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We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)(-), measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP∕6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.

An extension of the traditional Kirkwood-Buff (KB) theory of solutions is outlined which provides additional fluctuating quantities that can be used to characterize and probe the behavior of solution mixtures. Particle-energy and energy-energy fluctuations for local regions of any multicomponent solution are expressed in terms of experimentally obtainable quantities, thereby supplementing the usual particle-particle fluctuations provided by the established KB inversion approach. The expressions are then used to analyze experimental data for pure water over a range of temperatures and pressures, a variety of pure liquids, and three binary solution mixtures – methanol and water, benzene and methanol, and aqueous sodium chloride. In addition to providing information on local properties of solutions it is argued that the particle-energy and energy-energy fluctuations can also be used to test and refine solute and solvent force fields for use in computer simulation studies.

The theoretical basis of two-frequency saturation is given here in the framework of Provotorov theory. The parameters influencing the saturation efficiency are discussed and studied experimentally using a liquid-crystalline test system. It is shown that double-frequency irradiation can be extremely efficient when the irradiation frequencies are placed at opposite sides of the characteristic frequency of the spin system, and that the frequency separation in the double-frequency irradiation can be varied over a large range. Provotorov theory is also shown to provide good insights into the experimental findings, which would otherwise be difficult to obtain from simulations.

X-ray absorption spectroscopy (XAS) and small angle x-ray scattering (SAXS) were utilized to study the effect of fluoride (F(-)) anion in aqueous solutions. XAS spectra show that F(-) increases the number of strong H-bonds, likely between F(-) and water in the first hydration shell. SAXS data show a low-Q scattering intensity increase similar to the effect of a temperature decrease, suggesting an enhanced anomalous scattering behavior in F(-) solutions. Quantitative analysis revealed that fluoride solutions have larger correlation lengths than chloride solutions with the same cations but shorter compared to pure water. This is interpreted as an increased fraction of tetrahedral low-density structures in the solutions due to the presence of the F(-) ions, which act as nucleation centers replacing water in the H-bonding network and forming stronger H-bonds, but the presence of the cations restricts the extension of strong H-bonds.

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.

The technologically important properties of room temperature ionic liquids (RTILs) are fundamentally linked to the ion-ion interactions present among the constituent ions. These ion-ion interactions in one RTIL (1-ethyl-3-methylimidazolium trifluoromethanesulfonate, [C(2)mim]CF(3)SO(3)) are characterized with transmission FTIR spectroscopy and polarized attenuated total reflection (ATR) FTIR spectroscopy. A quasilattice model is determined to be the best framework for understanding the ionic interactions. A novel spectroscopic approach is proposed to characterize the degree of order that is present in the quasilattice by comparing the dipole moment derivative calculated from two independent spectroscopic measurements: (1) the TO-LO splitting of a vibrational mode using dipolar coupling theory and (2) the optical constants of the material derived from polarized ATR experiments. In principle, dipole moment derivatives calculated from dipolar coupling theory should be similar to those calculated from the optical constants if the quasilattice of the RTIL is highly structured. However, a significant disparity for the two calculations is noted for [C(2)mim]CF(3)SO(3), indicating that the quasilattice of [C(2)mim]CF(3)SO(3) is somewhat disorganized. The potential ability to spectroscopically characterize the structure of the quasilattice, which governs the long-range ion-ion interactions in a RTIL, is a major step forward in understanding the interrelationship between the molecular-level interactions among the constituent ions of an ionic liquid and the important physical properties of the RTIL.

Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical∕molecular mechanical (QM∕MM) calculations at the MP2∕aug-cc-pVQZ level on a B3LYP∕aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM∕MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM∕MM multipoles is much closer than that from the site models to the potential from the QM∕MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.

X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ∼61% and ∼71% higher than in bulk water.

Water dynamics as reflected by the spectral diffusion of the water hydroxyl stretch were measured in w(0) = 2 (1.7 nm diameter) Aerosol-OT (AOT)/water reverse micelles in carbon tetrachloride and in isooctane solvents using ultrafast 2D IR vibrational echo spectroscopy. Orientational relaxation and population relaxation are observed for w(0) = 2, 4, and 7.5 in both solvents using IR pump-probe measurements. It is found that the pump-probe observables are sensitive to w(0), but not to the solvent. However, initial analysis of the vibrational echo data from the water nanopool in the reverse micelles in the isooctane solvent seems to yield different dynamics than the CCl(4) system in spite of the fact that the spectra, vibrational lifetimes, and orientational relaxation are the same in the two systems. It is found that there are beat patterns in the interferograms with isooctane as the solvent. The beats are observed from a signal generated by the AOT/isooctane system even when there is no water in the system. A beat subtraction data processing procedure does a reasonable job of removing the distortions in the isooctane data, showing that the reverse micelle dynamics are the same within experimental error regardless of whether isooctane or carbon tetrachloride is used as the organic phase. Two time scales are observed in the vibrational echo data, ~1 and ~10 ps. The slower component contains a significant amount of the total inhomogeneous broadening. Physical arguments indicate that there is a much slower component of spectral diffusion that is too slow to observe within the experimental window, which is limited by the OD stretch vibrational lifetime.

The "Swedish slow motion theory" [Nilsson and Kowalewski, J. Magn. Reson. 146, 345 (2000)] applied so far to Nuclear Magnetic Relaxation Dispersion (NMRD) profiles for solutions of transition metal ion complexes has been extended to ESR spectral analysis, including in addition g-tensor anisotropy effects. The extended theory has been applied to interpret in a consistent way (within one set of parameters) NMRD profiles and ESR spectra at 95 and 237 GHz for two Gd(III) complexes denoted as P760 and P792 (hydrophilic derivatives of DOTA-Gd, with molecular masses of 5.6 and 6.5 kDa, respectively). The goal is to verify the applicability of the commonly used pseudorotational model of the transient zero field splitting (ZFS). According to this model the transient ZFS is described by a tensor of a constant amplitude, defined in its own principal axes system, which changes its orientation with respect to the laboratory frame according to the isotropic diffusion equation with a characteristic time constant (correlation time) reflecting the time scale of the distortional motion. This unified interpretation of the ESR and NMRD leads to reasonable agreement with the experimental data, indicating that the pseudorotational model indeed captures the essential features of the electron spin dynamics.

We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the "Mercedes-Benz" (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water's heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water's large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state.

Fatty acids constitute one of the main components of the lipid lamellae in the top layer of the skin, known as the stratum corneum, which acts as a barrier to foreign substances entering the body and to water leaving the body. To better understand the mechanics of the skin, a molecular-level understanding of the structure of the lamellae needs to be investigated. As a first step toward this goal, the current work involves the development of a coarse-grained model for fatty acids in an amorphous and a crystalline state. In order to retain the structural details of the atomistic molecules, radial distribution functions have been used to provide target data against which the coarse-grained force field is optimized. The optimization was achieved using the method developed by Reith, Pütz, and Müller-Plathe with a damping factor introduced into the updating scheme to facilitate the convergence against the crystalline radial distribution functions. Using this approach, a transferable force field has been developed for both crystalline and amorphous systems that can be used to describe fatty acids of different chain lengths. We are unaware of any other coarse-grained model in the literature that has been developed to study solid phases. Additionally, the amorphous force field has been shown to accurately model mixtures of different free fatty acids based on the potentials derived from pure lipid systems.

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all (13)C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.

A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1-2 eV) energy REC are of the same types as those observed in electron capture/transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of z(n)-1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M-H](-) NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of c(n)+1 ions. Instead, c(n) ions arose without hydrogen/proton transfer albeit with lower abundances than that observed for z(n)-1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the c(n) ions than for the z(n)-1 ions. The mechanisms for the N-C(alpha) bond cleavage are discussed.

The (13)C NMR signal of acetic acid 1-(13)C-AcH is enhanced by polarization transfer from hyperpolarized (129)Xe using a thermal mixing procedure. 1-(13)C-AcH acid and hyperpolarized (129)Xe are mixed as gases to disperse (129)Xe in the acetic acid. The mixture is frozen with liquid N(2) at 0.5 T. The magnetic field is then momentarily dropped to allow for exchange of spin polarization between (13)C and (129)Xe. After polarization exchange the magnetic field is raised to its original value and the mixture is thawed, resulting in a solution of polarization enhanced 1-(13)C-AcH. A (13)C nuclear spin polarization enhancement of 10 is observed compared to its thermal polarization at 4.7 T. This polarization enhancement is approximately three orders of magnitude lower than that predicted by theory. The discrepancy is attributed to the formation of either an inhomogeneous solid matrix and/or spin dynamics during polarization transfer. Despite the low polarization enhancement, this is the first report of polarization transfer from (129)Xe to (13)C nuclear spins achieved by thermal mixing for a proton-containing molecule of biomedical importance. If future work can increase the enhancement, this method will be useful in hyperpolarizing a wide range of (13)C enriched compounds important in biomedical and biophysical research.

The method developed in a previous paper [R. Mazo, J. Chem. Phys. 129, 154101 (2008)] for extracting information on the size of relative fluctuations in multicomponent systems is tested on ten binary systems and one ternary system. For the binary systems, it is found that the approximation works well for mole fractions in the range of 0.15-0.85 in most cases. For the ternary case, the method inherently yields less information and is valid only over a more restricted range for the case studied (chloroform-methanol-acetone). It is found that the predicted ratio of number fluctuations is approximately equal to the ratio of molar volumes of the components.

The HCN tetramer, diaminomaleonitrile, crystallizes in sheets with amine and nitrile groups of neighboring molecules in close proximity. This suggests the possibility of relatively facile acid-base addition to form a protopeptide polymer. We find that moderate heating under argon indeed results in an unmistakable reaction, with the abrupt transformation of pale crystallites to shrunken dark particles that become electrically conductive upon doping with iodine. Since nearly a quarter of the mass is lost in the process and the released gas condenses, polymerizes, and reacts with aqueous AgNO(3) like HCN, it seems likely that the dark solid is a polymer of HCN trimer. (13)C and (15)N solid state NMR spectra show the formation of new N-C bonds, and entirely different functional groups from those observed in polymers formed by liquid HCN. These include three different types of nitrogen functionalities and an absence of saturated carbon or nitrile. The observed chemical shifts, optical properties, and electrical conductivity are consistent with polymers of HCN trimer that have undergone cyclization to form poly-[aminoimidazole].

We evaluate exactly the statistical integral for an inhomogeneous one-dimensional counterion-only Coulomb gas between two charged boundaries and from this compute the effective interaction, or disjoining pressure, between the bounding surfaces. Our exact results are compared with the limiting cases of weak and strong coupling which are the same for 1D and 3D systems. For systems with a large number of counterions it is found that the weak coupling (mean-field) approximation for the disjoining pressure works perfectly and that fluctuations around the mean-field in 1D are much smaller than in 3D. In the case of few counterions it works less well and strong coupling approximation performs much better as it takes into account properly the discreteness of the counterion charges., Comment: 16 pages RevTex, 1 .eps figure

A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. With the new acquisition scheme, the range of magnetic field inhomogeneity rather than chemical shift is sampled in the indirect dimension. This enables a great reduction in acquisition time and amount of data, much improved over the original IDEAL implementation. It is applicable to both isolated and J-coupled spin systems in liquid. For the latter, apparent J coupling constants are magnified threefold in spectra obtained with this sequence. This allows a more accurate measurement of J coupling constants in the cases of small J coupling constants or large inhomogeneous fields. Analytical expression was derived based on intermolecular multiple-quantum coherence treatments. Solution samples that were purposely deshimmed and biological samples with intrinsic field inhomogeneities were tested. Experimental results demonstrate that this sequence retains useful structural information including chemical shifts, relative peak areas, and multiplet patterns of J coupling even when the field inhomogeneity is severe enough to almost erase all spectroscopic information with conventional 1D single-quantum coherence techniques. This sequence is more applicable to weakly coupled and uncoupled spin systems, potentially useful for studying metabolites in in vivo NMR spectroscopy and for characterizing technologically important new materials in combinatorial chemistry.

Due to the limited sensitivity of many nuclear magnetic resonance (NMR) applications, careful consideration must be given to the effect of NMR data processing on spectral noise. This work presents analytical relationships as well as simulated and experimental results characterizing the propagation of noise by unsymmetric covariance NMR processing, which concatenates two NMR spectra along a common dimension, resulting in a new spectrum showing spin correlations as cross peaks that are not directly measured in either of the two input spectra. It is shown how the unsymmetric covariance spectrum possesses an inhomogeneous noise distribution across the spectrum with the least amount of noise in regions whose rows and columns do not contain any cross or diagonal peaks and with the largest amount of noise on top of signal peaks. Therefore, methods of noise estimation commonly used in Fourier transform spectroscopy underestimate the amount of uncertainty in unsymmetric covariance spectra. Different data processing procedures, including the Z-matrix formalism, thresholding, and maxima ratio scaling, are described to assess noise contributions and to reduce noise inhomogeneity. In particular, determination of a Z score, which measures the difference in standard deviations of a statistic from its mean, for each spectral point yields a Z matrix, which indicates whether a given peak intensity above a threshold arises from the covariance of signals in the input spectra or whether it is likely to be caused by noise. Application to an unsymmetric covariance spectrum, obtained by concatenating two 2D (13)C-(1)H heteronuclear, single quantum coherence (HSQC) and (13)C-(1)H heteronuclear, multiple bond correlation (HMBC) spectra of a metabolite mixture along their common proton dimension, reveals that for sufficiently sensitive input spectra the reduction in sensitivity due to covariance processing is modest.

This report introduces a new approach that enhances nonlinear solution magnetic resonance signals from intermolecular dipolar interactions. The resulting signals can theoretically be as large as the full equilibrium magnetization. Simple, readily implemented pulse sequences using square-wave magnetization modulation simultaneously refocus all even order intermolecular multiple quantum coherences, leading to a substantial net signal enhancement, complex nonlinear dynamics, and improved structural sensitivity under realistic conditions.

Explicit expressions are developed for the chemical potential derivatives, partial molar volumes, and isothermal compressibility of solution mixtures involving four components at finite concentrations using the Kirkwood-Buff theory of solutions. In addition, a general recursion relationship is provided which can be used to generate the chemical potential derivatives for higher component solutions.

We consider a general double pulsed field gradient experiment with arbitrary experimental parameters and calculate an exact expression for the NMR signal attenuation from restricted geometries, which is valid at long wavelengths, i.e., when the product of the gyromagnetic ratio of the spins, the pulsed gradients' duration, and their magnitude is small compared to the reciprocal of the pore size. It is possible to observe microscopic anisotropy within the pore space induced by the boundaries of the pore, which can be used to differentiate restricted from free or multicompartmental diffusion and to estimate a characteristic pore dimension in the former case. Explicit solutions for diffusion taking place between parallel plates as well as in cylindrical and spherical pores are provided. In coherently packed cylindrical pores, it is possible to measure simultaneously the cylinders' orientation and diameter using small gradient strengths. The presence of orientational heterogeneity of cylinders is addressed, and a scheme for differentiating microscopic from ensemble anisotropy is proposed.

Laser induced charge transfer reactions of halogens in rare gas solids and liquids provide a powerful means for the study of condensed phase dynamics. Many-body effects with respect to both electronic and nuclear coordinates, and cooperative interactions with radiation fields, are some of the studied phenomena that are highlighted in this article.The pertinence of these ionic reactions to chemistry in solids is demonstrated in photodissociation studies of molecular halogens in rare gas matrices. The coexistence of both delocalized and localized charge transfer states in solid xenon doped with atomic halogens is presented and dynamical consequences—charge separation, self-trapping and energy storage—are discussed. Static and dynamic solvent effects in liquid phase harpoon reactions are considered. The characterization of cooperative excitations— two-photon, two-electron transitions—in liquid solutions is presented.

Intrinsically disordered regions (IDRs) often are fast evolving protein domains of low sequence complexity that can drive phase transitions and are commonly found in many proteins associated with neurodegenerative diseases, including the RNA processing factor TDP43. Yet, how phase separation contributes to the physiological functions of TDP43 in cells remains enigmatic. We combined systematic mutagenesis guided by evolutionary sequence analysis with a live-cell reporter assay of TDP43 phase dynamics to identify regularly-spaced hydrophobic motifs separated by flexible, hydrophilic segments in the IDR as a key determinant of TDP43 phase properties. This heuristic framework allowed us to customize the material properties of TDP43 condensates to determine effects on splicing function. Remarkably, mutants with increased or decreased phase dynamics, and even mutants that failed to phase separate, could mediate the splicing of a quantitative, single-cell splicing reporter and endogenous targets. We conclude that phase separation is not required for the function of TDP43 in splicing.

According to gap-phase dynamics theory, forests can be divided into four distinct patch types: gap patch (G), building patch (B), mature patch (M), and degeneration patch (D). Varying light conditions across patch types are one of the most important factors affecting the coexistence of vegetation. Mechanisms of coexistence can be understood through detailed knowledge of ecophysiological responses of codominant tree seedlings to patch types. The following study was conducted to determine ecophysiological responses of Cyclobalanopsis glauca (an evergreen broad-leaved species) and Bothrocaryum controversum (a deciduous broad-leaved species) to four different patch types. During the gap-phase dynamics, light intensity and the magnitude of change in the four different patches followed the order of: G B D M. Both species had the greatest photosynthetic capacity in the G patch. Dry leaf mass per area (LMA), Chlorophyll a + b concentration (Chl), carotenoids (Car), and nitrogen content per area (N a ) all responded to changes in light across patch type, but B. controversum showed greater sensitivity and changes than C. glauca. From G to M patch, the maximal quantum efficiency of PSII (F v /F m ) had a larger variation magnitude for B. controversum than for C. glauca. From G to M patch, B. controversum showed significant changes in gas exchange, while C. glauca showed only small changes. Ecophysiological trait partitioning of response to light in different patches provides a possible explanation of a coexistence mechanism.

The ultrafast gain and refractive index dynamics in AlInAs/AlGaAs quantum dot (QD) based semiconductor optical amplifiers is reported. Measurements in the forward bias regime indicate a complete gain recovery timescale of similar to 5 ps, while the phase dynamics occur over a much longer timescale. At increased pump powers, the impact of nonresonant carriers created by two-photon absorption is visible as an increased injection in both gain and phase dynamics. Reverse-biased measurements reveal a similar behavior to previous measurements on InAs QD devices.

Models useful in the dynamic method for KLa measurements are developed and compared. Particular attention is given to the gas phase dynamics and the oxygen electrode response time. Comparisons and error calculations are based on computer simulations. Correction factors are presented for a range of dimensionless parameters. In general, the errors resulting from neglecting the gas phase dynamics and the electrode response can be expected to be large.

The early vertebrate developmental process of somitogenesis involves bands of gene expression that form periodically at the posterior end of the presomitic mesoderm (PSM) and traverse it with decreasing width and velocity. We have constructed a chemical flow system that, based on the novel flow-distributed oscillator (FDO) mechanism of wave pattern formation, reproduces key physical features of the PSM and observe concentration waves having similar spatio-temporal behavior. This suggests that the gene expression waves can be understood qualitatively in terms of phase dynamics in an open flow of a self-oscillating medium and that chemical flow systems can be used to mimic and model biological pattern formation during axial growth. In fact, expressions for wavelength and wave velocity derived from phase dynamics are found to be in quantitative agreement with measurements from both the biological and the chemical systems. This indicates that they, despite their significant differences, have common dynamics.

Native mass spectrometry (MS) is used to elucidate the stoichiometry of protein complexes and quantify binding interactions by maintaining native-like, noncovalent interactions in the gas phase. However, ionization forces proteins into specific conformations, losing the solution-phase dynamics associated with solvated protein structures. Comparison of gas-phase structures to those in solution, or to other gas-phase ion populations, has many biological implications. For one, analyzing the variety of conformations that are maintained in the gas-phase can provide insight into a protein's solution-phase energy landscape. The gas-phase conformations of proteins and complexes can be investigated using ion mobility (IM) spectrometry. Specifically, drift tube (DT)-IM utilizes uniform electric fields to propel a population of gas-phase ions through a region containing a neutral gas. By measuring the mobility (K) of gas-phase ions, users are able to calculate an average momentum transfer cross section (DTCCS), which provides structural information on the ion. Conversely, in traveling-wave ion mobility spectrometry (TWIMS), TWCCS values cannot be derived directly from an ion's mobility but must be determined following calibration. Though the required calibration adds uncertainty, it is common to report only an average and standard deviation of the calculated TWCCS, accounting for uncertainty associated with replicate measurements, which is a fraction of the overall uncertainty. Herein, we calibrate a TWIMS instrument and derive TWCCSN2 and TWCCSN2→He values for four proteins: cytochrome c, ubiquitin, apo-myoglobin, and holo-myoglobin. We show that compared to reporting only the standard deviation of TWCCS, propagating error through the calibration results in a significant increase in the number of calculated TWCCS values that agree within experimental error with literature values (DTCCS). Incorporating this additional uncertainty provides a more thorough assessment of a protein ion's gas-phase conformations, enabling the structures sampled by native IM-MS to be compared against other reported structures, both experimental and computational.

Colloidal crystal phase dynamics is one of the hotspots on Condensed Matter Physics. Kossel-line diffraction method is an important way to measure the inner structure of colloidal crystal. The research on the model of colloidal crystal phase dynamics changing as the temperature will provide scientific basis to the preparation of colloidal crystal materials, especially in the condition of microgravity. Achieving high accuracy temperature control on the suspension of colloid crystal is a key work on the research of colloidal crystal phase dynamics. A proportional-integral-derivative (PID) control method based on pulse-width modulation (PWM) is proposed. Then, system identification on the heating system of the sample solution is used to get transfer function, and Hooke-Jeeves pattern search method is used to get optimal parameters of the PID controller. We obtain best temperature control accuracy (±0.1°C) as well as simulation results, after actual temperature control system uses the optimal parameters.

Multi-pulse heterodyne pump-probe measurements are used to investigate the reverse bias dynamics of InAs/GaAs quantum dots in a waveguide structure. Using a femtosecond pulse, we simultaneously populate high energy ground states and low energy excited states and measure the resulting gain and phase dynamics over the bandwidth of the pulse. We identify a ∼5 ps timescale in the phase dynamics which can be associated with low energy ground states outside the pulse bandwidth and may provide an explanation for the deterioration of monolithic mode locked laser performance at high reverse voltages. © 2011 American Institute of Physics., SCOPUS: ar.j, info:eu-repo/semantics/published

The physics of quantum dot based optical devices has been studied intensively due to their interesting blend of atomic and solid state properties. Recently, attention has been focused on their absorption properties and has led to QD materials finding favour in such applications as monolithic mode-locked lasers, electro-absorption modulators and saturable absorber mirrors. In this study we perform a detailed experimental investigation of the ultrafast absorption and phase dynamics of a QD InAs/GaAs structure under reverse bias conditions using single colour pump-probe measurements. Experimental results reveal the fundamental timescales and underlying dynamical processes occurring in such absorbers. We will also consider the impact of the observed absorption and phase dynamics on some current applications of QD absorbers.

In a previous work [ J. chem. Technol. Biotechnol. 34B , 121 (1984)] a rapid method was proposed for K L a estimation under growth conditions based on first moment analysis. The response curve of dissolved oxygen concentration is obtained by a sudden change in the stirrer speed while the aeration rate is held constant. The influence of the liquid diffusion film and electrode response on K L a estimation were considered but not the gas phase dynamics because it was assumed that the gas phase remained constant. In the present paper, a new model which considers the influence of the gas phase is proposed. The results show that the gas phase dynamics affect the K L a estimation, and its influence is more pronounced for higher values of K L a and for small aeration rates.

Polymer gels undergoing the oscillatory Belousov-Zhabotinsky (BZ) reaction are one of the few synthetic materials that exhibit biomimetic mechano-chemical transduction, converting mechanical input into chemical energy. Here, we consider self-oscillating BZ gels that are subjected to periodic mechanical forcing, and model the entrainment of the oscillatory gel dynamics to this external stimulus. The gel size is assumed to be sufficiently small that the chemo-mechanical oscillations are spatially uniform. The behavior of the system is captured by equations describing the kinetics of the oscillatory BZ reaction in the gel coupled to equations for the variations in gel size due to the inherent reaction and imposed force. We employ the phase dynamics approach for analyzing the entrainment of the BZ gel to force- and strain-controlled compressive deformations. The phase response curves are obtained using Malkin's method, and time-averaging is applied to extract the slow phase dynamics caused by the periodic forcing. We demonstrate that the entrainment of the self-oscillating BZ gel is sensitive to the chemo-mechanical coupling in gel, the mode of deformation, and the level of static compression. Kuramoto's model of phase oscillators is shown to be applicable if the external forcing is purely harmonic.

The detailed understanding of kinetic and phase dynamics taking place in lithium-ion batteries (LIBs) is crucial for optimizing their properties. It was previously reported that Fe1-xS/C nanocomposites display a superior performance as anode materials in LIBs. However, the underlying lithium storage mechanism was not entirely understood during the 1st cycle. In this work, in operando synchrotron techniques are used to track lithium storage mechanisms during the 1st (de)-lithiation process in the Fe1-xS/C nanocomposite. The combination of in operando techniques enables the uncovering of the phase fraction alternations and crystal structural variations on different length-scales. Additionally, the investigation of kinetic processes, morphological changes, and internal resistance dynamics is discussed. These results reveal that the phase transition of Fe1-xS → Li2Fe1-xS2 → Fe0 + Li2S occurs during the 1st lithiation process. The redox reaction of Fe2+ + 2e- ⇌ Fe0 and the Fe K-edge X-ray absorption spectroscopy (XAS) transformation process are confirmed by in operando XAS. During the 1st de-lithiation process, Fe0 and Li2S convert to Li2-yFe1-xS2 and Li+ is extracted from Li2S to form Li2-yS. The phase transition from Li2S to Li2-yS is not detected in previous reports. After the 1st de-lithiation process, amorphous lithiated iron sulfide nanoparticles are embedded within the remaining Li2S matrix.

We present a zero-dimensional kinetic model to characterise specifically the gas-phase dynamics of methane conversion in a nanosecond pulsed discharge (NPD) plasma reactor. The model includes a systematic approach to capture the nanoscale power discharges and the rapid ensuing changes in electric field, gas and electron temperature, as well as species densities. The effects of gas temperature and reactor pressure on gas conversion and product selectivity are extensively investigated and validated against experimental work. We discuss the important reaction pathways and provide an analysis of the dynamics of the heating and cooling mechanisms. H radicals are found to be the most populous plasma species and they participate in hydrogenation and dehydrogenation reactions, which are the dominant recombination reactions leading to C2H4 and C2H2 as main products (depending on the pressure).

Two-dimensional infrared (2D-IR) spectroscopy is used to measure the spectral dynamics of the metal carbonyl complex cyclopentadienyl manganese tricarbonyl (CMT) in a series of linear alkyl nitriles. 2D-IR spectroscopy provides direct readout of solvation dynamics through spectral diffusion, probing the decay of frequency correlation induced by fluctuations of the solvent environment. 2D-IR simultaneously monitors intramolecular vibrational energy redistribution (IVR) among excited vibrations, which can also be influenced by the solvent through the spectral density rather than the dynamical friction underlying solvation. Here, we report that the CMT vibrational probe reveals solvent dependences in both the spectral diffusion and the IVR time scales, where each slows with increased alkyl chain length. In order to assess the degree to which solute–solvent interactions can be correlated with bulk solvent properties, we compared our results with low-frequency dynamics obtained from optical Kerr effect (OKE) spectroscopy—performed by others—on the same nitrile solvent series. We find excellent correlation between our spectral diffusion results and the orientational dynamics time scales from OKE. We also find a correlation between our IVR time scales and the amplitudes of the low-frequency spectral densities evaluated at the 90-cm−1 energy difference, corresponding to the gap between the two strong vibrational modes of the carbonyl probe. 2D-IR and OKE provide complementary perspectives on condensed phase dynamics, and these findings provide experimental evidence that at least at the level of dynamical correlations, some aspects of a solute vibrational dynamics can be inferred from properties of the solvent.

Geophysical methods have the capacity to detect and characterize gas-phase dynamics in groundwater. Suitable methods can be deployed at surface or within boreholes depending on the required depth of investigation, spatial/temporal resolution, and geologic conditions. While the application of geophysical methods to monitor immiscible phase contaminants in the subsurface has been extensively documented, the effects of hydraulic properties and flow system conditions on the nature of the geophysical responses used to elucidate multi-phase fluid flow remains underdeveloped. A series of numerical 2-dimensional multi-phase flow and geophysical model simulations based on a controlled methane release experiment in the Borden unconfined sand aquifer was carried out to assess the influence of porous media hydraulic properties and flow system conditions on geophysical signatures associated with transient gas-phase saturation and gas migration behaviour. Specifically, the utility of electrical resistivity tomography (ERT) and ground-penetrating radar (GPR) to monitor gas-phase plume dynamics in shallow groundwater flow systems is examined. ERT and GPR responses to gas-phase distribution and migration during a 72-day methane gas injection and subsequent recovery period was calculated using a numerical multi-phase flow model (CFbio) simulating four distinct parameterizations of the sandy aquifer system. Geophysical models showed that ERT was effective at imaging the central position of the plume but was less effective at detecting thinner lateral migration pathways extending beyond the primary high gas saturation bulb. Conversely, GPR was able to detect thin gas pools emanating from the primary gas bulb and small-scale vertical preferential pathways arising from capillary boundaries with contrasting saturations; however, gradational boundaries proved to be more difficult to resolve using GPR. This study demonstrates that ERT and GPR can be very useful tools in combination for longer-term monitoring of stray gas leakage from decommissioned hydrocarbon wells in shallow granular media freshwater aquifers, especially given the likelihood of strong lateral migration.

Multivalent polymers are a key structural component of many biocondensates. When interacting with their cognate binding proteins, multivalent polymers such as RNA and modular proteins have been shown to influence the liquid-liquid phase separation (LLPS) boundary to control condensate formation and to influence condensate dynamics after phase separation. Much is still unknown about the function and formation of these condensed droplets, but changes in their dynamics or phase separation are associated with neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer’s Disease. Therefore, investigation into how the structure of multivalent polymers relates to changes in biocondensate formation and maturation is essential to understanding and treating these diseases. Here, we use a coarse-grain, Brownian Dynamics simulation with reactive binding that mimics specific interactions in order to investigate the difference between non-specific and specific multivalent binding polymers. We show that non-specific binding interactions can lead to much larger changes in droplet formation at lower energies than their specific, valence-limited counterparts. We also demonstrate the effects of solvent conditions and polymer length on phase separation, and we present how modulating binding energy to the polymer can change the organization of a droplet in a three component system of polymer, binding protein, and solvent. Finally, we compare the effects of surface tension and polymer binding on the condensed phase dynamics, where we show that both lower protein solubilities and higher attraction/affinity of the protein to the polymer result in slower droplet dynamics. We hope this research helps to better understand experimental systems and provides additional insight into how multivalent polymers can control LLPS.

This paper presents the results of dynamic behavior modeling of phase states (solid and liquid) of water clusters ((H2O)8, (H2O)10, and (H2O)12) by molecular dynamics method. The initial configurations of the clusters were cube for octamer, pentagonal prism for decamer, and fused-cube structure for dodecamer. The different analytical interaction potentials (TIPnP (n = 3, 4), SPC, and SPC/E) were applied to the phase dynamics of water octamer to choose the most appropriate potential for the study. The dynamic criteria based on the molecule’s potential energy distribution were applied for identification of solid and liquid phases of decamer and dodecamer. The most probable conformers of decamer and dodecamer in different phases were obtained.