Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection

Mathematical modeling of viral replication dynamics, based on sequential measurements of levels of virion-associated RNA in plasma during antiretroviral treatment, has led to fundamental new insights into human immunodeficiency virus type 1 pathogenesis. We took advantage of the simian immunodeficiency virus (SIV)-infected macaque model to perform detailed measurements and mathematical modeling during primary infection and during treatment of established infection with the antiretroviral drug (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA). The calculated clearance half-life for productively infected cells during resolution of the peak viremia of primary infection was on the order of 1 day, with slightly shorter clearance half-lives calculated during PMPA treatment. Viral reproduction rates upon discontinuation of PMPA treatment after 2 weeks were approximately twofold greater than those obtained just prior to initiation of treatment in the same animals, likely reflecting accumulation of susceptible target cells during treatment. The basic reproductive ratio (R0) for the spread of SIV infection in vivo, which represents the number of productively infected cells derived from each productively infected cell at the beginning of infection, was also estimated. This parameter quantifies the extent to which antiviral therapy or vaccination must limit the initial spread of virus to prevent establishment of chronic disseminated infection. The results thus provide an important guide for efforts to develop vaccines against SIV and, by extension, human immunodeficiency virus.     

Modeling ion implantation of HgCdTe

Ion implantation of boron is used to create n on p photodiodes in vacancy-doped mercury cadmium telluride (MC.T). The junction is formed by Hg interstitials from the implant damage region diffusing into the MC.T and annihilating Hg vacancies. The resultant doping profile is n⁺/n^-/p, where the n⁺ region is near the surface and roughly coincides with the implant damage, the n^- region is where Hg vacancies have been annihilated revealing a residual grown-in donor, and the p region remains doped by Hg vacancy double acceptors. We have recently developed a new process modeling tool for simulating junction formation in MC.T by ion implantation. The interstitial source in the damage region is represented by stored interstitials whose distribution depends on the implant dose. These interstitials are released into the bulk at a constant, user defined rate. Once released, they diffuse away from the damage region and annihilate any Hg vacancies they encounter. In this paper, we present results of simulations using this tool and show how it can be used to quantitatively analyze the effects of variations in processing conditions, including implant dose, annealing temperature, and doping background.     

UTEC and Ferut: the University of Toronto's computation centre

Although not well known, the University of Toronto had a very early computer-development program and in 1952 was one of the first few institutions with an operable computer in North America. This article describes the university's initial attempt to build the UTEC computer and how it acquired the pioneering Ferut machine     

Biodegradation of monoaromatic hydrocarbons in aquifer columns amended with hydrogen peroxide and nitrate

The ability of indigenous microorganisms to degrade benzene, toluene, ethylbenzene and xylenes (BTEX) in laboratory scale flow-through aquifer columns was tested separately with hydrogen peroxide (110 mg/l) and nitrate (330 mg/l as NO₃⁻) amendments to air-saturated influent nutrient solution. The continuous removal of individual components from all columns relative to the sterile controls provided evidence for biodegradation. In the presence of hydrogen peroxide, the indigeneous microorganisms degraded benzene and toluene (> 95%), meta- plus para-xylene (80%) and ortho-xylene (70%). Nitrate addition resulted in 90% removal of toluene and 25% removal of ortho-xylene. However, benzene, ethylbenzene, meta- and para-xylene concentrations were not significantly reduced after 42 days of operation. Following this experiment, low dissolved oxygen (< 1 mg/l) conditions were initiated with the nitrate-amended column influent in order to mimic contaminated groundwater conditions distal from a nutrient injection well. Toluene continued to be effectively degraded (> 90%), and more than 25% of the benzene, 40% of the ethylbenzene, 50% of the meta- plus para-xylenes and 60% of the ortho-xylene were removed after several months of operation.     

Quantum chemical studies of Li cation binding to polyalkyloxides

A quantum chemical study of the binding of Li⁺ cation to polyalkyloxides has been carried out. The lithium cation interaction with three polyalkyloxides (polyethylene oxide (PEO), polytrimethylene oxide (PTMO), and polypropylene oxide (PPO)) has been investigated using ab initio molecular orbital theory at the HF/6-31G^* level with molecular models for the polymers. Coordination by one to six oxygens was considered. In addition, higher level calculations were carried out using G3(MP2) theory for coordination of Li⁺ by one oxygen. For coordination of lithium by one oxygen, the binding energy ordering is PTMO>PPO>PEO, with PTMO having the largest lithium cation affinity. The same ordering is found for larger coordination numbers with the exception of coordination by six oxygens, where the ordering changes due to the steric interactions.     

Deformation behavior of HCP Ti-Al alloy single crystals

Single crystals of Ti-Al alloys containing 1.4, 2.9, 5, and 6.6 pct Al (by weight) were oriented for 〈a〉 slip on either basal or prism planes or loaded parallel along the c-axis to enforce a nonbasal deformation mode. Most of the tests were conducted in compression and at temperatures between 77 and 1000 K. Trace analysis of prepolished surfaces enabled identification of the twin or slip systems primarily responsible for deformation. Increasing the deformation temperature, Al content, or both, acted to inhibit secondary twin and slip systems, thereby increasing the tendency toward strain accommodation by a single slip system having the highest resolved stress. In the crystals oriented for basal slip, transitions from twinning to multiple slip and, finally, to basal slip occurred with increasing temperature in the lower-Al-content alloys, whereas for Ti-6.6 pct Al, only basal slip was observed at all temperatures tested. A comparison of the critically resolved shear stress (CRSS) values for basal and prism slip as a function of Al content shows that prism slip is favored at room temperature in pure Ti, but the stress to activate these two systems becomes essentially equal in the Ti-6.6 pct Al crystals over a wide range of temperatures. Compression tests on crystals oriented so that the load was applied parallel to the c-axis showed extensive twinning in lower Al concentrations and 〈c+a〉 slip at higher Al concentrations, with a mixture of 〈c+a〉 slip and twinning at intermediate compositions. A few tests also were conducted in tension, with the load applied parallel to the c-axis. In these cases, twinning was observed, and the resolved shear for plastic deformation by twinning was much lower that that for 〈c+a〉 slip observed in compression loading. This article is based on a presentation made in the symposium entitled “Defect Properties and Mechanical Behavior of HCP Metals and Alloys” at the TMS Annual Meeting, February 11–15, 2001, in New Orleans, Louisiana, under the auspices of the following ASM committees: Materials Science and Critical Technology Sector, Structural Materials Division, Electronic, Magnetic & Photonic Materials Division, Chemistry & Physics of Materials Committee, Joint Nuclear Materials Committee, and Titanium Committee.     

Network topology and the theory of rubber elasticity

The earliest investigations on rubber elasticity, commencing in the 19th century, were necessarily limited to phenomenological interpretations. The realisation that polymers consist of very long molecular chains. commencing c. 1930, gave impetus to the molecular theory of rubber elasticity (1932-). according to which the high deformability of an elastomer, and the elastic force generated by deformation, stem from the configurations accessible to long molecular chains. Theories of rubber elasticity put forward from 1934-1946 relied on the assumption that the junctions of the rubber network undergo displacements that are affine in macroscopic strain. The theory of James and Guth (1947) dispensed with this premise, and demonstrated instead that the mean positions of the junctions of a ‘phantom’ network consisting of Gaussian chains devoid of material properties are affine in the strain. The vital significance of the distinction between the actual distribution of chain vectors in a network and their distribution if the junctions would be fixed at their mean positions went unnoticed for nearly 30 years. Experimental investigations, commencing with the incisive work of Gee in 1946. revealed large departures from the relationship of stress to strain predicted by the theories cited. This discrepancy prompted extensive studies, theoretical and experimental, during succeeding years. Inquiry into the fundamentals of polymer networks, formed for example by interlinking very long polymer molecules, exposed the need to take account of network imperfections, typically consisting of chains attached at only one end to a network junction. Various means were advocated to make corrections for these imperfections. The cycle rank ζ of the network has been shown (1976) to be the fundamental measure of its connectivity, regardless of the junction functionality and pattern of imperfections. Often overlooked is the copious interpenetration of the chains comprising typical elastomeric networks. Theories that attempt to represent such networks on a lattice are incompatible with this universal feature. Moreover, the dense interpenetration of chains may limit the ability of junctions in real networks to accommodate the fluctuations envisaged in the theory of phantom networks. It was suggested in 1975 that departures from the form predicted for the elastic equation of state are due to constraints on the fluctuations of junctions whose effect diminishes with deformation and with dilation. Formulation of a self-consistent theory based on this suggestion required recognition of the non-affine connection between the chain vector distribution function and the macroscopic strain in a real network, which may partake of characteristics of a phantom network in some degree. Implementation of the idea was achieved through postulation of domains of constraint affecting the equilibrium distribution of fluctuations of network junctions from their mean positions. This led in due course to a theory that accounts for the relationship of stress to strain virtually throughout the ranges of strain accessible to measurement. The theory establishes connections between structure and elastic properties. This is achieved with utmost frugality in arbitrary parameters.     

Properties of Carbopol Solutions as Models for Yield-Stress Fluids

ABSTRACT: The effect of pH on the non-Newtonian viscosity (η)of aqueous Carbopol 940 solutions is presented with high resolution (pH increments about 0.4) between pH = 2.8 and 12.7. Aqueous NaOH was used to adjust pH of 1.48 wt % Carbopol solutions. A Contraves viscometer was used to measure steady-flow shear stress at known shear rate (γ) over the range γ= 8 to 195 s⁻¹. Yield stresses and shear-thinning η(γ) were observed. Data were fitted with a Herschel-Bulkley model, whose parameters (including yield stress) were expressed as functions of pH. Comparisons were made of η(γ) to the dynamic viscometric properties η'(ω) and η*(ω) for comparable ranges of γ and frequency (ω): A fairly close match was found between η and η* but η«η'. pH dependence included previously unreported extrema of h(pH) in the range of pH = 6.2 to 6.6. Because of sensitive control of rheological properties with pH, Carbopol solutions can be used to mimic a great range of shear-thinning and yield-stress behavior that should make them useful for model studies directed toward process and equipment design and evaluation.