

On the stationary points of the TAP free energy

In the context of the p-spin spherical model, we introduce a method for the computation of the number of stationary points of any nature (minima, saddles, etc.) of the TAP free energy. In doing this we clarify the ambiguities related to the approximations usually adopted in the standard calculations of the number of states in mean field spin glass models.Comment: 11 pages, 1 Postscript figure, plain Te