Student Abstracts
ASTROPHYSICS
What Lies Beneath the Surface? Europa’s Icy
Enigma
Lissa C.F. Ong
I tested the hypothesis that chaos areas on Europa may be the
result of impactor penetration into a ductile subsurface. In laboratory
experiments, ice projectiles were shot at velocities from 100 to 400 meters per
second into layered ice targets consisting of ice over water, ice over slush,
and ice over snow. Ice thicknesses varied from 0.5 cm to 4 cm. Three impact
types were produced: non-penetrating craters, simple holes, and complete
fragmentation. Non-penetrating craters correspond to recognized craters on
Europa. Simple holes correspond to equant chaos. Complete fragmentation is
analogous to blocky chaos. Impact type progresses from non-penetrating craters
to complete fragmentation with increasing energy and/or decreasing ice
thickness. Chaos boundaries correspond with observed impactor-penetration
walls, and small craters surrounding candidate penetration features on Europa
may represent secondary cratering. Measurements of over 2000 crater and chaos
features from Galileo SSI images
produced a combined exponential size-frequency distribution with craters
dominating at small sizes and chaos at larger sizes. Limited overlap between
the crater and chaos size-frequency distributions is the result of variable
crustal thickness and a possible second chaos formation mechanism. My results
suggest that chaos formation on Europa has been dominated by impactor
penetration into a liquid or slush sub-surface layer. This exogenic mechanism
for chaos formation differs strongly from other proposed mechanisms, and avoids
the issues of energy magnitude and buoyancy.
Chemical Abundances of 20 Planetary Nebulae
Davis V. Stevenson
The beautiful planetary nebulae that make up the late stages
of low-mass star evolution can help us understand more about the evolution of
stars like our sun. In particular, the delicate balance between a star’s
mass and the CNO cycle can be explored by studying the elemental abundances of
planetary nebulae. The differences in oxygen abundances between Type I and Type
II planetary nebulae should indicate whether the CNO cycle is depleting oxygen
within the more massive progenitor stars of the Type I planetary nebulae.
One notable difference in this study as compared to previous
research is that the stronger [S III] lines 9069 Å, 9532 Å in the
near-infrared were used instead of the weak [S III] 6312 Å emission line
in order to more accurately determine the abundances of sulfur within the
planetary nebulae. This increased sulfur reliability will then allow for a more
reliable S/O ratio for the objects. This S/O ratio is used to compare the
amount of oxygen between the Type I and Type II planetary nebulae.
Chemical abundances of 20 Type I planetary nebulae were
calculated, and the data seems indicative of some oxygen depletion within the
progenitor stars, but is not strong enough to draw definitive conclusions to
that effect.
Adaptive Optics in Williamstown and the Restoration of a
Solar Telescope
Galen M. Thorp
This thesis is the result of two independent projects. My
work in the field of adaptive optics is detailed in Chapter Two, while the
remaining three chapters begin with a theory behind solar observing and then
detail my work on the solar telescope. The only major connection between the
two sections is that they both made use of the Astronomy Department’s
Phillips Webcam. I have some observational results, namely images and data that
show the adaptive optics system isn’t feasible, as well as images of the
Sun that demonstrate the further potential for the solar telescope, but they
were not gathered with the intent of producing groundbreaking research. This
thesis should be considered a labor of instrumentation: I have attempted to
engineer a unique adaptive optics system and furthered the restoration of an
aged solar telescope while integrating it with modern imaging devices.
Observations of Pluto and Its Atmosphere in 2002
David R. Ticehurst
In 2002, a team of scientists from Williams College observed
the planet Pluto passing in front of a star, an occultation. The observations
were made from the University of Hawaii’s 2.2-meter telescope at Mauna Kea
Observatory. The existence of Pluto’s nitrogen and methane atmosphere has
been known since the 1970’s and was probed during an occultation in 1988.
Our data shows that Pluto’s atmosphere has expanded since 1988 even though
Pluto’s distance from the Sun has increased since then. Our data also
shows the presence of spikes in the intensity during various parts of the
occultation. Such features were also observed in 1988. The source of these
spikes may be due to variations in the atmospheric density. These observations
present a strong case for a spacecraft mission to study Pluto. NASA’s New
Horizons probe is currently scheduled for launch in 2006 and arrival at Pluto in
2015.
BIOLOGY
Systematic Genetic Array Analysis and Competition Studies
Reveal Novel Roles for the Yeast tRNA-Modifying Enzyme Pus4
tRNA modification is a complex, mysterious process. One
particularly intriguing modification is the transformation of uridine to
pseudouridine (ɵ) at position 55; this modification occurs in
>90% of the tRNA sequences analyzed across three domains of life, yet its
function is not at all well understood. In order to gain greater insight into
the function of this near-universal modification and the yeast enzyme that
catalyzes the modification, Pus4, co-culture competition studies and systematic
genetic array (SGA) analysis were performed. The co-culture studies clearly
established that pus4É¢ mutants are at a competitive disadvantage
compared to wild-type cells. This establishes that PUS4 and/or the
ɵ55 modification have a positive effect on cellular fitness, thus
providing a rationale for their evolutionary conservation. In addition, the SGA
analysis performed revealed a number of genes that appear to have synthetic
genetic interactions with pus4. Random spore analysis has preliminarily
confirmed 32 of these candidates, which encompass genes in a diverse array of
processes, including tRNA modification, protein synthesis, metabolism, and genes
of uncharacterized function. In addition, a plasmid was constructed that, based
on mutation of a conserved catalytic amino acid residue, should encode a
catalytically inactive form of pus4, under the control of its natural promoter.
This plasmid will be useful in determining if PUS4, like its E. coli ortholog
TruB, has a modification-independent function.
Reconfiguration of Song Recognition in the Adult Zebra Finch
Brain
Gregory DelPrete
As closed-ended learners, male zebra finches normally go
through one song learning process, which concludes with song crystallization at
about 90 days of age. Thereafter, the bird will sing only this crystallized
song unless some form of outside intervention induces song plasticity. This
song learning process results in a representation of a bird’s own
individual song in the high vocal center (HVC) and other song production nuclei
in the brain. Thus, a recording of a bird’s own song will elicit a more
robust response from auditory response neurons within HVC than will any other
sound stimuli. The bird will reenter a period of song plasticity and
crystallized song will change, however, if one half of the bird’s vocal
organ, the syrinx, is uncoupled from the brain. A region of the brain that is
normally required for proper song learning, but not necessary for adult song
production, LMAN, must be intact in order for this nerve-damage-induced
plasticity to occur. This suggests that song plasticity corresponds with
plasticity in the brain itself. In this study, the right half of the syrinx was
denervated in adult male zebra finches, causing the subjects to alter their
crystallized songs. Recordings of each subject’s own song before and
after nerve injury were presented to each bird after song recrystallized. In
none of the six subjects studied did HVC respond most strongly to intact,
crystallized song. All six birds showed the greatest HVC response for one of
their own songs recorded after nerve damage, and five of the six subjects showed
increased responses to songs that contained new features not seen in original
song. These results suggest that, under certain circumstances, brain plasticity
is possible in male zebra finches during a phase of life when this normally
would not be the case.
Microsatellite Isolation from the House Finch
(Carpodacus mexicanus): A Protocol for
Implementing Microsatellite Markers in the Study of Cultural Evolution.
Tory A. Hendry
In order to develop a protocol for the study of song dialects
and cultural evolution based on the use of molecular markers we attempted to
isolate microsatellite loci from the House Finch,
Carpodacus mexicanus. We tested a new
procedure for this isolation, involving several microsatellite enrichment
methods and the use of the non-palindromic restriction enzyme BseYI to create
unique sticky ends. This procedure was not successful, as we were not able to
isolate any new loci, and it showed little promise for future work. We also
tested both microsatellite and non-microsatellite genetic markers on a sample of
birds from two different dialect regions to determine their relatedness and
found these two types of markers did not behave similarly. Using microsatellite
loci we were able to determine that differences in song pattern do not serve as
a barrier to interbreeding amongst neighboring populations in this species. We
also found intriguing evidence that eastern House Finch populations may be
lacking in genetic diversity and genetically divergent on a large scale.
Characterization of the Internal Promoter within the virB
Operon of Agrobacterium
tumefaciens
Jacqueline M. Hom
Agrobacterium
tumefaciens incites crown gall disease on wounded dicotyledonous plants
by exporting both DNA and proteinaceous virulence factors across the bacterial
membrane system using a Type IV secretion system (T4SS) encoded on the
endogenous tumor inducing (Ti plasmid. This T4SS is comprised of
virB and
virD4 gene products. The
virB operon is under the
transcriptional control of the acetosyringone (AS)-inducible vir promoter. In
addition, the virB operon in the Ti
plasmid pTiA6 in the wild-type A.
tumefaciens strain, A348, contains an additional promoter embedded
between virB6 and
virB7. Through the use of a reporter
gene fusion and β-galactosidase liquid assays, the
virB internal promoter was further
characterized. By cloning the analogous
virB internal promoter sequence from
pTiC58 in the wild-type A. tumefaciens
strain C58 into a promoterless lacZ
construct and performing β-galactosidase liquid assays, we determined that
pTiC58 does not contain an internal promoter analogous to the one found in the
virB operon of A348. To investigate
whether traffic through the VirB-D4 T4SS affects internal promoter activity, we
studied the effect of T4SS-mediated plasmid translocation on pTiA6
virB internal promoter activity
measured from β-galactosidase liquid assays.
virB internal promoter activity did not
differ between a wild-type A.
tumefaciens strain carrying a broad host range plasmid and the same
wild-type A. tumefaciens strain that
did not carry a broad host range plasmid. Further, a clean deletion of the
VirB-D4 T4SS component, VirD4, did not result in abnormal internal promoter
activity, indicating that the VirD2-dependent drop in internal promoter activity
that is observed under vir-inducing
conditions is not mediated through VirD4. A construct that was expected to
insert the lacZ reporter gene
downstream of the internal promoter in the context of the entire
virB operon did not exhibit significant
β-galactosidase activity and therefore did not give conclusive data about
the virB internal promoter activity in its naturally occurring context. These
results are consistent with a working model, which predicts that the
virB internal promoter directs
constitutive transcription of VirB8 in order to nucleate assembly of the T4SS
immediately upon plant wounding.
HSP27 Is Required for Neural Development in Zebrafish
Courtney E. Juliano
Heat shock proteins (HSP’s) are highly conserved
proteins whose expression is induced in response to heat shock. They act as
molecular chaperones by helping to fold or re-fold proteins after a thermal
event and by targeting misfolded proteins to degradative machinery within the
cell. One particular HSP that is highly conserved in vertebrates is the small
HSP27. This protein functions in neuronal and non-neuronal differentiation,
conveying resistance to apoptosis, and providing protection against oxidative
stress.
Importantly, HSP27 is also implicated in actin regulation in
a variety of cell types, functioning primarily as an actin-capping protein or as
an actin-stabilizing protein. HSP27 localizes to dynamic structures at the
leading edge of motile cells where the protein’s association with actin
translates to a broader role in cell motility. More recent evidence points to
the fact that HSP27 is present in vertebrate neuronal cells and, more
specifically, in neuronal growth cones. Growth cones navigate by translating
cues from the environment into changes in the actin and/or microtubule
cytoskeleton, allowing individual axons to migrate along specific trajectories.
Based on its role as an actin regulatory molecule, it seems
likely that HSP27 may mediate axon outgrowth and/or guidance by regulating the
actin dynamics in neurons. I have examined the expression of HSP27 in zebrafish
embryos over the course of development and found that it is expressed in neurons
throughout the nervous system. In addition, I have performed loss-of-function
analysis, which revealed that, in the absence of HSP27, axon outgrowth defects
are observed. In summary, the results are consistent with HSP27 playing a role
in axon outgrowth.
Di-butyryl-cAMP Effects Spinal
Cord Regeneration in the Goldfish (Carassius
auratus)
Michelle M. Kron
A spinal cord crush at the spino-medullary level results in
the loss of function below the wound in goldfish,
Carassius
auratus. Miraculously these animals recover swimming, feeding,
equilibrium and startle responses a few months after injury (Zottoli and
Freemer, 2003). However, not all central neurons (i.e. nerve cells confined to
the central nervous system) contribute to this behavioral recovery. For
example, a pair of identifiable nerve cells, the Mauthner cells (M-cells),
morphologically regenerate after injury but the growth follows aberrant pathways
and ultimately does not contribute to the recovery of startle responses that it
is known to initiate in normal fish.
A pair of Mauthner cells (M-cells) are located on either side
of the midline in the medulla oblongata of the goldfish brain. These neurons
can be identified by their large size and characteristic extracellular negative
field recorded near the axon hillock-initial segment region. This initial region
is encased in a specialized structure called the axon cap, a structure
surrounded by a ring of glial cells. The axon cap can be divided into a central
and peripheral zone based on the input types each portion receives.
Cyclic adenosine monophosphate (cAMP) and its analogues
mediate a broad spectrum of events such as promoting neurite growth (Cai et al.,
2001) and act as axon guidance cues (Song et al., 1998). Recent studies in
larval zebrafish have demonstrated that dibutyryl-cAMP (db-cAMP), a membrane
permeable analogue, injected on the plasmalemma of damaged M-cells
“converts” the cell from a non-regenerating state to a regenerating
one. In fact, the cAMP activated growth is directed caudally and results in the
return of function (Bhatt et al., in press). In this study, we first verified
that we could reliably inject a visible tracer, Horse Radish Peroxidase (HRP)
into specific portions of the axon cap. Using the information gained through HRP
injection, we localized db-cAMP injections to specific portions of the cap
region of damaged M-cells in the adult goldfish to determine whether db-cAMP
could facilitate morphological and ultimately functional regeneration.
We saw that db-cAMP stimulates all injected M-axons to
regenerate and that db-cAMP enhances growth of injected M-axons past the wound
site. Most remarkable is that this growth occurred in 20 days compared to the
lesser growth by control M-axons in 30 days. Our results support the findings of
Bhatt et al. (in press) that cAMP can enhance M-cell regeneration and indicate
that cAMP also has significant effects in an adult model. These results have
profound implications for possible reversal of abortive regeneration and
possible functional regeneration in mammals.
Synchronous Segment Formation in the Polychaete
Capitella Capitata
Marina Vivero
The developmental mechanisms of polychaete segmentation have
not been thoroughly characterized, although they are the best representatives of
the annelid phylum. Our project examines segment formation in the polychaete
Capitella capitata by describing the spatial and temporal patterns of cell
proliferation that give rise to segments during development. Immunostaining
Capitella with an antibody against HH3, which targets rapidly dividing cells,
reveals a distinct progression of cell proliferation in the trunk region of the
trochophore larva. There are four abrupt increases in cell proliferation during
the first 96 hours of development. Cells along the extent of the
anterior-posterior body axis begin to divide simultaneously in the
ventral-lateral region of the larva at 46 hours after development commences.
Cell proliferation continues to increase until stripes of cells in the ventral
region of the trunk begin to divide simultaneously at 77 hours; when
morphological boundaries become visible, it is clear that each ventral stripe
corresponds to a single segment. Both of these events indicate that segment
formation in Capitella is synchronous. This temporal mechanism of segmentation
is atypical among the polychaetes, but a comparison of the spatial distributions
of rapidly dividing segmental precursors suggests that the spatial
characteristics of segment formation in
Capitella may still be common in the
annelid phylum.
CHEMISTRY
Progress toward the Total Synthesis of Hennoxazole A:
Completion of the
C16—C25
Victoria D. Bock
An efficient synthesis of the
C16–C25
triene fragment of antiviral marine natural product hennoxazole A is obtained in
nine steps from commercially available
(S)-3-butyn-2-ol with an overall yield
of 16.3%. A high yielding, stereoselective [2,3]-Wittig-Still rearrangement is
utilized to establish the geometry of the
C20–C21
Z-trisubstituted alkene. A key
fragment coupling between a
C8–C15
bisoxazole system and the
C16–C25
triene fragment provides validation of our approach toward hennoxazole A. This
model coupling and subsequent deprotection of the
C13 protecting group are accomplished
smoothly in two steps with a 75.1% yield overall.
Examination of the Role of the Linker Histone H5 in Chicken
Erythrocyte
Daniel R. Calnan
Mammalian erythrocytes undergo a process of enucleation as
they mature. In their functional form, mammalian erythrocytes do not contain any
genetic material, and are essentially ‘bags of hemoglobin.’ Avian
and amphibian erythrocytes do not undergo the enucleation process and, therefore
are nucleated in their functional form. However, no transcription or
replication occurs in these nucleated, mature erythrocytes. The DNA is
essentially held in an inert state.
The DNA within these nucleated erythrocytes is packaged in
the same manner as it is in transcribing and replicating cells within the
chicken with one exception. The typical chicken cell has the linker histone H1
(A and B) present in the nucleosome (the basic, repeating unit of packaging in
chromatin). In the erythrocyte nucleosome, a variant of H1, named H5, is
present in a four to one ratio over H1. The incorporation of H5 inactivates the
erythrocyte nucleus and holds the DNA in an inert state.
The goal of this project is to compare the strength of
binding of H1 and H5 to chicken erythrocyte chromatin. To achieve this,
erythrocyte chromatin was isolated from chicken blood. This chromatin was then
characterized by gel electrophoresis and thermal denaturation. The linker
histones were selectively stripped off using elevated salt concentrations and
the stripped chromatin was recovered. This stripped chromatin was characterized
in the same manner as the whole chromatin.
A Snapshot of PCB Levels in the Hoosic River
PCB Levels
in Sediment, Crayfish, and Brown Trout in the Tri-State Area
Elaine K. Denny
From the 1950s to the 1970s, Sprague Electric Company (SEC)
of North Adams, Massachusetts, used polychlorinated biphenyls (PCBs) in its
manufacture of capacitors. Although the plant closed at the end of the 1970s,
PCBs continued to leach into the river from contamination at the former SEC
site. Later studies estimated that approximately 20 pounds of PCBs were
entering the Hoosic River each year from waste buried near the plant. As
probable carcinogens, these PCBs posed potential health threats to citizens
using the river downstream of the SEC. Finally, in 2000 a cleanup effort was
launched, the landfill was contained, and large amounts of contaminated dirt
were removed to prevent PCBs from entering the Hoosic. After the cleanup and
prior to this study, however, no research had been conducted investigating to
what extent these highly stable, persistent pollutants continue to exist in the
Hoosic ecosystem.
This study sought to measure what levels of PCBs remain in
the river four years after the remediation of the SEC site. We sampled
riverbank soil from Adams, Massachusetts, to the Vermont/New York border in
hopes of identifying trends in PCB dispersion. We focused primarily on
recreational sites to gain a better understanding of what levels of PCBs
recreational users of the Hoosic would encounter on a regular basis.
Additionally, we studied PCB levels in crayfish and brown trout to investigate
how PCBs continue to bioaccumulate. We also conducted these studies so we could
compare our results to previous studies on the same species, thereby gaining a
better understanding of how PCB levels may have changed since the SEC cleanup in
2000.
Progress toward the Total Synthesis of Jerangolid D
Adrian A. Dowst
Jerangolid D is a secondary metabolite produced by the
myxobacterium Sorangium cellulosum
(strain So ce 307). A structural variant of jerangolid D exhibits potent
antifungal activity against the developing cells
of Hansenula anomala by a mechanism
that is believed to be similar to ambruticin, a more well-known myxobacterial
isolate. Jerangolid D bears an appealing structure from a synthetic point of
view. It contains two asymmetric dihydropyran-based ring systems and four
stereogenic centers, one of which is in a doubly-allylic location.
In this work, we propose a total synthesis of the natural
product. Our synthetic route utilizes a three-step sequence that was previously
developed by the Smith group for establishing asymmetric dihydropyran-based ring
systems. Using the experience from synthesizing the kavalactones, this aldol
– homologation – lactonization sequence will be applied to both
rings of jerangolid D. The stereochemistry at the doubly allylic can be
approached by replicating the asymmetric hydroformylation reaction used by
Jacobsen in his total synthesis of ambruticin. Intercepting his route provides a
reliable method of establishing a potentially difficult structural
component.
Reactions through the cyclization of the first ring of
jerangolid D were successful. However, single nucleophilic addition to this
lactone was not as straightforward. To avoid mixtures of starting material,
desired product, and overaddition material, a sulfone-based route was attempted.
Although addition of a sulfone-stabilized anion was successful, desulfonation
proved to be difficult. Both modifications of the sulfone approach and new
synthetic strategies are proposed as alternatives.
A Kinetic Model for the HIV-1 Rev Pathway
Jeffrey J. Ishizuka
A kinetic model for the HIV-1 Rev protein was developed by
drawing upon the literature to formulate a set of differential equations
modeling the behavior of Rev and its various associated factors over time.
Several sets of results were presented demonstrating the possibility of
oscillations in the concentration of these factors. Finally, these results were
analyzed and future directions for the project were discussed.
A Library of Benzocanthinones
Charles E. Jakobsche
A six molecule library, containing the canthine alkaloid,
benzocanthinone, one known benzocanthinone derivative and four previously
unsynthesized isomeric compounds was successfully synthesized. Each synthetic
scheme contained two similar key steps, first the base-catalyzed formation of an
amide bond and second the radical induced intramolecular cyclization of an aryl
halide. The productivity of the cyclization step on a variety of relevant
starting materials was analyzed to understand better the scope of this
reaction’s effectiveness.
Probing Changes to the Electronic Structure of Substituted
Triphenylene and Triimide Molecules for Use in Liquid Crystalline Donor/Acceptor
Complexes
Steven T. Scroggins
Mixtures of substituted triphenylene molecules with triimide
have been shown to form materials in which donor/acceptor behavior causes the
molecules stack in an alternating fashion. At certain temperatures, some of
these mixtures display liquid crystalline properties. The degree of the
donor/acceptor interaction is determined by the donor properties of the
triphenylene’s electron-rich π system and the acceptor properties of
the electron-poor triimide. The proximity in energy of the HOMO of the
triphenylene and the LUMO of the triimide determines the strength of the
donor/acceptor interaction. In our work, we have shown that changes to the
substituent groups on the triphenylene may change the strength of this
interaction, affecting both the HOMO-LUMO energy gap and the mixtures’
liquid crystalline properties. We have also probed ways of tuning the electronic
properties of the triimide by creating hydrogen-bonded supramolecular complexes.
We did not find NMR or IR spectroscopy to be useful in characterizing these
supramolecular complexes, but CV experiments on mixtures of triimide with
certain compounds (N, N'-diethylthiourea, 2-guanidinobenzimidazole) show that
their hydrogen-bonding interactions with triimide may be used to modulate the
electronic properties of the molecule. So far, we have been unable to measure
the extent of this change or characterize its effect on the donor/acceptor
complexes formed by the triimide with the substituted triphenylenes.
Synthesis of Novel Chiral Platinum Bioxazoline Complexes
for Use as Anti-Tumor Agents
Edward A. Wydysh
The discovery of cisplatin as an effective anti-tumor agent
and the subsequent determination of its mode of action led to the synthesis of
many related structures in hope of synthesizing a more powerful drug. This
paper begins with describing the ways in which cisplatin is believed to lead to
cell death, highlighting several important components. Furthermore, the means
by which the body detoxifies cisplatin are also brought to focus. The knowledge
of these biological processes is taken into account, and various structural
components necessary for a more active drug are outlined.
The ability of a bioxazoline ligand to bind to platinum,
prevent attack of cellular thiols, and allow for the introduction of chirality
indicates that this functionality is worth pursuing. The bioxazoline ligands
were first synthesized in several steps from enatiomerically pure amino acids as
previously described in literature. The real synthetic achievement accomplished
is the creation of the platinum-bioxazoline complexes.
Both enantiomers of
4,4’-diisopropyl-2,2’-bioxazoline platinum-diiodide as well as both
enantiomers of 4,4’-dimethyl-2,2’-bioxazoline platinum-diiodide were
synthesized in 3.75% and 22% yield, respectively.
S,S-4,4’-dimethyl-2,2’-bioxazoline
platinum-dichloride was synthesized in 18.9% yield from the corresponding
diiodide, and
S,S-4,4’-diisopropyl-2,2’-bioxazoline
platinum-dichloride was synthesized in 16.5% yield from the corresponding
diiodide starting material. The reactive intermediate in the scheme from the
diiodide to the dichloride product is the diaqua compound, which was synthesized
for both enantiomers of the methyl and isopropyl compounds and subsequently
remained in solution throughout the following reaction.
The ability of the
S,S diaqua methyl and isopropyl
compounds to bind to the nucleotide dGMP was also examined. It was determined
that the novel platinum complexes bind to the nucleotide exactly as cisplatin
does, at the N7 nitrogen.
Finally, an experiment to determine the extent of complex
binding to double-stranded DNA was begun, in which the melting temperature of
the non-platinated double-stranded DNA determined corresponds to that described
in literature. The attempted reaction of the complex with single stranded DNA
and a portion of the subsequent purification of DNA are described.
COMPUTER SCIENCE
Cache-Conscious Memory Allocation
Christopher Cyll ’04
Today, almost all software uses on dynamic memory allocation.
In some programming languages, it is impossible to even write “Hello
World!” without implicitly calling the allocator. However, the costs of
dynamic memory allocation on cache performance are relatively unstudied. This
work explores the effects of dynamic memory allocation on cache performance, as
well as methods to make memory allocators cache-conscious. We use profiling
techniques to build custom memory allocators. These allocators contain
statically generated memory layouts that arrange memory in a cache-conscious
manner for previously analyzed workloads. We demonstrate performance gains
resulting from these cache-conscious allocators and analyze the cache
performance of different memory layout strategies. We provide an open source
foundation to aid in future research that is fully compatible with all standard
C allocation functions.
GEOSCIENCES
Petrology and Evolution of a Monoclinally-Folded, Paleorift
Lava Sequence, Vatnsdalsfjall, Northwest Iceland
Katherine C. Ackerly
The Hvammur-Breidin area of southern Vatnsdalsfjall in
northwest Iceland lies 15 km east of an abandoned rift zone that was an active
spreading center from 15–7 Ma. It contains an unusual and dramatically
well-exposed monoclinal flexure that deforms a 150 m-thick sequence of late
Tertiary volcanics produced during the waning stages of rift activity. The lavas
in the sequence dip to the west up to 44º and maintain a constant thickness
up to the fold axis, which trends north-south. In the trough of the monocline
is a thick basaltic unit, the Hjallin Lens, that was originally mapped as an
intrusion but has been reinterpreted as extrusive (McClanahan, 2004). In this
study, the evolution of the monocline is described and related to a change in
magmatic processes that ultimately led to the eruption of the Hjallin Lens
basalt.
Overlying the monocline sequence and underlying the Hjallin
Lens, an intervening sequence of thin basalt flows leading upwards to a thick
lahar thickens from ~30 to 100 m into the trough of the monocline. This middle
sequence contains low-angle unconformities and minor faults that suggest
structural adjustment concurrent with its emplacement. A major fault that
post-dates the eruption of the flows in the monocline and predates the
deposition of the lahar is inferred to have displaced the monocline sequence
just east of its fold axis, with 150 m of normal slip to the west.
Flows that are part of the monocline (M sequence) and those
that overlie the monocline (O sequence) are mutually distinct in terms of
petrography and geochemistry. The M sequence contains several silicic units
(rhyolite, dacite, and rhyodacite tuff) interlayered with a wide variety of
basalts, including weakly porphyritic intergranular basalt, coarse-grained
ophitic basalt, olivine basalt, and plagioclase-ultraphyric basalt. In
contrast, basalts in the O sequence are all fine-grained and intergranular.
Volcanic rocks from both the M and the O sequences are
subalkaline. Bivariate plots of major oxides against MgO reveal a general
fractionation trend involving both sequences, in which the O sequence and
Hjallin Lens basalts are the most highly evolved differentiates. With respect
to increasing SiO2, M and O basalts
characterize two distinct trends, and a high degree of compositional variation
exists within the M sequence. Basalts from both sequences are enriched in
lighter, incompatible elements (Th and Rb), characteristic of plume-associated
mid-ocean ridge basalt. The degree of enrichment among the M-sequence basalts
is varied but increases somewhat upsequence. Both M and O basalts have Zr/Nb
ratios of <10, also a signature of plume influence, and a substantial gap in
Zr and Nb abundance occurs between the M and O sequences.
Two new
40Ar/39Ar
dates, one from the top of the M sequence (7.62 ± 0.32 Ma) and one from the
Hjallin Lens (6.98 ± 0.18 Ma; McClanahan, 2004) bracket a 0.60–1.14
m.y. window for the formation of the monocline, major displacement of the
monocline along the normal fault, and the eruption of the O sequence. The
monocline is interpreted to have formed incrementally during eruption of the O
sequence above an upward-propagating normal fault. The structure is likely due
to local subsidence caused by extension, and it provided a topographic
depression for the ponding of the thick Hjallin Lens basalt flow during a new
phase of magmatism.
Changes in a Fringing Reef Complex, St. John, U.S. Virgin
Islands
Emily C. Clinch
Data collected by five expeditions, spanning 36 years, shows
that the Mary Creek reef complex (MCRC) is shallowing and that
Acropora palmata colonies in the MCRC,
after experiencing a severe decline in the 1980s, have begun to repopulate the
reef. Analysis of five airphotos taken between 1965 and 1999 shows that all
three reef lobes of the MCRC have decreased in size since 1983, and the
westernmost reef lobe has decreased by more than 50% since 1965. Bathymetric
data from 1968, 1998, and 2004, show conclusively that the backreef lagoon is
experiencing shallowing at a rate of approximately 3.2 cm/year.
The backreef lagoon infilling is not attributable to in-situ
algal sediment production, nor to an increase in storm events. However, the
progressive infilling may be related to regular storm transport of sediment over
the reef crest.
We observed approximately 70
A. palmata colonies in the MCRC, a
substantial increase over the population observed in 1998.
Depositional History of the Plio-Pleistocene Arroyo Blanco
Basin on
Carmen Island, Baja California Sur, Mexico
James M. Eros
Plio-Pleistocene basin and ramp deposits are exposed at many
sites along the southern Baja California coast of the Gulf of California. These
deposits give an important record of the opening of the Gulf of California at
about 5 Ma. However, most of these basins record only part of the
Plio-Pleistocene history. Arroyo Blanco on Carmen Island, located 25 km
offshore of the town of Loreto, provides access to a substantially complete
record of Pliocene and Pleistocene ramp, terrace and rocky-shore environments in
the context of a large carbonate basin.
The Arroyo Blanco Basin on Carmen Island covers about 3.3
km2 and includes at least 61 m of
conformable strata measured normal to bedding plane. Satellite imagery (TM and
ASTER data) was used to evaluate possible deposits and their relationships and
to expedite fieldwork. These data were also used for mapping basin and terrace
features. A stratigraphic column for the basin was constructed to differentiate
between limestone, conglomerate and clay-pan deposits. In addition, four marine
terraces were identified on the truncated east side of the basin, at 12, 37, 58
and 68 m elevation above sea level. A possible fifth terrace may exist at 72 m
elevation. A biostratigraphic column was constructed using important index
fossils such as the pecten Argopecten
svedrupi (Lower Pliocene), the echinoids
Clypeaster bowersi (Lower-Middle
Pliocene), Encope shepherdi (Middle
Pliocene), and Encope grandis subsp.
inezana (Pleistocene); the gastropod
Turitella gonostoma (Pleistocene), and
the coral Pocillopora robusta
(Pleistocene). All Pliocene deposits are conformable, and Lower Pleistocene
deposits sit conformably on these deposits. The origin of the basin is set at
roughly 5 Ma to include the upper Lower Pliocene. The Plio-Pleistocene boundary
is set tentatively at about 47 m up section, or roughly 50 m above present sea
level. Eight thin sections were made from samples of representative strata, and
these support field interpretations of deposits as rhodalgal calcarudite
limestones with a minor volcanic lithic component.
All larger scale bedding in the basin shows a consistent
synsedimentary slope of 4-6° along about 0.8 km dip. Thick rhodalgal
calcarudite/calcarenite facies indicate predominant current and offshore-storm
deposition (~64%). Less prevalent and thinly bedded units of conglomerates
(~15%) indicate periodic terrestrial runoff, probably related to onshore
chubascos. Pecten-rich strata (~21%)
indicate periods of relatively calm background deposition related to nearshore
processes. Finally, horizontal red clay beds indicate back-beach or shallow
intertidal subaerial deposits (< 1%). These are left undisturbed in their
original horizontality. These clay beds act as a ‘mega-geopetal’
device that allows for the recalculation of true ramp thickness as a function of
vertical accumulation on a slope. At Arroyo Blanco, this true thickness is 153
m. While other basins in the Gulf show evidence for tectonic tilt, Arroyo
Blanco Basin does not.
In general, the Arroyo Blanco Basin strata indicate prolonged
relative marine transgression in a sizeable basin dominated by rhodalgal facies.
The thickness is theorized to be related to prolonged subsidence of the basin,
as can be seen from the continuous development of a carbonate ramp. There are a
few possible indicators of regressive periods, namely red clay beds and possible
shallow-water sedimentation, in the form of channel flow in three of the
conglomerate beds. After a period of subsidence ranging from the upper lower
Pliocene to at least the lower Pleistocene, the sediments of Arroyo Blanco
underwent uplift relative to sea level. This began with a period of relative
sea level low-stand and the formation of a Pleistocene beach deposit that
currently caps the stratigraphy of the basin. The basin subsequently
experienced episodic uplift during the Pleistocene. At least four marine
terraces were cut into the Pliocene substrate, leaving evidence of Pleistocene
rocky shorelines, including sorted, red algae coated cobble deposits, bored
surfaces, gastropods and corals.
The basin is bounded to the southwest by a normal fault
cutting all four Pleistocene terrace deposits and normally offsetting
Pleistocene deposits along its margin. Also, tectonic uplift since the Lower
Pleistocene has been considerable.
Comparison of these deposits to other basins, including Punta
El Bajo (northern Loreto Basin), Arroyo El Mangle, deposits at the base of the
Concepcion Peninsula, and Punta Chivato indicate that the Arroyo Blanco deposits
are exceptional for the thickness of their rhodalgal facies. Additionally, this
site provides an important master-record of conformable Pliocene and Pleistocene
strata for the entire Gulf of California.
Characterization of High-Angle Faults on the Island of
Syros, Greece
Eli D. Lazarus
Faults on the Aegean island of Syros, part of the Cycladic
archipelago southeast of mainland Greece, record the complex tectonic history of
the Mediterranean region following blueschist metamorphism. The Cyclades are in
the Attic-Cycladic crystalline belt, a series of high-pressure, low-temperature
metamorphic core complexes derived from subduction between microplates during
the Alpine orogeny. Beginning approximately 30–25 Ma, collision in the
Mediterranean gave way to post-orogenic extension (Jolivet and Faccenna, 2000)
and exhumation of the Aegean blueschist terranes by low-angle normal faults and
detachments in a back-arc setting (Okrush and Bröcker, 1990). Although
Syros is famous for its exposures of high-grade metamorphic rocks, the
island’s high-angle normal faults with well-developed breccia zones have
not been studied in detail. It is uncertain whether the high-angle normal faults
are synchronous with or younger than the large-scale normal faults responsible
for Aegean blueschist exhumation. Three high-angle faults are located along
Syros’ western coast at Cape Diapori, the northernmost tip of the island;
the western end of Cape Katakefalos; and on the Charasonas headland near the
Grotto of St. Stephanos. The faults are arranged en echelon, strike
NW–SE, dip >60º, and have throws no greater than 30 m. All three
breccia zones contain similar fault products, primarily equidimensional angular
marble fragments in a cohesive, finely ground carbonate matrix. No schist
clasts are evident in the breccia. Field observations and petrographic
descriptions provide the context for fluid-inclusion analyses of fault material
from each of the breccia zones, which help constrain ambient conditions during
faulting. Fluid inclusions in crystalline quartz from a fault-related vein at
Diapori show homogenization temperatures of 140–150ºC and freezing
temperatures of –2.9 to –0.9ºC; the latter suggest a fluid
composition of 1.5–4.7 wt% NaCl. Fluid inclusions in crystalline quartz
from breccia matrix at Charasonas contain at least three fluids with
homogenization temperatures of 140–160, 200–210, and
220–240ºC. Freezing temperatures of –5.9 to –5.4ºC
suggest a fluid composition of 8.5–9.0 wt% NaCl. Petrographic evidence
suggests brittle deformation during faulting; brittle deformation tends to occur
in low-temperature environments at shallow crustal levels. The three faults
occur at or near the tips of the western peninsulas, and may be isolated parts
of a NW–SE-trending graben with a W-dipping plane on its NE side and an
E-dipping plane to the SW.
The Elusive Intrusive: A Petrologic, Structural, and
Geochemical Analysis of a Large Igneous Body in Vatnsdalsfjall, Northwest
Iceland
Paige M. McClanahan
The Hjallin Lens is a thick, lenticular basaltic unit in the
Vatnsdalsfjall Ridge near the southern end of the Skagi Peninsula in northwest
Iceland. The extensive volcanic and intrusive units that define the geology of
this region are products of a unique interplay between the mid-Atlantic
spreading ridge and the Iceland plume. While no longer active today, the region
was the site of prolific volcanic activity between 7 and 15 Ma. The Hjallin
Lens was first interpreted by Annells (1968) as a shallow-level, olivine-free
tholeiitic laccolith. However, petrographic, geochemical, and geochronologic
analyses, coupled with extensive field observations, have yielded support for an
alternate interpretation: that the lens is in fact an extrusive feature,
representing the ponding of a thick basaltic flow in a pre-existing topographic
low.
The Hjallin Lens is exposed on the western flank of the
Vatnsdalsfjall ridge. It extends approximately 3000 m in the NNW–SSE
direction and up to 800 m in the ENE–WSW direction. The lens reaches its
greatest thickness (over 150 m) near its southern end. The lithology of the
lens is virtually uniform throughout: the rock is a very hard, fine-grained,
aphyric, non-vesiculated basalt that has cooled into sharply defined columnar
joints. Petrographic analysis revealed that the lens basalt contains small,
scattered phenocrysts of plagioclase and, less frequently, clinopyroxene. Its
groundmass is composed of roughly equal amounts of intergranular clinopyroxene,
plagioclase, and a significant amount (15-40%) of ilmenite and other opaque
minerals. Geochemically, the lens rock can be classified as a tholeiitic,
sub-alkaline basalt, with trace-element signatures (Zr/Nb<10; enrichment in
incompatible elements) that indicate a plume overprint on N-MORB geochemistry.
The striking textural, mineralogical, and geochemical homogeneity of the Hjallin
Lens indicates that the entire body must have cooled rapidly at the surface,
without any internal differentiation.
The lens is underlain by a rhyolitic ash flow tuff along a
sharply defined contact. At the southern end of the lens, the ash flow tuff is
underlain by a poorly lithified sediment with well-preserved specimens of
carbonized and silicified organic material. The upper contact of the sediment
with the ash flow tuff is sharp; at its base, however, the sedimentary unit
grades into a much coarser, polymict lahar. The presence of these relatively
undisturbed surficial units immediately below the lens is further evidence that
the lens basalt is extrusive and that it buried surficial units.
New
Ar40/Ar39
dating indicates an age of 6.98 ± 0.18 Ma for the lens basalt. A
topographically, but not necessarily stratigraphically, higher basalt unit
located 1 km ENE of the lens was dated at 7.35 ± 0.19 Ma (Auerbach, 2004).
A basalt from the monocline beneath the lens has an age of 7.62 ± 0.32 Ma
(Ackerly, 2004).
The Hjallin Lens thus appears to be a thick, homogenous
extrusive. Its thickness could be due to its unique position immediately
adjacent to a large monoclinal fold structure (Ackerly, 2004).
Extension-related down-dropping, perhaps reinforced by crustal loading from
accumulating lavas, resulted in the creation of the monocline and the formation
of a topographic low. As it erupted, the lava flowed down into this valley,
where it pooled and subsequently crystallized rapidly.
MATHEMATICS
Triangle Sequence Revisited: An In-Depth Look at Triangle
Iterations
Christopher Stine Calfee
Purely periodic triangle sequences correspond to cubic
irrationals alpha and beta. We will show a variety of methods for finding the
irreducible cubic polynomials corresponding to both alpha and beta. Finally, we
will explore some of the interesting
polynomials which emerge from the
sequences that are purely periodic of periodicity length one.
Minimal Blow-ups of Spherical Coxeter Complexes and their
Homotopy
Eric Hershel Engler
The goal of my thesis is to find a presentation for the
fundamental group of projective
spherical Coxeter complexes with minimal blow-ups.
It is based on work by Davis,
Januszkiewicz and Scott (DJS), who prove that
the fundamental group is the kernel of a map p from a group OW that acts
on the universal cover of the space onto the underlying group W. DJS prove this
result for abstract systems, and thus translating their work is non-trivial, in
fact very difficult. We translate their work into the language of
graph-associahedra developed by the SMALL 2004 configuration spaces group and
specifically compute OW and p. Given these computations, we calculate the
fundamental group of these spaces (through dimension six) using java code and a
computational algebra package called GAP. From these results, we develop a
conjecture for the first homology group.
Double Bubbles in
S3,
H3, and Gauss Space
Neil Reardon Hoffman
This
thesis is the near completion of work done by the 2001-2003 Geometry Groups to
prove the double bubble conjecture in the three-sphere
S
3 and hyperbolic three-space
H3
in the cases where we can apply Hutchings theory:
• in
S3,
both enclosed volumes and the complement occupy at least 10% of the volume of
S3
• in
H3,
the smaller volume is at least 85% that of the larger
and in Gauss space
Gm
for three-equal-volume double bubbles. A balancing argument and asymptotic
analysis reduce the problem in
S3
and
H3
to some computer checking. The computer analysis has been designed and fully
implemented in
S3.
In
H3,
it has been only partially implemented.
Completions of UFDs with Semi-Local Formal Fibers
David Jensen
Let (T,M) be a complete local ring such that |T/M|
= |T|. Given a finite set
of incomparable non-maximal prime ideals
C of T, we provide necessary and
sufficient conditions for T to be the completion of a local UFD A
with semi-local generic formal fiber
with maximal ideals the elements of C. We also
prove an extension of this result where A contains a height one prime
ideal with semi-local formal fiber with
maximal ideals the elements of C. In
addition, we discuss the possibility of forcing our UFD A to be
excellent.
Identifying Best Rational Approximations through Sharp
Diophantine Inequalities
Kari Frazer Lock
Using the theory of continued fractions, we produce a new
sharp Diophantine inequality involving an irrational number and a rational
approximation to that number, such that the only solutions are precisely all the
“best rational approximates” to the given irrational number; that
is, the complete list of its convergents. This work generalizes and extends
previously known results appearing in the literature. We also identify the best
rational approximates when simultaneously approximating a finite number of
generalized golden ratios in the same quadratic field.
Rotating Linkages in a Normed Plane
Jonathan Lovett
In this paper, we examine the implications of rotating
linkages in generalized norms. We prove that fully rotating a rhombus with both
diagonals implies that the norm is linearly equivalent to Euclidean or that the
triangle has a certain exceptional property. We also demonstrate that the same
is implied by full rotation of some non-exceptional isosceles triangle with
median or right triangle with median. In addition, we prove that all triangles
can be fully rotated in any norm, and that that rotation is continuous if the
norm is strictly convex.
Totally Geodesic Seifert Surfaces in Hyperbolic Complements
of Knots in 3-Manifolds
Aaron Daniel Magid
A rich class of hyperbolic 3-manifolds can be represented as
the complement of a knot or link in a closed orientable 3-manifold. For these
cusped manifolds, we are interested in finding totally geodesic Seifert
surfaces, surfaces whose boundary is the knot or link. We consider knot
complements for knots embedded in Euclidean 3-manifolds, spherical 3-manifolds,
and S2 x
S1. We show that all of the closed
Euclidean 3-manifolds contain a hyperbolic knot with totally geodesic Seifert
surface. Additionally, we show that
S2 x
S1 and all lens spaces L(p,q)
contain a hyperbolic knot with totally geodesic Seifert surface. Also, we give
examples of some immersed totally geodesic surfaces in knot complements in the
3-sphere.
The Farey-Bary Map Revisited
Andrew Noah Marder
Two generalizations of the Minkowski ?(x) function are given.
As ?(x) maps quadratic irrationals to rational numbers, it is shown that both
generalizations send natural classes of pairs of cubic irrational numbers in the
same cubic number field to pairs of rational numbers. It is also shown that
these functions satisfy an analog to the fact that ?(x), while continuous and
increasing, has derivative zero almost everywhere. Both extend earlier work of
Beaver-Garrity on the Farey-Bary map.
PHYSICS
Energy Yield and Visual Impact Studies of the Berlin Wind
Project
Samuel M. Arons
The Berlin Wind Project is a Williams College-sponsored study
of the potential for electricity generation by a 7-9-turbine wind farm at Berlin
Pass (Berlin, NY). Two questions must be addressed in assessing the
project’s viability. (1) How much energy could the proposed wind farm
produce in a year? (2) What would be the turbines’ visual impact? In
this thesis, I present both the answers to these questions and the techniques
necessary to obtain them.
I first conclude that AWS Truewind’s wind resource maps
predict energy yield with an accuracy of approximately 16±3% in the
northern Berkshire/Taconic region, and that the maps also predict directional
distributions quite reasonably. I next conclude that a 7-turbine wind farm at
Berlin Pass could produce 35±4% million kW-hr per year, or 163±21% of
Williams College’s 2002-2003 energy use on average. Because of natural
fluctuations in wind speed, this value could vary by as much as an additional
±10% from year to year. Furthermore, since the prevailing winds at the
Pass blow from the WNW and the ridgeline runs NNE-SSW, turbine shading should
not cause substantial energy losses—though there would likely be some
losses from a moderate SSW wind component. (Assuming a net turbine cost (sale
price + installation) of $1.24 million ($8.65 million for 7 turbines) and an
average wholesale electricity price of $38/MW-hr the farm could pay for itself
in 6.5±.84 years ignoring the time value of money.
In addition, based on the results of the visual impact
study—some 59 potential views of the wind farm from various locations
within a 20 km radius of the Pass—I conclude that the turbines are likely
to be visible from quite a few locations throughout the region. However, from a
number of these locations the turbines may appear to be quite small and could
remain unnoticed by all but the most careful observers.
In light of these results, my recommendation to the College
is to continue researching the Project while maintaining an open dialog with the
local communities.
Measuring the Two-Step
6P1/2
-> 7S1/2
-> 7P1/2
378nm/1301nm Transition in Atomic Thallium
Mark H. Burkhardt
This thesis presents program towards measurements of the
7S1/2 ->
7P1/2 E1 transition in atomic
thallium. Since the ground state of thallium’s valence electron is the
6P1/2 state, the
6P1/27 ->S1/2 transition
must also be driven.
The feasibility of such a two-step excitation using present equipment will be
demonstrated. Measurements will initially be made in a vapor cell environment,
and they will lead up to a measurement of the Stark shift in an atomic beam
environment. High-precision measurements such as this will provide valuable
information regarding atomic wave functions and electroweak theory, which will
help to refine the Standard Model.
A Passively Mode-Locked All-Fiber Erbium-Ytterbium Doped
Laser with a Polarization Sensitive Nonlinear-Optical Loop Mirror
Paul M. Crittenden
Successful operation of a pulsed erbium-ytterbium co-doped
all-fiber laser is reported. The laser is capable of lasing at 1.55 µm
using a 1.06 µm Nd: YAG laser pump source. The employment of a
polarization sensitive nonlinear-optical loop mirror (NOLM) has led to passive
mode-locking. Pulses trains lasting on the order of hours have been achieved.
Interpretation of pulse spectra and autocorrelations has shown these pulses to
be approximately 1-2 picoseconds in duration. A new model of the NOLM has been
formulated incorporating fiber birefringence and polarization. This model
suggests a technique for exploiting birefringence in the fiber to shift the
switching threshold of the NOLM.
The Primary Sequence Limit of pre-mRNA Splice Site
Detection
Eric G. Daub
Traditional bioinformatics methods scan primary sequences for
patterns. In cases such as RNA splicing or editing, however, cellular action
may depend in some way on the RNA’s secondary structure. If the
information content of the primary sequence is small, how accurate can primary
sequence methods be? We study the problem of donor pre-mRNA splicing, where the
dataset is sufficiently large that the sequence overlaps between real and decoy
sequences, which limit the performance of primary sequence methods, can be
quantified. We propose a model that with sufficient training approaches the
optimal accuracy permitted by primary sequence analyses, and we assess the
accuracy of a class of primary sequence methods generally by studying how they
scale with dataset size.
Four-Wave Mixing and Other Observations of Quantum-Confined
Excitons
Jesse W. Dill
Though quantum-confined semiconductors have been studied at
length and are currently used in some applications of opto-electronics, little
is known about the effect of quantum confinement on their ultrafast dynamics.
In this thesis, we continue previous work in the Bolton lab that established
models and materials choices for this work. We analyze four-wave mixing
observations of the ultrafast exciton dynamics in
In0.04Ga0.96As
quantum wells. When compared across a range of well widths that span the
transition from two- to three-dimensional excitons, these data show that
increasing exciton confinement dampens their interactions with one another and
with phonons significantly. In the future, these data will be combined with
pump-probe spectroscopy techniques to further quantify the results.
The Discrete Wigner Function Based on Finite Fields:
Similarity Classes and Transformations
Matthew J. Hoffman
The continuous Wigner function provides a way of representing
the quantum states of systems with continuous degrees of freedom. As not all
systems have continuous degrees of freedom, Wigner functions have also been
developed for discrete quantum systems. There are many different discrete
Wigner functions for a system with N
orthogonal states. One popular version is defined on a
2N x
2N discrete phase space, whereas the
one we use in this thesis is defined on a
N x
N discrete phase space. Another
feature of our discrete Wigner function is that the field of real numbers that
labels the axes of continuous phase space is replaced by a
finite field having
N elements. There exists such a field
if and only if N is a power of a prime;
so our formulation can be applied directly only to systems for which the
state-space dimension takes such a value. While this constraint appears
limiting, we note that any quantum computer based on qubits meets the condition
and can thus be represented using our Wigner function. In this thesis, we
present our description of the discrete Wigner function and look at a number of
questions that arise from this construction. First, there are a number of
different ways to define the Wigner function for a given
N, but how many of these are actually
fundamentally different? We define and prove some things about a notion of
similarity for any value of N, and then
we present a method for calculating the number of similarity classes. Another
question is: "What happens when you apply a unitary transformation to the Wigner
function?" We develop a method for analyzing the effect of such a
transformation and use it to look at a two-qubit version of Grover’s
search algorithm.
Captivating and Chilling: Progress toward BEC via Laser
Trapping
Leon A. Webster
The production of a Bose Einstein condensate (BEC) in dilute
gases requires extremely low temperatures and high density. This thesis
describes progress on the laser systems required to cool and confine RB-87 atoms
to their Bose-condensed phase. It includes work on the magneto-optical trap,
which uses a magnetic field and 780nm diode lasers, and the far-detuned dipole
trap, which uses a 100W carbon dioxide laser focused to a spot roughly
40µm.
PSYCHOLOGY
Dose-Dependent Effects of Estradiol on Learning Following
4-Vessel Occlusion
Nicolas A. Bamat
Ischemic events such as cardiac arrest and stroke affect over
a million people in the United States every year. Cognitive deficits following
such events are often associated with damage to the hippocampus. Using animal
and cell culture models, estradiol administration has been shown to protect the
hippocampus from such damage. Furthermore, in male rats it has been shown in
that estrogen-mediated neuroprotection from ischemic injury can be demonstrated
in behavioral models of learning and memory dependent on the hippocampus. The
present study examined whether this behavioral neuroprotection is dependent on
sex or the level of estradiol using a 2x3x2 design [(Sex: Male and Female) x
(Hormone: Placebo, Low Estradiol (.25mg/pellet), High Estradiol (2.5mg/pellet))
x (Surgery: Ischemia and Sham)]. Gonadectomized male and female rats were
implanted with 21-day time-release hormone pellets on PND 35 and experienced
transient global ischemia via four-vessel occlusion or a sham surgery two weeks
later. A week following surgical procedures, all rats were tested on a
non-hippocampally dependent visible platform Morris Water Maze (MWM) variant and
then on the hippocampally dependent hidden platform MWM. Blood samples were
obtained via cardiac puncture to determine plasma estradiol levels on the day of
ischemia. Estradiol levels were quantified using radioimmunoassay (RIA). No
sex differences were observed in either the visible or hidden platform tasks.
Subjects treated with high estradiol performed significantly worse than those
pretreated with placebo capsules on the visible platform task. Sham subjects
receiving high estradiol performed significantly worse than subjects receiving
low estradiol on the MWM. However, this result was reversed in ischemic
subjects, with high estradiol subjects outperforming subjects from the low
estradiol group. These findings suggest a differential dose-dependent response
in performance on the MWM in ischemic and non-ischemic animals.
What You Don’t Know Can Hurt Me:
Projection of
Privately Known Context Information onto Naive Observers
Omri Bloch
Individuals make frequent errors when it comes to determining
how they appear in the eyes of others. Specifically, individuals tend to
misestimate how others will judge them on the basis of their behavior or
performance, often expecting to be judged more harshly than they actually are.
This thesis explores one reason for this phenomenon: individuals’ tendency
to project their own awareness of context information onto observers.
Individuals tend to evaluate their own performance based on certain contextual
information (e.g., comparisons with their own past performances, with others, or
with ideal standards) that may not be known to observers. In three studies, I
show that individuals tend to expect observers to judge them in light of such
context information even when they know that observers are not aware of it. In
other words, individuals expect observers to make a comparative judgment of them
and their performance, rather than an absolute one, even when the standard of
comparison is private and is available only to the individuals themselves.
Based upon this research, I conclude that when actors have a salient standard of
comparison against which to judge their own performance that is unknown to
observers, there will tend to be a divergence between how actors are judged and
how they expect to be judged.
A Longitudinal Study of the Emergence of Symbolic Thinking
in Young Children
Reka D. Daroczi
Twenty-six children took part in a longitudinal study of
symbolic thought. At time2 (age 36
months), children were tested in four domains related to symbolic functions:
completing pretend narratives, performance on a model room task
(representational thought), language comprehension, and fantasy proneness. The
narrative completion task measured children’s ability to engage in and
provide endings to pretend narratives that were presented to them. The
representational task investigated the children’s ability to understand
that an object can stand for another. Language comprehension was measured using
the third edition of the Peabody Picture Vocabulary Test, and fantasy proneness
was assessed through mothers’ reports of their children’s play
activities. Some of these domains were positively correlated to each other,
although only the correlation between the performance on the narrative
completion task and the score on the fantasy proneness measure was significant.
At time1 (age range from 25 to 30
months, M = 28 months), children were assessed on four related dimensions of
symbolic thought. After analyzing the longitudinal relationships between
time1 and
time2, the principal conclusion is that
children who are prone towards fantasy-oriented activities and engage frequently
in pretend play perform well on independent measures of representational
thinking (e.g., model room task) and on a measure of narrative
construction.
The Effects of Gestational and Lactational Iron Deficiency
on the
Development of Anxiety Behavior in Rats
Rosemary Eseh
Studies on the behavioral effects of iron deficiency (ID)
have focused on the postnatal or adult periods. In addition, little attention
has been paid to ID effects on affective behavior although alterations in the
relevant neurotransmitter system, GABA, have been documented. In this
experiment, two measures of anxiety, ultrasonic vocalizations (USV) and elevated
plus maze (EPM) were used to investigate the consequences of maternal ID.
Female Long-Evans rats were assigned randomly to one of three diet groups: low
iron (10-20ppm Fe), standard (60ppm Fe) or lab chow (250ppm Fe) diet. Diets
started seven days prior to mating and continued until ten days after birth
(PN10), after which all dams were iron replete with the lab chow diet. USVs
after maternal separation was used to test for anxiety in neonates and EPM was
used for adults. Maternal behavior, growth, and activity were also assessed.
Blood samples taken from pups on PN10 revealed a significant decrement in serum
iron and a compensatory increase in total iron binding capacity in the low iron
groups compared to the control groups. Relative to the two control groups, the
low iron group weighed less on PN1, and this weight difference persisted in
adulthood. In neonates, the rate of USVs in the low iron group was
significantly higher than the two control groups, and their general activity was
significantly less than the controls’. Maternal behavior was not
significantly different across groups. By adulthood, anxiety behavior and motor
activity in the low iron group were comparable to controls. This study shows
that prenatal deficiency results in anxiety behavior, low weight and decreased
activity. These deficits, except for weight, were reversed with iron repletion.
Future research is needed to elucidate the mechanism of ID effects on anxiety
and the persistent weight deficit.
What Are They Thinking? The Relationship between Conflict
and Causal Attributions in Parent-Teen Relationships
Janette L. Funk
While the role that attributions play in marital
relationships has been studied extensively there is very little research on the
role of attributions in parent-teen relationships. The studies conducted on
parental attributions often concern parents of young children and generally do
not include fathers or teenagers. Two studies addressed causal attributions and
their relationship to conflict and teen adjustment. Study 1 included 60 mothers
and 21 fathers and assessed the relationship between internal, stable, global,
and responsibility attributions regarding 11 hypothetical negative teen
behaviors, and conflict and teen adjustment. This study also included two
exploratory questions concerning the relationship between these attributions and
the age of the teen and the relationship between parental responses to negative
behavior and causal attributions. A multiple regression with internality,
stability, globality, and responsibility as predictor variables, regressed on
conflict, was significant. The results also indicated that the globality of
parental attributions was a significant predictor of both conflict and teen
adjustment. Study 2 included 27 teenagers, 22 mothers, and 8 fathers and
elicited participants’ articulated thoughts concerning two audiotaped
parent-teen conflicts using Davison, Robins and Marcia’s
(1983) Articulated Thoughts in Simulated
Situations paradigm. Teens’ reports of conflict was negatively correlated
to the frequency of perspective taking and positively correlated to the
frequency of automatic thoughts. Parents and teens did not make stable or
global attributions during the ATSS procedure. In addition, affective responses
during the conflicts and the exploratory topic of the tipping point were
examined. Finally, the limitations and implications of both studies are
discussed and possibilities for future studies are explored.
Who You Are and What You Think: The Effects of
Children’s Perception of Status on Aggressive Responding and Broader
Indices of Adjustment
Rebecca D. Herlan
In this study, sociometric interviews were conducted to
determine children’s actual and perceived social status in the classroom.
On the basis of these scores, five groups of children
(Overestimators, Underestimators, High
Accurates, Low Accurates, and Averages) were identified and recruited to
participate in an experimental paradigm designed to measure aggressive
responding to positive or negative feedback. Based on Bushman and
Baumeister’s (1998) work, we expected those children who overestimated
their social status to respond most aggressively to negative feedback. We also
expected that they would positively distort negative feedback in predictable
ways. Finally, we expected
Overestimators to report the lowest
frequency of internalizing problems on self-report measures, but to receive
higher ratings for externalizing problems according to parent- and peer-report.
Contrary to expectations,
Overestimators did not respond most
aggressively in the experimental paradigm; rather it was the
Underestimators who responded more
aggressively than any other group. In addition,
Overestimators did not distort the
negative feedback they received. However, with regard to broader indices of
adjustment, Overestimators and
Low Accurates were rated as most
aggressive by their peers.
Overestimators also reported fewer
depressive symptoms and higher scores on self-perceived conduct than three of
the other groups.