Kinetic Components Research Articles

Triggering and Delivery Algorithms for AGN Feedback

Abstract We compare several common subgrid implementations of active galactic nucleus (AGN) feedback, focusing on the effects of different triggering mechanisms and the differences between thermal and kinetic feedback. Our main result is that pure thermal feedback that is centrally injected behaves differently from feedback with even a small kinetic component. Specifically, pure thermal feedback results in excessive condensation and smothering of the AGN by cold gas because the feedback energy does not propagate to large enough radii. We do not see large differences between implementations of different triggering mechanisms, as long as the spatial resolution is sufficiently high, probably because all of the implementations tested here trigger strong AGN feedback under similar conditions. In order to assess the role of resolution, we vary the size of the “accretion zone” in which properties are measured to determine the AGN accretion rate and resulting feedback power. We find that a larger accretion zone results in steadier jets but can also allow too much cold gas condensation in simulations with a Bondi-like triggering algorithm. We also vary the opening angle of jet precession and find that a larger precession angle causes more of the jet energy to thermalize closer to the AGN, thereby producing results similar to pure thermal feedback. Our simulations confirm that AGNs can regulate the thermal state of cool-core galaxy clusters and maintain the core in a state that is marginally susceptible to thermal instability followed by precipitation.

Protonation Kinetics Compromise Liposomal Fluorescence Assay of Membrane Permeation.

The membrane permeation of weak acids and bases couples to the ambient pH and can be studied using pH-sensitive dyes as reporters. Such fluorescence measurements with aliphatic amine drugs have revealed biexponential kinetics of permeation into liposomes (Eyer et al. J. Controlled Release 2014, 173, 102). Permeability coefficients have been obtained using the faster of the two kinetic components. Here, the origin of the biexponential kinetics is studied with a kinetic rate model that in addition to drug permeation accounts for the protonation of the drug and the dye. Surprisingly, the experimental readout is found to strongly depend on the rates of protonation. The analysis demonstrates that fluorescence studies of drug permeation relying on pH-sensitive proxies should be accompanied by comprehensive modeling of the relevant kinetic processes.

Ultrafast Spectroscopic Investigation of Energy Transfer in Site-Directed Mutants of the Fenna-Matthews-Olson (FMO) Antenna Complex from Chlorobaculum tepidum.

Ultrafast transient absorption (TA) and time-resolved fluorescence (TRF) spectroscopic studies were performed on several mutants of the bacteriochlorophyll (BChl) a-containing Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum. These mutants were generated to perturb a particular BChl a site and determine its effects on the optical spectroscopic properties of the pigment-protein complex. Measurements conducted at 77 K under both oxidizing and reducing conditions revealed changes in the dynamics of the various spectral components as compared to the data set from wild-type FMO. TRF results show that under reducing conditions all FMO samples decay with a similar lifetime in the ∼2 ns range. The oxidized samples revealed varying fluorescence lifetimes of the terminal BChl a emitter, considerably shorter than those recorded for the reduced samples, indicating that the quenching mechanism in wild-type FMO is still present in the mutants. Global fitting of TA data yielded similar overall results, and in addition, the lifetimes of early decaying components were determined. Target analyses of TA data for select FMO samples generated kinetic models that better simulate the TA data. A comparison of the lifetime of excitonic components for all samples reveals that the mutations affect mainly the early kinetic components, but not that of the lowest energy exciton, which reflects the flexibility of energy transfer in FMO.

Database-Centric Method for Automated High-Throughput Deconvolution and Analysis of Kinetic Antibody Screening Data.

The state-of-the-art industrial drug discovery approach is the empirical interrogation of a library of drug candidates against a target molecule. The advantage of high-throughput kinetic measurements over equilibrium assessments is the ability to measure each of the kinetic components of binding affinity. Although high-throughput capabilities have improved with advances in instrument hardware, three bottlenecks in data processing remain: (1) intrinsic molecular properties that lead to poor biophysical quality in vitro are not accounted for in commercially available analysis models, (2) processing data through a user interface is time-consuming and not amenable to parallelized data collection, and (3) a commercial solution that includes historical kinetic data in the analysis of kinetic competition data does not exist. Herein, we describe a generally applicable method for the automated analysis, storage, and retrieval of kinetic binding data. This analysis can deconvolve poor quality data on-the-fly and store and organize historical data in a queryable format for use in future analyses. Such database-centric strategies afford greater insight into the molecular mechanisms of kinetic competition, allowing for the rapid identification of allosteric effectors and the presentation of kinetic competition data in absolute terms of percent bound to antigen on the biosensor.

Probing Electrode Heterogeneity using Fourier-Transformed Alternating Current Voltammetry: Protocol Development

Fourier-transformed large amplitude alternating current voltammetry (FTACV) provides a sensitive analytical tool for the discrimination of electrode reactions that are complicated by surface heterogeneity. In this paper, it is shown how the FTACV response at a dual-electrode system comprised of different electrode materials having different heterogeneous charge transfer (k01 and k02) can be resolved into its individual electrode kinetics components without prior knowledge of the electrode size ratio (θ1:θ2). This is possible when one process is reversible and the other is quasi-reversible; achievable by careful selection of the FTACV frequency. The applicability of the FTACV method over a wide range of electrode kinetic values and size ratios is considered for conditions under which numerical simulations based on a 1D diffusion model are adequate to describe the mass transport problem.

The Evolution of Quantum Confinement in CsPbBr3 Perovskite Nanocrystals

Colloidal nanocrystals (NCs) of lead halide perovskites are considered highly promising materials that combine the exceptional optoelectronic properties of lead halide perovskites with tunability from quantum confinement. But can we assume that these materials are in the strong confinement regime? Here, we report an ultrafast transient absorption study of cubic CsPbBr3 NCs as a function of size, compared with the bulk material. For NCs above ∼7 nm edge length, spectral signatures are similar to the bulk material–characterized by state-filling with uncorrelated charges–but discrete new kinetic components emerge at high fluence due to bimolecular recombination occurring in a discrete volume. Only for the smallest NCs (∼4 nm edge length) are strong quantum confinement effects manifest in TA spectral dynamics; focusing toward discrete energy states, enhanced bandgap renormalization energy, and departure from a Boltzmann statistical carrier cooling. At high fluence, we find that a hot-phonon bottleneck effect ...

Identifying the sensitive area in adaptive observation for predicting the upstream Kuroshio transport variation in a 3-D ocean model

Using the conditional nonlinear optimal perturbation (CNOP) approach, sensitive areas of adaptive observation for predicting the seasonal reduction of the upstream Kuroshio transport (UKT) were investigated in the Regional Ocean Modeling System (ROMS). The vertically integrated energy scheme was utilized to identify sensitive areas based on two factors: the specific energy scheme and sensitive area size. Totally 27 sensitive areas, characterized by three energy schemes and nine sensitive area sizes, were evaluated. The results show that the total energy (TE) scheme was the most effective because it includes both the kinetic and potential components of CNOP. Generally, larger sensitive areas led to better predictions. The size of 0.5% of the model domain was chosen after balancing the effectiveness and efficiency of adaptive observation. The optimal sensitive area OSen was determined accordingly. Sensitivity experiments on OSen were then conducted, and the following results were obtained: (1) In OSen, initial errors with CNOP or CNOP-like patterns were more likely to yield worse predictions, and the CNOP pattern was the most unstable. (2) Initial errors in OSen rather than in other regions tended to cause larger prediction errors. Therefore, adaptive observation in OSen can be more beneficial for predicting the seasonal reduction of UKT.

Energy partition, scale by scale, in magnetic Archimedes Coriolis weak wave turbulence.

Magnetic Archimedes Coriolis (MAC) waves are omnipresent in several geophysical and astrophysical flows such as the solar tachocline. In the present study, we use linear spectral theory (LST) and investigate the energy partition, scale by scale, in MAC weak wave turbulence for a Boussinesq fluid. At the scale k^{-1}, the maximal frequencies of magnetic (Alfvén) waves, gravity (Archimedes) waves, and inertial (Coriolis) waves are, respectively, V_{A}k,N, and f. By using the induction potential scalar, which is a Lagrangian invariant for a diffusionless Boussinesq fluid [Salhi et al., Phys. Rev. E 85, 026301 (2012)PLEEE81539-375510.1103/PhysRevE.85.026301], we derive a dispersion relation for the three-dimensional MAC waves, generalizing previous ones including that of f-plane MHD "shallow water" waves [Schecter et al., Astrophys. J. 551, L185 (2001)AJLEEY0004-637X10.1086/320027]. A solution for the Fourier amplitude of perturbation fields (velocity, magnetic field, and density) is derived analytically considering a diffusive fluid for which both the magnetic and thermal Prandtl numbers are one. The radial spectrum of kinetic, S_{κ}(k,t), magnetic, S_{m}(k,t), and potential, S_{p}(k,t), energies is determined considering initial isotropic conditions. For magnetic Coriolis (MC) weak wave turbulence, it is shown that, at large scales such that V_{A}k/f≪1, the Alfvén ratio S_{κ}(k,t)/S_{m}(k,t) behaves like k^{-2} if the rotation axis is aligned with the magnetic field, in agreement with previous direct numerical simulations [Favier etal., Geophys. Astrophys. Fluid Dyn. (2012)] and like k^{-1} if the rotation axis is perpendicular to the magnetic field. At small scales, such that V_{A}k/f≫1, there is an equipartition of energy between magnetic and kinetic components. For magnetic Archimedes weak wave turbulence, it is demonstrated that, at large scales, such that (V_{A}k/N≪1), there is an equipartition of energy between magnetic and potential components, while at small scales (V_{A}k/N≫1), the ratio S_{p}(k,t)/S_{κ}(k,t) behaves like k^{-1} and S_{κ}(k,t)/S_{m}(k,t)=1. Also, for MAC weak wave turbulence, it is shown that, at small scales (V_{A}k/sqrt[N^{2}+f^{2}]≫1), the ratio S_{p}(k,t)/S_{κ}(t) behaves like k^{-1} and S_{κ}(k,t)/S_{m}(k,t)=1.

Light intensity dependent photosynthetic electron transport in eelgrass (Zostera marina L.)

Responses of electron transport to three levels of irradiation (20, 200, and 1200 μmol photons m−2 s−1 PAR; exposures called LL, ML and HL, respectively) were investigated in eelgrass (Zostera marina L.) utilizing the chlorophyll a fluorescence technique. Exposure to ML and HL reduced the maximum quantum yield of photosystem II (PSII) (Fv/Fm) and the maximum slope decrease of MR/MRO (VPSI), indicating the occurrence of photoinhibition of both PSII and photosystem I (PSI). A comparatively slow recovery rate of Fv/Fm due to longer half-life recovery time of PSII and 40% lower descending amplitude compared to other higher plants implied the poor resilience of the PSII. Comparatively, PSI demonstrated high resilience and cyclic electron transport (CEF) around PSI maintained high activity. With sustained exposure, the amplitudes of the kinetic components (L1 and L2), the probability of electron transfer from PSII to plastoquinone pool (ψET2o), and the connectivity among PSII units decreased, accompanied by an enhancement of energy dissipation. Principle component analysis revealed that both VPSI and Fv/Fm contributed to the same component, which was consistent with high connectivity between PSII and PSI, suggesting close coordination between both photosystems. Such coordination was likely beneficial for the adaption of high light. Exposure to LL significantly increased the activity of both PSI and CEF, which could lead to increased light harvesting. Moreover, smooth electron transport as indicated by the enhancement of L1, L2, ψET2o and the probability of electron transport to the final PSI acceptor sides, could contribute to an increase in light utilization efficiency.

Evaluation of long-heating kinetic process of edible oils using ATR-FTIR and chemometrics tools.

Long thermal oxidative kinetic and stability of four different edible oils (colza, corn, frying, sunflower) from various brands were surveyed with the use of attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) combined with multivariate curve resolution-alternative least square (MCR-ALS). Sampling from the heated oils (at 170°C) was performed each 3h during a 36-h period. Changes in the ATR-FTIR spectra of the oil samples in the range of 4000-550cm-1 were followed as a function of heating time. MCR-ALS was utilized to resolve the concentration and spectral profiles of three detected kinetic components. Three variations in resolved concentration profiles were related to the thermal-deduction of triacylglycerol of unsaturated acid, appearance of hydroperoxides form of triacylglycerols and generation of secondary oxidation products. The kinetic profiles of these species were dependent on the type of oil. The proposed method can define a new way to monitor the oils' quality.

Mapping the kinetic Sunyaev-Zel’dovich effect toward MACS J0717.5+3745 with NIKA

Measurement of the gas velocity distribution in galaxy clusters provides insight into the physics of mergers, through which large scale structures form in the Universe. Velocity estimates within the intracluster medium (ICM) can be obtained via the Sunyaev-Zel’dovich (SZ) effect, but its observation is challenging both in term of sensitivity requirement and control of systematic effects, including the removal of contaminants. In this paper we report resolved observations, at 150 and 260 GHz, of the SZ effect toward the triple merger MACS J0717.5+3745 (z = 0.55), using data obtained with the NIKA camera at the IRAM 30 m telescope. Assuming that theSZ signal is the sum of a thermal (tSZ) and a kinetic (kSZ) component and by combining the two NIKA bands, we extract for the first time a resolved map of the kSZ signal in a cluster. The kSZ signal is dominated by a dipolar structure that peaks at −5.1 and + 3.4σ, corresponding to two subclusters moving respectively away and toward us and coincident with the cold dense X-ray core and a hot region undergoing a major merging event. We model the gas electron density and line-of-sight velocity of MACS J0717.5+3745 as four subclusters. Combining NIKA data with X-ray observations from XMM-Newton and Chandra, we fit this model to constrain the gas line-of-sight velocity of each component, and we also derive, for the first time, a velocity map from kSZ data (i.e. that is model-dependent). Our results are consistent with previous constraints on the merger velocities, and thanks to the high angular resolution of our data, we are able to resolve the structure of the gas velocity. Finally, we investigate possible contamination and systematic effects with a special care given to radio and submillimeter galaxies. Among the sources that we detect with NIKA, we find one which is likely to be a high redshift lensed submillimeter galaxy.

Solvation Dynamics and Proton Transfer in Diethylaminohydroxyflavone.

4'-N,N-Diethylamino-3-hydroxyflavone (DEAHF) exhibits dual fluorescence in most solvents as a result of a rapid excited-state intramolecular proton transfer reaction. The high sensitivity of its dual emission to solvent polarity and hydrogen bonding make DEAHF of interest as a ratiometric fluorescence sensor. In addition, prior work has suggested that the rate of this proton transfer should depend on solvent relaxation in an unusual manner. It has been proposed that rapid solvation of the initially excited reactant should retard reaction. The present work tests this idea by using femtosecond Kerr-gated emission spectroscopy to measure the reaction kinetics of DEAHF in mixtures of propylene carbonate (PC) + acetonitrile (ACN). This mixture was chosen to maintain constant solvent polarity and thereby constant reaction energies while varying solvation times ∼10-fold with composition. The reaction kinetics observed in these mixtures are multiexponential, consisting of resolvable components of ∼2 and ∼30 ps and a small fraction of reaction faster than detectable by the 400 fs resolution of the experiment. Average reaction times increase by approximately a factor of 2 as a function of ACN mole fraction, primarily as a result of changes to the slower kinetic component. This trend is opposite to the composition dependence of solvation times, thereby supporting the unusual role of polar solvation dynamics in this proton transfer. In n-alkane solvents, where electrostatic coupling is minimized, frictional properties of the solvent do not influence reaction rates.

Ultrafast Nonadiabatic Dynamics of Electronically Excited 2-Methyl Furan

Excited-state dynamics of 2-methyl furan has been studied by femtosecond time-resolved photoelectron imaging. The molecule 2-methyl furan was simultaneously excited to the n = 3 Rydberg series of S-1[(1)A ''(pi 3s)], (1)A'(pi 3p(x)), (1)A ''(pi 3p(y)) and (1)A ''(pi 3p(z)) and the valence state of (1)A ''(pi pi*) by two 400 nm photons and subsequently probed by two 800 nm photons. The average lifetime of the Rydberg series and the valence state was measured to be on the time scale of 50 fs by the time-dependent ion yield of the parent ion. Ultrafast internal conversions among these excited states were observed and extracted from the time-dependences of the photoelectron kinetic energy components of these excited states in the photoelectron kinetic energy spectra. Furthermore, it is identified that the (1)A'(pi pi*) state might play an important role in internal conversions among these excited states. The Rydberg-valence mixings, which result in numerous conical intersections, act as the driving force to accomplish such ultrafast internal conversions.

Chemodynamics of metal ion complexation by charged nanoparticles: a dimensionless rationale for soft, core-shell and hard particle types.

Soft nanoparticulate complexants are defined by a spatial confinement of reactive sites and electric charges inside their 3D body. In turn, their reactivity with metal ions differs significantly from that of simple molecular ligands. A revisited form of the Eigen mechanism recently elucidated the processes leading to metal/soft particle pair formation. Depending on e.g. particle size and metal ion nature, chemodynamics of nanoparticulate metal complexes is controlled by metal conductive diffusion to/from the particles, by intraparticulate complex formation/dissociation kinetics, or by both. In this study, a formalism is elaborated to achieve a comprehensive and systematic identification of the rate-limiting step governing the overall formation and dissociation of nanoparticulate metal complexes. The theory covers the different types of spherical particulate complexants, i.e. 3D soft/permeable and core-shell particles, and hard particles with reactive sites at the surface. The nature of the rate-limiting step is formulated by a dynamical criterion involving a power law function of the ratio between particle radius and an intraparticulate reaction layer thickness defined by the key electrostatic, diffusional and kinetic components of metal complex formation/dissociation. The analysis clarifies the intertwined contributions of particle properties (size, soft or hard type, charge, density or number of reactive sites) and aqueous metal ion dehydration kinetics in defining the chemodynamic behavior of nanoparticulate metal complexes. For that purpose, fully parameterized chemodynamic portraits involving the defining features of particulate ligand and metal ion as well as the physicochemical conditions in the local intraparticulate environment, are constructed and thoroughly discussed under conditions of practical interest.

Dissociative photoionization of 1,2-dichloroethane in intense near-infrared femtosecond laser field

We experimentally demonstrate the dissociative photoionization of 1,2-C2H4Cl2 molecules in femtosecond laser field by time-of-flight mass spectrum and dc-slice imaging technology. Our results show the low kinetic energy components are from the dissociative ionization process of singly charged molecular ions, and the positive charge assignment are greatly influenced by the appearance energy of the fragment ions. The high kinetic energy components result from Coulomb explosion of multi-charged molecular ions, and the different angular distribution of these fragments along CC and CCl bond dissociation can be explained by the potential energy surfaces of the molecular ions.

KREO: Kinetic Responsive Envelop by Origami

One of the most interesting fields of contemporary research is addressed to the realization of kinetic building components. It can be obtained by using foldable surfaces, that are light surfaces which increase their strength thanks to the folds. They could be useful to form envelopes, coverings, shading elements or entire pavilions. KREO is classifiable in this field; it is an experimentation concerning geometric modelling and fold texture, in relation with kinematism. In addition, in KREO project, tests of composite materials are carried out with CNR of Catania, to evaluate the most useful of them, to this purpose.

Detection of the Excited-State NH2 (Ã 2A1) in the Ultraviolet Photodissociation of Methylamine.

Ion-imaging and dispersed fluorescence spectroscopy are employed for the photodissociation dynamics study of methylamine in the photolysis wavelength range 205-213 nm. The methyl radical product is found to populate a wide range of ro-vibrational states, among which the CH3 fragment generated in the v = 0 state shows a bimodal kinetic energy distribution. The internal energy analysis of the NH2 counterproduct indicates that a lower kinetic energy component, which was observed only with the CH3(v=0) fragment, energetically matches the electronically excited Ã2A1 state. The dispersed fluorescence spectrum, whose band structure is assigned to the Ã2A1 → X̃2B1 transition, provides evidence of the CH3(v=0) + NH2(Ã2A1) pathway. The branching mechanism of the product pathway is discussed in terms of nuclear dynamics in the long-range region, where the conical intersection between the excited- and ground-state potential energy surfaces can play a significant role.

Folding of a Zinc-Finger ββα-Motif Investigated Using Two-Dimensional and Time-Resolved Vibrational Spectroscopy.

Small proteins provide good model systems for studying the fundamental forces that control protein folding. Here, we investigate the folding dynamics of the 28-residue zinc-finger mutant FSD-1, which is designed to form a metal-independent folded ββα-motif, and which provides a testing ground for proteins containing a mixed α/β fold. Although the folding of FSD-1 has been actively studied, the folding mechanism remains largely unclear. In particular, it is unclear in what stage of folding the α-helix is formed. To address this issue we investigate the folding mechanism of FSD-1 using a combination of temperature-dependent UV circular dichroism (UV-CD), Fourier transform infrared (FTIR) spectroscopy, two-dimensional infrared (2D-IR) spectroscopy, and temperature-jump (T-jump) transient-IR spectroscopy. Our UV-CD and FTIR data show different thermal melting transitions, indicating multistate folding behavior. Temperature-dependent 2D-IR spectra indicate that the α-helix is the most stable structural element of FSD-1. To investigate the folding/unfolding re-equilibration dynamics of FSD-1, the conformational changes induced by a nanosecond T-jump are probed with transient-IR and transient dispersed-pump-probe (DPP) IR spectroscopy. We observe biexponential T-jump relaxation kinetics (with time constants of 80 ± 13 ns and 1300 ± 100 ns at 322 K), confirming that the folding involves an intermediate state. The IR and dispersed-pump-probe IR spectra associated with the two kinetic components suggest that the folding of FSD-1 involves early formation of the α-helix, followed by the formation of the β-hairpin and hydrophobic contacts.

Photoluminescent Nanocrystals in a Multicomponent Aluminoborosilicate Glass

In this study, stable and nonexpensive aluminoborosilicate glasses with different photoluminescence colors were synthesized by doping with Pb(II), Ba(II) and sodium halides. While glasses with NaF and NaCl exhibit no (or very low) luminescence, glasses doped with NaBr and NaI display room-temperature photoluminescence at 435 and 530 nm, respectively. The observed room-temperature photoluminescence is attributed to nanocrystals whose presence is revealed by transmission electron microscopy. The crystalline nature of the particles, which are pointed out as barium-lead halides, is also revealed by anisotropy measurements for Br and I doped samples. Time-resolved luminescence measurements show a second-order kinetics component combined with a first-order nonradiative rate constant. The photoluminescence properties here described are important for the future design of new optical materials or devices based on lead halide nanocrystals.

Let Students Derive, by Themselves, Two-Dimensional Atomic and Molecular Quantum Chemistry from Scratch

Hands-on exercises are designed for undergraduate physical chemistry students to derive two-dimensional quantum chemistry from scratch for the H atom and H2 molecule, both in the ground state and excited states. By reducing the mathematical complexity of the traditional quantum chemistry teaching, these exercises can be completed independently by students who have basic calculus skills. Students are expected to convert the Laplacian into the polar coordinates; solve the Schrodinger equations for the two-dimensional H atom; write out the electron configurations and atomic terms for many-electron atoms; solve the Schrodinger equations for the H2 molecule; obtain its potential energy surfaces in the ground state and excited states; examine the individual kinetic, attractive, and repulsive energy components; and plot and visualize the bonding and antibonding molecular orbitals of the two-dimensional H2. In summary, various exercises are designed for students to derive quantum chemistry for atoms and molecules...