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Countercurrent distribution of biological cells

Detailed physiochemical studies of dextran/poly(ethylene glycol) (PEG) two phase systems were carried out to characterize and provide understanding of the properties of the systems which determine cell partition and the electrophoretic behavior of phase drops responsible for electric field driven phase separation. A detailed study of the electrostatic and electrokinetic potentials developed in these systems was carried out. The salt partition was examined both in phase systems and with pure polymer solutions via equilibrium dialysis and mechanism of sulfate, chloride and phosphate partition shown to be exclusion by PEG rather than binding by dextran. Salt partition was shown to have a strong effect on the polymer compositions of the phases as well, an effect which produces large changes in the interfacial tension between them. These effects were characterized and the interfacial tension shown to obey a power law with respect to its dependence on the length of the tie line describing the system composition on a phase diagram. The electrostatic potential differences measured via salt bridges were shown to obey thermodynamic predictions. The electrophoretic mobilities measured were utilized to provide a partial test of Levine's incomplete theory of phase drop electrophoresis. The data were consistent with Levine's expression over a limited range of the variables tested.

Brooks, D. E.↗

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.↗

A Proposed Pathway for the Nucleation and Crystal Growth of the Tetragonal Form of Lysozyme

A number of factors, the shape and charge distribution anisotropy, multiple components in the solution (buffer + counter ion, precipitant, protein, and water), conformational flexibility, and large numbers of intermolecular contacts, all serve as complicating variables in understanding the nucleation and growth mechanism for macromolecules. Intermolecular contacts include hydrogen bonds, van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and give specificity while the others are weaker, more prevalent, and more promiscuous, i.e., can lead to a range of possible molecular interactions. We propose that for tetragonal lysozyme, and by extension many other monomeric proteins, there is a solution-phase assembly process to form 4(sub 3) helix structures that are the basic unit for nucleation. The formation of these structures is continuous and concentration dependent. They subsequently also servc as growth units, with that process then being a recapitulation of the nucleation process. The advantages of solution phase assembly are the immediate burying of the strongest interactions, removing them from subsequent participation in the nucleation and growth process, and the introduction of symmetry into the system, which also assists in the assembly process.

Pusey, Marc L.↗

A Model for Tetragonal Lysozyme Crystal Nucleation and Growth

Macromolecular crystallization is a complex process, involving a system that typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only a few 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 be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be difficult or 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. This model has been developed from experimental evidence based upon face growth rate, AFM, and fluorescence energy transfer data for the nucleation and growth of tetragonal lysozyme crystals.

Pusey, Marc L.↗

Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

Two properties are particularly germane to the transition from chemistry to biology. One is the emergence of complex molecules (polymers) capable of performing non-trivial functions, such as catalysis, energy transduction or transport across cell walls. The other is the ability of several functions to work in concert to provide reproductive advantage to systems hosting these functions. Biological systems exhibit these properties at remarkable levels of efficiency and accuracy in a way that appears effortless. However, dissection of these properties reveals great complexities that are involved. This opens a question: how a simple, ancestral system could have acquired the required properties? Other questions follow. What are the chances that a functional polymer emerges at random? What is the minimum structural complexity of a polymer to carry out a function at a reasonable level of efficiency? Can we identify concrete, protobiologically plausible mechanisms that yield advantageous coupling between different functions? These and similar questions are at the core of the main topic of this session: how soulless chemistry became life? Clearly, we do not have complete answers to any of these questions. However, in recent years a number of new and sometimes unexpected clues have been brought to light. Of particular interest are proteins because they are the main functional polymers in contemporary cells. The emergence of protein functions is a puzzle. It is widely accepted that a well ]defined, compact structure (fold) is a prerequisite for function. It is equally widely accepted that compact folds are rare among random amino acid polymers. Then, how did protein functionality start? According to one hypothesis well folded were preceded by their poorly folded, yet still functional ancestors. Only recently, however, experimental evidence supporting this hypothesis has been presented. In particular, a small enzyme capable of ligating two RNA fragments with the rate of 106 above background was evolved in vitro. This enzyme does not look like any contemporary protein. It is very flexible and its structure is kept together just by a single salt bridge between a charged residue and a coordinating zinc. A similar picture emerges from studies of simple transmembrane channels that mimic those in ancestral cells. Again, they are extremely flexible and do not form a conventional pore. Yet, they efficiently mediate ion transport. Studies on simple proteins that are on-going in several laboratories hold promise of revealing crucial links between chemical and biological catalysis and other ubiquitous cell functions. Interaction between composition, growth and division of protobiologically relevant vesicles and metabolic reactions that they encapsulate is an example of coupling between simple functions that promotes reproduction and evolution. Recent studies have demonstrated possible mechanisms by which vesicles might have evolved their composition from fatty acids to phospholipids, thus facilitating a number of new cellular functions. Conversely, it has been also demonstrated that an encapsulated metabolism might drive vesicle division. These are, again, examples of processes that might have driven the transition from chemistry to biology.

Pohorille, Andrew↗

Proteins with Novel Structure, Function and Dynamics

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828‐831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81‐83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha‐helix or beta‐sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Proteins↗

Nucleation and Growth According to Lysozyme

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme that may be very germane to other monomeric proteins. The first species formed is postulated to be a dimer. Through repeating associations involving the same intermolecular interactions this becomes the 4(sub 3) helix, that in turn serves as the basic unit for nucleation and crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub 3)2(sub 1)2(sub 1) unit cell are filled. From the above, the process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the solution parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. Lysozyme is atypical in the breadth of its crystallization conditions; many proteins only crystallize under narrowly defined conditions, pointing to the criticality of the empirical balancing process. Lack of a singularly defined association pathway leads to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. When two molecules self associate the resulting species will have an axis of symmetry. Subsequent interactions between two associated species having equivalent interactions will also have symmetry. Only a few unique sets of interactions are required to give any of the commonly found space groups for monomeric proteins. This model and what it suggests will be discussed.

Pusey, Marc L.↗

A Proposed Model for Protein Crystal Nucleation and Growth

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme, based upon fluorescence, light, neutron, and X-ray scattering data, size exclusion chromatography experiments, dialysis kinetics, AFM, and modeling of growth rate data, from this and other laboratories. The first species formed is postulated to be a 'head to side' dimer. Through repeating associations involving the same intermolecular interactions this grows to a 4(sub 3) helix structure, that in turn serves as the basic unit for nucleation and subsequent crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates subsequent helix-helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub3)2(sub 1),2(sub 1) unit cell are filled. The process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the growth parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. In the general case for proteins the lack of a singularly defined association pathway may lead to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. This model, its basis, how it fits into the currently understood osmotic second virial coefficient approach to crystallization, and what it suggests will be discussed.

Pusey, Marc↗

Zinc-rich coatings: A market survey

Zinc-rich coatings with both organic and inorganic binders were considered for coastal bridges which require more corrosion protection than inland bridges because of exposure to salt spray and fog. Inorganics give longer protection and may be applied without a finish coat; those currently available are harder to apply than organics. The NASA potassium silicate/zinc - dust coating appears to provide longer protection, resist thermal shock, and overcome the application problem. Panels coated with the formulation withstood 5308 hours in a salt spray chamber with no rusting or blistering.

Lizak, R.↗

Anti-Corrosion Coating

NASA-Goddard developed a zinc-rich coating with a special binder that exhibits longer life and booths with the air purifiers. superior adhesion characteristics-so that only a single coat is required. Unlike conventional coatings, . the NASA compound is easy to mix and it requires no straining before application; its materials also cost less. Thus the new coating offers cost advantages in materials, labor hours per application, and fewer applications over a given time span. The NASA coating is now undergoing test on a number of coastal area structures. In a cooperative effort with the Philadelphia Mayor's Science and Technology Council, the coating has been applied to sample sections of the Frankford Elevated System's steel support structure. On the West Coast, it is being tested on facilities of the Pillar Point Satellite Tracking Station, Pillar Point, Cat. and on segments of the Golden Gate Bridge. It is also undergoing evaluation as an undercoating to protect road equipment against de-icing salts; the coating was applied to the underside of a truck and its performance is being recorded periodically by the Vermont Department of Highways. NASA has issued patent licenses to two paint companies and the coating is expected to be commercially available this year.

Source record↗

An investigation of several aspects of LANDSAT-5 data quality

Band-to-band registration, geodetic registration, interdector noise, and the modulation transfer function (MTE) are discussed for the Palmer County; TX scene. Band combinations for several LANDSAT 4 and LANDSAT 5 scenes; the geodetic registration test for the Sacramento, CA area; periodic noise components in TM band 5; and grey level measurements by detector for Great Salt Lake (UT) dark water forescans and backscans are considered. Results of MTF analyses of the San Mateo Bridge and of TM high resolution and aerial Daedalus scanner imagery are consistent and appear to be repeatable. An oil-on-sand target was constructed on the White Sands Missile Range in New Mexico. The two-image analysis procedure used is summarized.

Wrigley, R. C.↗

Synthesis of perfluoroalkylene dianilines

The objective of this contrast was to optimize and scale-up the synthesis of 2,2-bis(4-aminophenyl)-hexafluoropropane and 1,3-bis(4-aminophenyl)hexafluoropropane, as well as to explore avenues to other perfluoroalkyl-bridged dianilines. Routes other than Friedel-Crafts reaction leading to 2,2-bis(4-aminophenyl)hexafluoropropane were investigated. The processes utilizing bisphenol-AF were all unsuccessful; reactions aimed at the production of 4-(hexafluoro-2-halo-isopropyl)aniline from the hydroxyl intermediate failed to yield the desired products. Tailoring the conditions of the Friedel-Crafts reaction of 4-(hexafluoro-2-hydroxyisopropyl)aniline, aniline, and aluminum chloride by using hydrochloride salts and selecting optimum reagent ratios, reaction times, and temperature resulted in approx. 20% yield of pure crystallized 2,2-bis(4-aminophenyl)hexafluoropropane in 0.2 mole reaction batches. Yields up to approx. 40% were realized in small, approx. 0.01 mole, batches. The synthesis of 1,3-bis(4-aminophenyl)hexafluoropropane starting with perfluoroglutarimidine was reinvestigated. The yield of the 4-step reaction sequence giving 1,3-bis(4-acetamidophenyl)hexafluoropropane was raised to 44%. The yield of the subsequent hydrolysis process was improved by a factor of approx. 2. Approaches to prepare other perfluoroalkyl-bridged dianilines were unsuccessful. Reactions reported to proceed readily with trifluoromethyl substituents failed when longer chain perfluoroalkyl groups were employed.

Paciorek, K. L.↗

Assessments of Potential Rock Coatings at Rocknest, Gale Crater with ChemCam

Many locations on Mars have low color contrast between the rocks and soils due to the rocks being "dusty"--basically having a surface that is spectrally similar to Martian soil. In general this has been interpreted as soil and/or dust clinging to the rock though either mechanical or electrostic processes. However, given the apparent mobility of thin films of water forming cemented soils on Mars and at Gale Crater, the possibility exists that some of these "dusty" surfaces may actually be coatings formed by thin films of water locally mobilizing soil/air fall material at the rock interface. This type of coating was observed by Spirit during an investigation of the rock Mazatzal which showed enhanced salts above "normal soil" and an enhancement of nano phase iron oxide that was ~ 10 micronmeters thick. We decided to use ChemCam to investigate the possibility of similar rock coatings forming at the Rocknest site at Gale Crater.

Gale Crater↗

Machine Learning the COSMO Model for Predicting Thermodynamics of Electrolyte Mixtures

Bottom-up design of electrolyte mixtures for battery systems requires predicting macro thermodynamic properties from molecular constituents. For instance, molten salt electrolyte batteries require conditions far above room temperature to operate. Therefore, discovering mixtures with increasingly lower eutectic melting points is desirable. A model that can approximate chemical activity is a valuable tool to search through the vast compositional design space. Machine learning can predict properties of materials such as vibrational free energies, electronic energy gaps, and thermal conductivities. Moreover, they can learn physical models such as interatomic potentials. The COSMO-SAC model uses theory and empirical parameterization to predict liquid-vapor and liquid-solid properties using first-principles calculations. However, obtaining activity coefficients required for parameterizing the COSMO-SAC model is costly and limited to a select chemical space. In this work, we explored if machine learning methods could improve the COSMO-SAC model and bridge density functional theory calculations to liquid phase thermodynamic properties. Our data-driven approach uses existing databases for sigma-profiles of organic solvents and reconciles their methodological differences via ensemble averaging. First, an optimal machine learning model is constructed for each dataset. Our machine learning algorithms use the sigma-profile as an input feature to predict binary mixtures' activity coefficients using multi-output regression. Each dataset uses different choices of functionals, methods, and basis sets. Therefore, our ensemble model attempts to predict corrected activity coefficients given the combination of all the model outputs. The activity coefficients used for training are generated using the COSMO-SAC model. This approach enables the extraction of meaningful information from the existing datasets to improve the COSMO-SAC model for obtaining thermodynamic properties of electrolyte mixtures. With the liquid phase activities, we can identify electrolyte mixtures that meet desired phase equilibria conditions.

Thermodynamics↗

Real Time Quantitative 3-D Imaging of Diffusion Flame Species

A low-gravity environment, in space or ground-based facilities such as drop towers, provides a unique setting for study of combustion mechanisms. Understanding the physical phenomena controlling the ignition and spread of flames in microgravity has importance for space safety as well as better characterization of dynamical and chemical combustion processes which are normally masked by buoyancy and other gravity-related effects. Even the use of so-called 'limiting cases' or the construction of 1-D or 2-D models and experiments fail to make the analysis of combustion simultaneously simple and accurate. Ideally, to bridge the gap between chemistry and fluid mechanics in microgravity combustion, species concentrations and temperature profiles are needed throughout the flame. However, restrictions associated with performing measurements in reduced gravity, especially size and weight considerations, have generally limited microgravity combustion studies to the capture of flame emissions on film or video laser Schlieren imaging and (intrusive) temperature measurements using thermocouples. Given the development of detailed theoretical models, more sophisticated studies are needed to provide the kind of quantitative data necessary to characterize the properties of microgravity combustion processes as well as provide accurate feedback to improve the predictive capabilities of the computational models. While there have been a myriad of fluid mechanical visualization studies in microgravity combustion, little experimental work has been completed to obtain reactant and product concentrations within a microgravity flame. This is largely due to the fact that traditional sampling methods (quenching microprobes using GC and/or mass spec analysis) are too heavy, slow, and cumbersome for microgravity experiments. Non-intrusive optical spectroscopic techniques have - up until now - also required excessively bulky, power hungry equipment. However, with the advent of near-IR diode lasers, the possibility now exists to obtain reactant and product concentrations and temperatures non-intrusively in microgravity combustion studies. Over the past ten years, Southwest Sciences has focused its research on the high sensitivity, quantitative detection of gas phase species using diode lasers. Our research approach combines three innovations in an experimental system resulting in a new capability for nonintrusive measurement of major combustion species. FM spectroscopy or high frequency Wavelength Modulation Spectroscopy (WMS) have recently been applied to sensitive absorption measurements at Southwest Sciences and in other laboratories using GaAlAs or InGaAsP diode lasers in the visible or near-infrared as well as lead-salt lasers in the mid-infrared spectral region. Because these lasers exhibit essentially no source noise at the high detection frequencies employed with this technique, the achievement of sensitivity approaching the detector shot noise limit is possible.

Kane, Daniel J.↗

Identifying Chemical Aerosol Signatures Using Optical Suborbital Observations: How Much Can Optical Properties Tell us about Aerosol Composition?

Improvements in air quality and Earth’s climate predictions require improvements of the aerosol speciation in chemical transport models, using observational constraints. Aerosol speciation (e.g., organic aerosols, black carbon, sulfate, nitrate, ammonium, dust or sea salt) is typically determined using in situ instrumentation. Continuous, routine surface network aerosol composition measurements are not uniformly widespread over the globe. Satellites, on the other hand, can provide a maximum coverage of the horizontal and vertical atmosphere but observe aerosol optical properties (and not aerosol speciation) based on remote sensing instrumentation. Combinations of satellite-derived aerosol optical properties can inform on air mass aerosol types (AMTs e.g., clean marine, dust, polluted continental). However, these AMTs are subjectively defined, might often be misclassified and are hard to relate to the critical parameters that need to be refined in models. In this paper, we derive AMTs that are more directly related to sources and hence to speciation. They are defined, characterized, and derived using simultaneous in situ gas-phase, chemical and optical instruments on the same aircraft during the Study of Emissions and Atmospheric Composition, Clouds, and Climate Coupling by Regional Surveys (SEAC4RS, US, summer of 2013). First, we prescribe well-informed AMTs that display distinct aerosol chemical and optical signatures to act as a training AMT dataset. These in situ observations reduce the errors and ambiguities in the selection of the AMT training dataset. We also investigate the relative skill of various combinations of aerosol optical properties to define AMTs and how much these optical properties can capture dominant aerosol speciation. We find distinct optical signatures for biomass burning (from agricultural or wildfires), biogenic and dust-influence AMTs. Useful aerosol optical properties to characterize these signatures are the extinction angstrom exponent (EAE), the single scattering albedo, the difference of single scattering albedo in two wavelengths, the absorption coefficient, the absorption angstrom exponent (AAE), and the real part of the refractive index (RRI). We find that all four AMTs studied when prescribed using mostly airborne in situ gas measurements, can be successfully extracted from at least three combinations of airborne in situ aerosol optical properties (e.g., EAE, AAE and RRI) over the US during SEAC4RS. However, we find that the optically based classifications for BB from agricultural fires and polluted dust include a large percentage of misclassifications that limit the usefulness of results relating to those classes. The technique and results presented in this study are suitable to develop a representative, robust and diverse source-based AMT database. This database could then be used for widespread retrievals of AMTs using existing and future remote sensing suborbital instruments/networks. Ultimately, it has the potential to provide a much broader observational aerosol data set to evaluate chemical transport and air quality models than is currently available by direct in situ measurements. This study illustrates how essential it is to explore existing airborne datasets to bridge chemical and optical signatures of different AMTs, before the implementation of future spaceborne missions (e.g., the next generation of Earth Observing System (EOS) satellites addressing Aerosol, Cloud, Convection and Precipitation (ACCP) designated observables).

Meloe S F Kacenelenbogen↗