Adsorption of Pb(II) and Cu(II) on α-quartz from aqueous solutions: influence of pH, ionic strength, and complexing ligands

Adsorption of aqueous Pb(II) and Cu(II) on α-quartz was studied as a function of time, system surface area, and chemical speciation. Experimental systems contained sodium as a major cation, hydroxide, carbonate, and chloride as major anions, and covered the pH range 4 to 8. In some cases citrate and EDTA were added as representative organic complexing agents. The adsorption equilibria were reached quickly, regardless of the system surface area. The positions of the adsorption equilibria were found to be strongly dependent on pH, ionic strength and concentration of citrate and EDTA. The addition of these non-adsorbing ligands resulted in a competition between chelation and adsorption. The experimental work also included the examination of the adsorption behavior of the doubly charged major cations Ca(II) and Mg(II) as a function of pH.

The theoretical description of the experimental systems was obtained by means of chemical equilibrium-plus-adsorption computations using two adsorption models: one mainly electrostatic (the James-Healy Model), and the other mainly chemical (the Ion Exchange-Surface Complex Formation Model). Comparisons were made between these two models.

The main difficulty in the theoretical predictions of the adsorption behavior of Cu(II) was the lack of the reliable data for the second hydrolysis constant(*β_2) The choice of the constant was made on the basis of potentiometric titratlons of Cu^(2+)

The experimental data obtained and the resulting theoretical observations were applied in models of the chemical behavior of trace metals in fresh oxic waters, with emphasis on Pb(II) and Cu(II).

A. An investigation of the relation between the tensile strength and (Brinell) hardness of non-ferrous alloys. B. A design of a fatigue testing machine for a college laboratory

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Organization and function of the phage Lambda chromosome

The process of prophage integration by phage λ and the function and structure of the chromosomal elements required for λ integration have been studied with the use of λ deletion mutants. Since att^φ, the substrate of the integration enzymes, is not essential for λ growth, and since att^φ resides in a portion of the λ chromosome which is not necessary for vegetative growth, viable λ deletion mutants were isolated and examined to dissect the structure of att^φ.

Deletion mutants were selected from wild type populations by treating the phage under conditions where phage are inactivated at a rate dependent on the DNA content of the particles. A number of deletion mutants were obtained in this way, and many of these mutants proved to have defects in integration. These defects were defined by analyzing the properties of Int-promoted recombination in these att mutants.

The types of mutants found and their properties indicated that att^φ has three components: a cross-over point which is bordered on either side by recognition elements whose sequence is specifically required for normal integration. The interactions of the recognition elements in Int-promoted recombination between att mutants was examined and proved to be quite complex. In general, however, it appears that the λ integration system can function with a diverse array of mutant att sites.

The structure of att^φ was examined by comparing the genetic properties of various att mutants with their location in the λ chromosome. To map these mutants, the techniques of heteroduplex DNA formation and electron microscopy were employed. It was found that integration cross-overs occur at only one point in att^φ and that the recognition sequences that direct the integration enzymes to their site of action are quite small, less than 2000 nucleotides each. Furthermore, no base pair homology was detected between att^φ and its bacterial analog, att^B. This result clearly demonstrates that λ integration can occur between chromosomes which have little, if any, homology. In this respect, λ integration is unique as a system of recombination since most forms of generalized recombination require extensive base pair homology.

An additional study on the genetic and physical distances in the left arm of the λ genome was described. Here, a large number of conditional lethal nonsense mutants were isolated and mapped, and a genetic map of the entire left arm, comprising a total of 18 genes, was constructed. Four of these genes were discovered in this study. A series of λdg transducing phages was mapped by heteroduplex electron microscopy and the relationship between physical and genetic distances in the left arm was determined. The results indicate that recombination frequency in the left arm is an accurate reflection of physical distances, and moreover, there do not appear to be any undiscovered genes in this segment of the genome.

Studies on the role of histones in the structure and function of chromatin

Studies on the dissociation of histones from chromatin by increasing concentrations of sodium deoxycholate (DOC) have shown that histrone II is removed at lowest concentrations of DOC, while slightly higher concentrations remove histones III and IV. Still higher concentrations remove histone I.

The complete separation of chromatin and ¹⁴C-DOC by sucrose sedimentation indicated that the binding of DOC to chromatin is readily and completely reversible.

The dissociation of histones from chromatin by increasing concentrations of related cholanic acids and some of their conjugated derivatives were studied. The results suggested that the driving force for the interaction between the cholanic acid anion and histones is the lowering of the activity coefficient of the cholanic acid anion which occurs when it is partially removed from solution by interaction with hydrophobic regions of the positively charged histones.

The role of histones in the structure of chromatin has been studied by comparing the effects of selective removal of histones from chromatin by increasing concentrations of DOC with those caused by NaCl (removes histone I at lowest concentrations, while higher concentrations remove histones II, III, and IV). Properties studied included thermal denaturation, sedimentation velocity, flow dichroism, relaxation times of molecules oriented in a flow field, and the irreversible disruption of a 130 S, cross-linked component of sheared chromatin. The data indicated that none of the structural or chemical parameters with which these properties are correlated show a dependence on the presence of one particular histone fraction.

The template activity (ability to prime a 0.2 M KC1 DNA-dependent RNA synthesis system catalyzed by E. coli RNA polymerase) increases from that of native chromatin (approximately 25 per cent of that pure DNA) to that of pure DNA in a fashion which shows a nearly linear relationship to the amount of histone coverage of the template. The precipitability of partially dehistonized chromatin samples in 0.15 M NaCl shows a large dependence on the presence of histone I.

Connectivity and Function of the Primate Insula

The insula is a mammalian cortical structure that has been implicated in a wide range of low- and high-level functions governing one’s sensory, emotional, and cognitive experiences. One particular role of this region is considered to be processing of olfactory stimuli. The ability to detect and evaluate odors has significant effects on an organism’s eating behavior and survival and, in case of humans, on complex decision making. Despite such importance of this function, the mechanism in which olfactory information is processed in the insula has not been thoroughly studied. Moreover, due to the structure’s close spatial relationship with the neighboring claustrum, it is not entirely clear whether the connectivity and olfactory functions attributed to the insula are truly those of the insula, rather than of the claustrum. My graduate work, consisting of two studies, seeks to help fill these gaps. In the first, the structural connectivity patterns of the insula and the claustrum in a non-human primate brain is assayed using an ultra-high-quality diffusion magnetic resonance image, and the results suggest dissociation of connectivity — and hence function — between the two structures. In the second study, a functional neuroimaging experiment investigates the insular activity during odor evaluation tasks in humans, and uncovers a potential spatial organization within the anterior portion of the insula for processing different aspects of odor characteristics.

Sequence-function relationships in E. coli transcriptional regulation

Understanding how transcriptional regulatory sequence maps to regulatory function remains a difficult problem in regulatory biology. Given a particular DNA sequence for a bacterial promoter region, we would like to be able to say which transcription factors bind there, how strongly they bind, and whether they interact with each other and/or RNA polymerase, with the ultimate objective of integrating knowledge of these parameters into a prediction of gene expression levels. The theoretical framework of statistical thermodynamics provides a useful framework for doing so, enabling us to predict how gene expression levels depend on transcription factor binding energies and concentrations. We used thermodynamic models, coupled with models of the sequence-dependent binding energies of transcription factors and RNAP, to construct a genotype to phenotype map for the level of repression exhibited by the lac promoter, and tested it experimentally using a set of promoter variants from E. coli strains isolated from different natural environments. For this work, we sought to ``reverse engineer'' naturally occurring promoter sequences to understand how variations in promoter sequence affects gene expression. The natural inverse of this approach is to ``forward engineer'' promoter sequences to obtain targeted levels of gene expression. We used a high precision model of RNAP-DNA sequence dependent binding energy, coupled with a thermodynamic model relating binding energy to gene expression, to predictively design and verify a suite of synthetic E. coli promoters whose expression varied over nearly three orders of magnitude.

However, although thermodynamic models enable predictions of mean levels of gene expression, it has become evident that cell-to-cell variability or ``noise'' in gene expression can also play a biologically important role. In order to address this aspect of gene regulation, we developed models based on the chemical master equation framework and used them to explore the noise properties of a number of common E. coli regulatory motifs; these properties included the dependence of the noise on parameters such as transcription factor binding strength and copy number. We then performed experiments in which these parameters were systematically varied and measured the level of variability using mRNA FISH. The results showed a clear dependence of the noise on these parameters, in accord with model predictions.

Finally, one shortcoming of the preceding modeling frameworks is that their applicability is largely limited to systems that are already well-characterized, such as the lac promoter. Motivated by this fact, we used a high throughput promoter mutagenesis assay called Sort-Seq to explore the completely uncharacterized transcriptional regulatory DNA of the E. coli mechanosensitive channel of large conductance (MscL). We identified several candidate transcription factor binding sites, and work is continuing to identify the associated proteins.

Fabrication, Characterization, And Deformation of 3D Structural Meta-Materials

Current technological advances in fabrication methods have provided pathways to creating architected structural meta-materials similar to those found in natural organisms that are structurally robust and lightweight, such as diatoms. Structural meta-materials are materials with mechanical properties that are determined by material properties at various length scales, which range from the material microstructure (nm) to the macro-scale architecture (μm – mm). It is now possible to exploit material size effect, which emerge at the nanometer length scale, as well as structural effects to tune the material properties and failure mechanisms of small-scale cellular solids, such as nanolattices. This work demonstrates the fabrication and mechanical properties of 3-dimensional hollow nanolattices in both tension and compression. Hollow gold nanolattices loaded in uniaxial compression demonstrate that strength and stiffness vary as a function of geometry and tube wall thickness. Structural effects were explored by increasing the unit cell angle from 30° to 60° while keeping all other parameters constant; material size effects were probed by varying the tube wall thickness, t, from 200nm to 635nm, at a constant relative density and grain size. In-situ uniaxial compression experiments reveal an order-of-magnitude increase in yield stress and modulus in nanolattices with greater lattice angles, and a 150% increase in the yield strength without a concomitant change in modulus in thicker-walled nanolattices for fixed lattice angles. These results imply that independent control of structural and material size effects enables tunability of mechanical properties of 3-dimensional architected meta-materials and highlight the importance of material, geometric, and microstructural effects in small-scale mechanics. This work also explores the flaw tolerance of 3D hollow-tube alumina kagome nanolattices with and without pre-fabricated notches, both in experiment and simulation. Experiments demonstrate that the hollow kagome nanolattices in uniaxial tension always fail at the same load when the ratio of notch length (a) to sample width (w) is no greater than 1/3, with no correlation between failure occurring at or away from the notch. For notches with (a/w) > 1/3, the samples fail at lower peak loads and this is attributed to the increased compliance as fewer unit cells span the un-notched region. Finite element simulations of the kagome tension samples show that the failure is governed by tensile loading for (a/w) < 1/3 but as (a/w) increases, bending begins to play a significant role in the failure. This work explores the flaw sensitivity of hollow alumina kagome nanolattices in tension, using experiments and simulations, and demonstrates that the discrete-continuum duality of architected structural meta-materials gives rise to their flaw insensitivity even when made entirely of intrinsically brittle materials.

Strength of thin-walled elliptical cylinders supported at the minor axis

In this investigation it was found that the instability failure of curved sheet is nearly independent of the type of loading and is primarily a function of the maximum stress, radius-thickness ration and modulus of elasticity. A method of correlating the critical stress of thin sheet under several different types of loading is given. An explanation for the experimental critical stress of thin walled cylinders under bending being greater than that for pure compression is given. The strength of unstiffened thin walled circular nose sections under pure bending was found to be controlled by local instability of the section, rather than a large scale instability. The equation of local instability of curved sheet gives values which are in fair agreement with those found experimentally.

The strength of elliptical cylinders supported at the minor axis under bending plus shear loads is governed primarily by the bending strength, and is little effected by the sheer force unless the amount of shear is quite large with respect to the moment. The effect of increasing the amount of elliptically greatly reduces the bending and shear strength of nose sections. Under torsional loads the stress at buckling falls off as the ration of the major to minor axis increases but the failure stress decreases at a slower rate than the buckling stress. The length effect of semi-circular sections under torsion is similar to that of a circular tube, and can be obtained by Donnell's theoretical equation.

Microscopic Origin of Macroscopic Strength in Granular Media: A Numerical and Analytical Approach

Constitutive modeling in granular materials has historically been based on macroscopic experimental observations that, while being usually effective at predicting the bulk behavior of these type of materials, suffer important limitations when it comes to understanding the physics behind grain-to-grain interactions that induce the material to macroscopically behave in a given way when subjected to certain boundary conditions.

The advent of the discrete element method (DEM) in the late 1970s helped scientists and engineers to gain a deeper insight into some of the most fundamental mechanisms furnishing the grain scale. However, one of the most critical limitations of classical DEM schemes has been their inability to account for complex grain morphologies. Instead, simplified geometries such as discs, spheres, and polyhedra have typically been used. Fortunately, in the last fifteen years, there has been an increasing development of new computational as well as experimental techniques, such as non-uniform rational basis splines (NURBS) and 3D X-ray Computed Tomography (3DXRCT), which are contributing to create new tools that enable the inclusion of complex grain morphologies into DEM schemes.

Yet, as the scientific community is still developing these new tools, there is still a gap in thoroughly understanding the physical relations connecting grain and continuum scales as well as in the development of discrete techniques that can predict the emergent behavior of granular materials without resorting to phenomenology, but rather can directly unravel the micro-mechanical origin of macroscopic behavior.

In order to contribute towards closing the aforementioned gap, we have developed a micro-mechanical analysis of macroscopic peak strength, critical state, and residual strength in two-dimensional non-cohesive granular media, where typical continuum constitutive quantities such as frictional strength and dilation angle are explicitly related to their corresponding grain-scale counterparts (e.g., inter-particle contact forces, fabric, particle displacements, and velocities), providing an across-the-scale basis for better understanding and modeling granular media.

In the same way, we utilize a new DEM scheme (LS-DEM) that takes advantage of a mathematical technique called level set (LS) to enable the inclusion of real grain shapes into a classical discrete element method. After calibrating LS-DEM with respect to real experimental results, we exploit part of its potential to study the dependency of critical state (CS) parameters such as the critical state line (CSL) slope, CSL intercept, and CS friction angle on the grain's morphology, i.e., sphericity, roundness, and regularity.

Finally, we introduce a first computational algorithm to ``clone'' the grain morphologies of a sample of real digital grains. This cloning algorithm allows us to generate an arbitrary number of cloned grains that satisfy the same morphological features (e.g., roundness and aspect ratio) displayed by their real parents and can be included into a DEM simulation of a given mechanical phenomenon. In turn, this will help with the development of discrete techniques that can directly predict the engineering scale behavior of granular media without resorting to phenomenology.