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Cross-Linking Studies of Lysozyme Nucleation

Tetragonal chicken egg white crystals consist of 4(sub 3) helices running in alternating directions, the helix rows having a two fold symmetry with each other. The unit cell consists of one complete tetrameric turn from each of two adjacent helices (an octamer). PBC analysis indicates that the helix intermolecular bonds are the strongest in the crystal, therefore likely formed first. AFM analysis of the (110) surface shows only complete helices, no half steps or bisected helices being found, while AFM line scans to measure the growth step increments show that they are multiples of the 4(sub 3) helix tetramer dimensions. This supports our thesis that the growth units are in fact multiples of the four molecule 4(sub 3) helix unit, the "average" growth unit size for the (110) face being an octamer (two turns about the helix) and the (101) growth unit averaging about the size of a hexamer. In an effort to better understand the species involved in the crystal nucleation and growth process, we have initiated an experimental program to study the species formed in solution compared to what is found in the crystal through covalent cross-linking studies. These experiments use the heterobifunctional cross-linking agent aminoethyl-4-azidonitroanaline (AEANA). An aliphatic amine at one end is covalently attached to the protein by a carbodiimide-mediated reaction, and a photo reactive group at the other can be used to initiate crosslinking. Modifications to the parent structure can be used to alter the distance between the two reactive groups and thus the cross-linking agents "reach". In practice, the cross-linking agent is first coupled to the asp101 side chain through the amine group. Asp101 lies within the active site cleft, and previous work with fluorescent probes had shown that derivatives at this site still crystallize in the tetragonal space group. This was also found to be the case with the AEANA derivative, which gave red tetragonal crystals. The protein now has a reactive group that can be photoactivated at a specific point in the nucleation or crystal growth process to "capture" protein molecules bound within reach of the crosslinking agent. If those bound protein molecules have a defined geometric relationship with the capturing molecule, such as would be found in a crystal, then the photoreacted cross-linking site should be consistent. Random protein interactions, typical of an amorphous precipitate or interaction, would show a random cross-linking reaction. The results of these and other experiments will be presented.

Forsythe, Elizabeth↗

Conference on Cloud Physics, Tucson, Ariz., October 21-24, 1974, Proceedings

Condensation and ice nucleation processes are considered, taking into account measurements of cloud nuclei and aerosol size spectra in the semiarid Southwest, the formation of sulfates and the enhancement of cloud condensation nuclei in clouds, biogenic sources of atmospheric ice nuclei, and the experimental determination of the deposition coefficient of water vapor onto ice. Other topics discussed are related to precipitation growth processes, the role of ice in cloud systems, cloud modeling, measurements in Colorado hailstorms during the national hail research experiment, cloud measurements, and measurement techniques. Attention is also given to cloud electrification, zero-gravity experiments, and the control of cloud development by larger scale motions. Individual items are announced in this issue.

Source record↗

Characterization of a New Phase and Its Effect on the Work Characteristics of a Near-Stoichiometric Ni30Pt20Ti50 High-Temperature Shape Memory Alloy (HTSMA)

A new phase observed in a nominal Ni30Pt20Ti50 (at.%) high temperature shape memory alloy has been characterized using transmission electron microscopy and 3-D atom probe tomography. This phase forms homogeneously in the B2 austenite matrix by a nucleation and growth mechanism and results in a concomitant increase in the martensitic transformation temperature of the base alloy. Although the structure of this phase typically contains a high density of faults making characterization difficult, it appears to be trigonal (-3m point group) with a(sub o) approx. 1.28 nm and c(sub o) approx. 1.4 nm. Precipitation of this phase increases the microhardness of the alloy substantially over that of the solution treated and quenched single-phase material. The effect of precipitation strengthening on the work characteristics of the alloy has been explored through load-biased strain-temperature testing in the solution-treated condition and after aging at 500 C for times ranging from 1 to 256 hours. Work output was found to increase in the aged alloy as a result of an increase in transformation strain, but was not very sensitive to aging time. The amount of permanent deformation that occurred during thermal cycling under load was small but increased with increasing aging time and stress. Nevertheless, the dimensional stability of the alloy at short aging times (1-4 hours) was still very good making it a potentially useful material for high-temperature actuator applications.

Garg, A.↗

Preconditioning of overcast-to-broken cloud transitions by riming in marine cold air outbreaks

Marine cold air outbreaks (CAOs) commonly form overcast cloud decks that transition into broken cloud fields downwind, dramatically altering the local radiation budget. In this study, we investigate the impact of frozen hydrometeors on these transitions. We focus on a CAO case in the NW Atlantic, the location of the multi-year flight campaign ACTIVATE (Aerosol Cloud meTeorology Interactions oVer the western ATlantic Experiment). We use MERRA-2 (Modern-Era Retrospective analysis for Research and Applications, version 2) reanalysis fields to drive large eddy simulations with mixed-phase two-moment microphysics in a Lagrangian framework. We find that transitions are triggered by substantial rain (rainwater paths >25 g m−2), and only simulations that allow for aerosol depletion result in sustained breakups, as observed. Using a range of diagnostic ice nucleating particle concentrations, Ninp, we find that increasing ice progressively accelerates transitions, thus abbreviating the overcast state. Ice particles affect the cloud-topped boundary layer evolution, primarily through riming-related processes prior to substantial rain, leading to (1) a reduction in cloud liquid water, (2) early consumption of cloud condensation nuclei, and (3) early and light precipitation cooling and moistening below cloud. We refer to these three effects collectively as “preconditioning by riming”. Greater boundary layer aerosol concentrations available as cloud condensation nuclei (CCN) delay the onset of substantial rain. However, cloud breakup and low CCN concentration final stages are found to be inevitable in this case, due, primarily, to liquid water path buildup. An ice-modulated cloud transition speed suggests the possibility of a negative cloud–climate feedback. To address prevailing uncertainties in the model representation of mixed-phase processes, the magnitude of ice formation and riming impacts and, thereby, the strength of an associated negative cloud–climate feedback process, requires further observational evaluation by targeting riming hot spots with in situ imaging probes that allow for both the characterization of ice particles and abundance of supercooled droplets.

Marine cold air outbreaks↗

Tridymite and maghemite formation in an Fe-SiO smoke

Grains produced in porous Fe-SiO smoke are analyzed by means of electron microscopy to determine their crystallographical, morphological, and chemical properties. The nucleation of metal oxide condensates takes place as the vapor evolves in a condensation-flow apparatus, initially producing simple crystalline phases. Fe nucleation follows, and the subsequent heterogeneous nucleation of quenched mixed high-Fe silica grains exhibits associated Fe-depletion, eventually producing pure silica grains. The coalescence exhibited by the pure silica grains is compatible with the higher surface energy found in the pure silica phase. During coagulation the grains melt and anneal to a chemically pure mixture of alpha- and beta-tridymite, and the precipitation of amorphous silica material is observed. The settling of grains in evolving solar nebula is theorized to be related to the stickiness of this material, and maghemite is suggested to contribute to the Fe/Si fractionation in solar nebula.

Rietmeijer, F. J. M.↗

Kinetic Roughening and Energetics of Tetragonal Lysozyme Crystal Growth

Lysozyme crystal growth rates over 5 orders of magnitude in range can be described using a layer-by-layer model where growth occurs by 2D nucleation on the crystal surface. Based upon the 2D nucleation model of layer growth, the effective barrier for growth was determined to be gamma = 1.3 plus or minus 0.3 x 10(exp -13) erg/molecule, corresponding to a barrier of 3.2 plus or minus 0.7 k(sub B)T, at 22 C. For solution supersaturation, In c/c(sub eq) greater than or equal to 1.9 plus or minus 0.2, the nucleation model would not predict or consistently estimate the highest observable crystal growth rates. As such, a kinetic roughening hypothesis where crystal growth occurs by a continuous mode was implemented for all growth rate data obtained above In c(sub r)/c(sub eq) greater than or equal to 2. That is, independent of the solution conditions that vary with either buffer pH, temperature or precipitant concentration, crystal growth occurs by the continuous addition of molecules anywhere on the crystal surface, above a roughening solution supersaturation. The energy barrier, E(sub c), for the continuous growth process is determined as 6.1 plus or minus 0.4 x 10(exp -13) erg/molecule or 15 plus or minus 1 k(sub B)T at 22 C.

Gorti, Sridhar↗

Polymer morphologh

All polymeric materials in their final application are aggregates of many molecules. For linear macromolecules, these aggregates are highly entangled and their macroscopic properties are affected in a little-known way by the interpenetration and entanglements of the molecules. Over the years, we have done occasional investigations of single molecule single crystals and found that there are many unsolved questions about their nucleation, growth, kinetically determined shape, and ultimate path to equilibrium morphology on annealing. This initial work could be extended by a study of the applicability of microgravity methods for the production and study of the formation of single molecule particles. The production of separated molecules of sufficient size to produce phase-like behavior would involve perhaps a spray of solutions containing single molecules, followed by evaporation of the volatiles, or precipitation out of dispersion droplets. Other methods may involve Langmuir films etc., as shown in our prior work. The microgravity environment should enhance the efficiency of any of these methods by avoiding the joining of growing particles by reduction of convection and settling due to density differences. Once produced, the single molecule droplets are to be quenched into the glassy state and analyzed morphologically and thermally. Their shape alone can be used for molecular mass determination (an old problem that suffered from the need to estimate the shape of collapsed (flat) droplets on a surface). Next would be the study of changes of properties as a function of time, temperature, and molecular mass (and distribution) on fusion to macroscopic single phases.

Wunderlich, Bernhard↗

The South Residual CO2 Cap on Mars: Investigations with a Mars Global Climate Model

The CO2 cycle is one of the three controlling climate cycles on Mars. One aspect of the CO2 cycle that is not yet fully understood is the existence of a residual CO2 ice cap that is offset from the south pole. Previous investigations suggest that the atmosphere could control the placement of the south residual cap (e.g., Colaprete et al., 2005). These investigations show that topographically forced stationary eddies in the south during southern hemisphere winter produce colder atmospheric temperatures and increased CO2 snowfall over the hemisphere where the residual cap resides. Since precipitated CO2 ice produces higher surface albedos than directly deposited CO2 ice, it is plausible that CO2 snowfall resulting from the zonally asymmetric atmospheric circulation produces surface ice albedos high enough to maintain a residual cap only in one hemisphere. Our current work builds on these initial investigations with a version of the NASA Ames Mars Global Climate Model (GCM) that includes a sophisticated CO2 cloud microphysical scheme. Processes of cloud nucleation, growth, sedimentation, and radiative effects are accounted for. Simulated results thus far agree well with the Colaprete et al. study—the zonally asymmetric nature of the atmospheric circulation produces enhanced snowfall over the residual cap hemisphere throughout much of the winter season. However, the predicted snowfall patterns vary significantly with season throughout the cap growth and recession phases. We will present a detailed analysis of the seasonal evolution of the predicted atmospheric circulation and snowfall patterns to more fully evaluate the hypothesis that the atmosphere controls the placement of the south residual cap.

climate cycles on Mars↗

In situ oxidation studies on /001/ copper-nickel alloy thin films

High-resolution transmission electron microscopy studies are reported of (001)-oriented single crystalline thin films of Cu-3%Ni, Cu-4.6%Ni, and Cu-50%Ni alloy which were prepared by vapor deposition onto (001) NaCl substrates and subsequently annealed at around 1100 K and oxidized at 725 K at low oxygen partial pressure. At all alloy concentrations, Cu2O and NiO nucleated and grew independently without the formation of mixed oxides. The shape and growth rates of Cu2O nuclei were similar to rates found earlier. For low-nickel alloy concentrations, the NiO nuclei were larger and the number density of NiO was less than that of Cu-50%Ni films for which the shape and growth rates of NiO were identical to those for pure nickel films. Phenomena involving a reduced induction period, surface precipitation, and through-thickness growth are also described. The results are consistent with previously established oxidation mechanisms for pure copper and pure nickel films.

Heinemann, K.↗

Studies of Ice Nucleating Aerosol Particles in Arctic Cloud Systems

The focus of this research is to improve the understanding of ice nucleating aerosol particles (IN) and the role they play in ice formation in Arctic clouds. IN are important for global climate issues in a variety of ways. The primary effect is their role in determining the phase (liquid or solid) of cloud particles. The microscale impact is on cloud particle size, growth rate, shape, fall speed, concentration, radiative properties, and scavenging of gases and aerosols. On a larger scale, ice formation affects the development of precipitation (rate, amount, type, and distribution), latent heat release (rate and altitude), ambient humidity, the persistence of clouds, and cloud albedo. The overall goals of our FIRE 3 research are to characterize the concentrations and variability of Arctic IN during the winter-spring transition, to compare IN measurements with ice concentrations in Arctic clouds, and to examine selected IN samples for particle morphology and chemical there are distinguishable chemical signatures. The results can be combined with other measurements of aerosols, gaseous species, and cloud characteristics in order to understand the processes that determine the phase and concentration of cloud particles.

Rogers, David C.↗

A Theory of the von Weimarn Rules Governing the Average Size of Crystals Precipitated from a Supersaturated Solution

More than 75 years ago, von Weimarn summarized his observations of the dependence of the average crystal size on the initial relative concentration supersaturation prevailing in a solution from which crystals were growing. Since then, his empirically derived rules have become part of the lore of crystal growth. The first of these rules asserts that the average crystal size measured at the end of a crystallization increases as the initial value of the relative supersaturation decreases. The second rule states that for a given crystallization time, the average crystal size passes through a maximum as a function of the initial relative supersaturation. Using a theory of nucleation and growth due to Buyevich and Mansurov, we calculate the average crystal size as a function of the initial relative supersaturation. We confirm the von Weimarn rules for the case where the nucleation rate is proportional to the third power or higher of the relative supersaturation.

Barlow, Douglas A.↗

Carbon Nanotube Microarrays Grown on Nanoflake Substrates

This innovation consists of a new composition of matter where single-walled carbon nanotubes (SWNTs) are grown in aligned arrays from nanostructured flakes that are coated in Fe catalyst. This method of growth of aligned SWNTs, which can yield well over 400 percent SWNT mass per unit substrate mass, exceeds current yields for entangled SWNT growth. In addition, processing can be performed with minimal wet etching treatments, leaving aligned SWNTs with superior properties over those that exist in entangled mats. The alignment of the nanotubes is similar to that achieved in vertically aligned nanotubes, which are called "carpets. " Because these flakes are grown in a state where they are airborne in a reactor, these flakes, after growing SWNTs, are termed "flying carpets. " These flakes are created in a roll-to-roll evaporator system, where three subsequent evaporations are performed on a 100-ft (approx. =30-m) roll of Mylar. The first layer is composed of a water-soluble "release layer, " which can be a material such as NaCl. After depositing NaCl, the second layer involves 40 nm of supporting layer material . either Al2O3 or MgO. The thickness of the layer can be tuned to synthesize flakes that are larger or smaller than those obtained with a 40-nm deposition. Finally, the third layer consists of a thin Fe catalyst layer with a thickness of 0.5 nm. The thickness of this layer ultimately determines the diameter of SWNT growth, and a layer that is too thick will result in the growth of multiwalled carbon nanotubes instead of single-wall nanotubes. However, between a thickness of 0.5 nm to 1 nm, single-walled carbon nanotubes are known to be the primary constituent. After this three-layer deposition process, the Mylar is rolled through a bath of water, which allows catalyst-coated flakes to detach from the Mylar. The flakes are then collected and dried. The method described here for making such flakes is analogous to that which is used to make birefringent ink that is coated on U.S. currency. After deposition, the growth is carried out in a hot-filament chemical vapor deposition apparatus. A tungsten hot filament placed in the flow of H2 at a temperature greater than 1,600 C creates atomic hydrogen, which serves to reduce the Fe catalyst into a metallic state. The catalyst can now precipitate SWNTs in the presence of growth gases. The gases used for the experiments reported are C2H2, H2O, and H2, at rates of 2, 2, and 400 standard cubic centimeters per minute (sccm), respectively. In order to retain the flakes, a cage is constructed by spot welding stainless steel or copper mesh to form an enclosed area, in which the flakes are placed prior to growth. This allows growth gases and atomic hydrogen to reach the flakes, but does not allow the flakes, which rapidly nucleate SWNTs, to escape from the cage.

Schmidt, Howard K.↗

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1 %, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. Preliminary experiments show that the presence of the fluorescent probe does not affect the nucleation process or the quality of the X-ray data obtained.

Pusey, Marc L.↗

Homogeneous Aerosol Freezing in the Tops of High-Altitude Tropical Cumulonimbus Clouds

Numerical simulations of deep, intense continental tropical convection indicate that when the cloud tops extend more than a few kilometers above the liquid water homogeneous freezing level, ice nucleation due to freezing of entrained aqueous sulfate aerosols generates large concentrations of small crystals (diameters less than approx. equal to 20 micrometers). The small crystals produced by aerosol freezing have the largest impact on cloud-top ice concentration for convective clouds with strong updrafts but relatively low aerosol concentrations. An implication of this result is that cloud-top ice concentrations in high anvil cirrus can be controlled primarily by updraft speeds in the tops of convective plumes and to a lesser extent by aerosol concentrations in the uppermost troposphere. While larger crystals precipitate out and sublimate in subsaturated air below, the population of small crystals can persist in the saturated uppermost troposphere for many hours, thereby prolonging the lifetime of remnants from anvil cirrus in the tropical tropopause layer.

Jensen, E. J.↗

Repartitioning of NaCl and Protein Impurities in Lysozyme Crystallization

Nonuniform precipitant and impurity incorporation in protein crystals can cause lattice strain and, thus, possibly decrease the X-ray diffraction resolution. To address this issue, a series of crystallization experiments were carried out, in which initial supersaturation, NaCl concentration, protein purity level and crystallized fraction were varied. Lysozyme and protein impurities, as well as sodium and chloride were independently determined in the initial solution, supernatant and crystals. The segregation coefficients for Na(+) and Cl(-) were found to be independent of supersaturation and NaCl concentration, and decreased with crystallized fraction/crystal size. Numerical evaluation of the extensive body of data, based on a nucleation-growth- repartitioning model, suggests a core of approx. 40 microns in which salt is incorporated in much greater concentrations than during later growth. Small crystals containing higher amounts of incorporated NaCl also had higher protein impurity contents. This suggests that the excess salt is associated with the protein impurities in the core. X-ray topography revealed strain fields in the center of the crystals comparable in size to the inferred core. The growth rates of crystals smaller than 30-40 pm in size were consistently 1.5-2 times lower than those of larger crystals, presumably due to higher chemical potentials in the core.

Vekilov, Peter G.↗

A Model for Macromolecular Crystallization

Macromolecular crystallization is a complex process. involving a system which typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only several well defined contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can often be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric single chain macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. Experimental evidence, based upon face growth rate, AFM, and fluorescence energy transfer data, for a postulated model of the nucleation of tetragonal lysozyme crystals and how it transitions into crystal growth will be presented.

Pusey, Marc L.↗

Aircraft-Measured Indirect Cloud Effects from Biomass Burning Smoke in the Arctic and Subarctic

The incidence of wildfires in the Arctic and subarctic is increasing; in boreal North America, for example, the burned area is expected to increase by 200-300 over the next 50-100 years, which previous studies suggest could have a large effect on cloud microphysics, lifetime, albedo, and precipitation. However, the interactions between smoke particles and clouds remain poorly quantified due to confounding meteorological influences and remote sensing limitations. Here, we use data from several aircraft campaigns in the Arctic and subarctic to explore cloud microphysics in liquid-phase clouds influenced by biomass burning. Median cloud droplet radii in smoky clouds were 50 smaller than in background clouds. Based on the relationship between cloud droplet number (N(liq))/ and various biomass burning tracers (BBt/ across the multi-campaign dataset, we calculated the magnitude of subarctic and Arctic smoke aerosol-cloud interactions (ACI, where ACI = (1/3) x dln(N(liq))/dln(BBt)) to be 0.12 out of a maximum possible value of 0.33 that would be obtained if all aerosols were to nucleate cloud droplets. Interestingly, in a separate subarctic case study with low liquid water content (0.02 gm/ cu m) and very high aerosol concentrations (2000-3000 cu m) in the most polluted clouds, the estimated ACI value was only 0.06. In this case, competition for water vapor by the high concentration of CCN strongly limited the formation of droplets and reduced the cloud albedo effect, which highlights the importance of cloud feedbacks across scales. Using our calculated ACI values, we estimate that the smoke-driven cloud albedo effect may decrease shortwave radiative flux by 2 and 4 W/sq or more under some low and homogeneous cloud cover conditions in the subarctic, although the changes should be smaller in high surface albedo regions of the Arctic. We lastly show evidence to suggest that numerous northern latitude background Aitken particles can interact with combustion particles, perhaps impacting their properties as cloud condensation and ice nuclei. However, the influence of background particles on smoke-driven indirect effects is currently unclear.

Arctic↗

Growth Modes and Energetics of 101 Face Lysozyme Crystal Growth

From analyses of lysozyme 101 face growth rate data using a 2D nucleation model for layer-by-layer growth, we find the effective barrier for crystal growth to be gamma = 1.0 +/- 0.2 x 10(exp -13) erg/molecule. The magnitude of the effective barrier is 2.4 +/- 0.5 k(sub beta)T, at 22 C. We also find that beyond a critical solution supersaturation, sigma(sub c), crystal growth rates are more accurately described by a kinetic roughening hypothesis. Beyond sigma(sub c), crystals grow by the continuous addition of molecules anywhere on the crystal surface rather than layer-by-layer. The magnitude of the critical supersaturation (sigma(sub c), = 1.7 +/- 0.2) for a crossover from a layer-by-layer to continuous growth is found to be statistically independent of the solution conditions that vary with buffer pH, temperature or precipitant concentration. Using the experimentally determined values for gamma and sigma(sub c), we find the crystal growth unit to be comprised of 7 +/- 3 molecules. The energy barrier, E(sub c), for the continuous addition of the growth Units is 6.2 +/- 0.3 x 10(exp -13) erg/molecule or 15 +/1 1 k(sub beta)T at 22C.

Gorti, Sridhar↗