ScienceWeek

SCIENCEWEEK

September 19, 2003

Vol. 7 - Number 38B

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CONTENTS:

1. Cell Biology: Systems Analysis of Biological Cells
2. Medical Biology: Public Health and Medical Research
3. Environmental Stress and the Effects of Mutation
4. Paleoclimate: Mechanisms of Abrupt Climate Change
5. Condensed Matter: Superconductivity and Cooper Pairs
6. Quantum Physics: Control of Quantum Systems

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1. CELL BIOLOGY: SYSTEMS ANALYSIS OF BIOLOGICAL CELLS

The following points are made by Paul Nurse (Nature 2003
424:883):

1) Many of the properties that characterize living organisms are
also exhibited by individual cells. These include communication,
homeostasis, spatial and temporal organization, reproduction, and
adaptation to external stimuli. Biological explanations of these
complex phenomena are often based on the logical and
informational processes that underpin the mechanisms involved.
Two examples of this are the significance of the structure of
DNA, and the mechanisms that control gene expression. The
structure of DNA structure relates to heredity because of the
coding and replicative capacity of its polynucleotide sequence,
whereas the interactions of activators and repressors with
promoter regions are best understood in terms of the feedback
loops that regulate gene expression.

2) Most experimental investigations of cells, however, do not
readily yield such explanations, because they usually put greater
emphasis on molecular and biochemical descriptions of phenomena.
To explain logical and informational processes on a cellular
level, therefore, we need to devise new ways to obtain and
analyse data, particularly those generated by genomic and post-
genomic studies.

3) An important part of the search for such explanations is the
identification, characterization and classification of the
logical and informational modules that operate in cells. For
example, the types of modules that may be involved in the
dynamics of intracellular communication include feedback loops,
switches, timers, oscillators and amplifiers. Many of these could
be similar in formal structure to those already studied in the
development of machine theory, computing and electronic
circuitry. When these modules are coupled in space by processes
such as reaction diffusion and regulated cytoskeletal transport,
they help to provide a basis for the spatial organization of the
cell. The identification and characterization of these modules
will require extensive experimental investigation, followed by
realistic modelling of the processes involved. Such analyses
would allow a catalogue of the module types that operate in cells
to be assembled.

4) The next task is to identify the interacting molecules and
biochemical activities that generate the characteristic behaviors
of particular modules. This will be more difficult, involving
systematic mapping of particular module types to specific
molecules, biochemical activities and molecular interactions, and
assembling the information into databases. Some examples may be
useful in thinking about this. Proteins that can be attacked by
proteases are likely to be found in switching modules, as
destruction of a protein can bring about an irreversible switch
in the behavior of a regulatory network. Small G-protein GTPases
that bind to and then convert GTP to GDP could act as timers
because of the time it takes to execute this conversion. In turn,
GTPase timers can act as amplifiers if signals are continually
sent when in the GTP-bound state, or as components of
proofreading modules, as seen during protein translation.
Antagonistically acting protein kinases and phosphatases could
also act as amplifiers and switches.

Nature http://www.nature.com/nature

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ON ORGANIZATION AND MODULARITY IN METABOLIC NETWORKS

The following points are made by E. Ravasz et al (Science 2002
297:1551):

1) The identification and characterization of system-level
features of biological organization is a key issue of post-
genomic biology (1-3). The concept of modularity assumes that
cellular functionality can be seamlessly partitioned into a
collection of modules. Each module is a discrete entity of
several elementary components and performs an identifiable task,
separable from the functions of other modules (1,4,5). Spatially
and chemically isolated molecular machines or protein complexes
(such as ribosomes and flagella) are prominent examples of such
functional units, but more extended modules, such as those
achieving their isolation through the initial binding of a
signaling molecule, are also apparent.

2) Simultaneously, it is recognized that the thousands of
components of a living cell are dynamically interconnected, so
that the cell's functional properties are ultimately encoded into
a complex intracellular web of molecular interactions (2). This
is perhaps most evident with cellular metabolism, a fully
connected biochemical network in which hundreds of metabolic
substrates are densely integrated through biochemical reactions.
Within this network, however, modular organization (i.e., clear
boundaries between subnetworks) is not immediately apparent.
Indeed, recent studies have demonstrated that the probability
that a substrate can react with (k) other substrates [the degree
distribution P(k) of a metabolic network] decays as a power law
in all organisms, suggesting that metabolic networks have a
scale-free topology. A distinguishing feature of such scale-free
networks is the existence of a few highly connected nodes (e.g.,
pyruvate or coenzyme A), which participate in a very large number
of metabolic reactions. With a large number of links, these hubs
integrate all substrates into a single, integrated web in which
the existence of fully separated modules is prohibited by
definition.

3) In summary: Spatially or chemically isolated functional
modules composed of several cellular components and carrying
discrete functions are considered fundamental building blocks of
cellular organization, but their presence in highly integrated
biochemical networks lacks quantitative support. The authors
demonstrate that the metabolic networks of 43 distinct organisms
are organized into many small, highly connected topologic modules
that combine in a hierarchical manner into larger, less cohesive
units, with their number and degree of clustering following a
power law. Within Escherichia coli, the uncovered hierarchical
modularity closely overlaps with known metabolic functions. The
identified network architecture may be generic to system-level
cellular organization.

References (abridged):

1. L. H. Hartwell, J. J. Hopfield, S. Leibler, A. W. Murray,
Nature 402, C47 (1999)

2. H. Kitano, Science 295, 1662 (2002)

3. Y. I. Wolf, G. Karev, E. V. Koonin, Bioessays 24, 105 (2002)

4. D. A. Lauffenburger, Proc. Natl. Acad. Sci. U.S.A. 97, 5031
(2000)

5. C. V. Rao and A. P. Arkin, Annu. Rev. Biomed. Eng. 3, 391
(2001)

Science http://www.sciencemag.org

ScienceWeek http://www.scienceweek.com

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2. MEDICAL BIOLOGY: PUBLIC HEALTH AND MEDICAL RESEARCH

The following points are made by Claude Lenfant (New Engl. J.
Med. 2003 349:868):

1) During the 20th century, enormous progress was made in
improving the health and therefore the life span of all
Americans. The average life expectancy at birth increased by
nearly 30 years between 1900 and 2000. Although the largest gains
were made in the early part of the century, we still managed to
add another 1.5 years between 1990 and 2000.

2) Much of our continued success in extending life expectancy
over the past several decades is almost certainly due to research
supported by the US National Institutes of Health (NIH) and
generously funded by the American public. NIH-supported research
has not only made possible the development of new and improved
treatments for a wide range of human diseases; it has also
provided the knowledge of disease risk factors needed to
formulate effective approaches to prevent them. For example,
research supported by the National Heart, Lung, and Blood
Institute has identified important cardiovascular risk factors,
has established the effectiveness of approaches to prevent or
control them, and has assessed the effectiveness of treatment
interventions for established disease.

3) The lion's share of our recent gains in life expectancy in the
United States has come from reductions in rates of death from
heart disease and stroke. According to data provided by the
National Center for Health Statistics, life expectancy increased
by six years between 1970 and 2000, and nearly two thirds of that
increase can be attributed to reductions in mortality due to
cardiovascular disease. And although primary prevention has
played an important part in the reductions, it appears, at least
for coronary heart disease, that secondary prevention and other
treatments have had a significantly greater effect. According to
one analysis of the decline in mortality due to coronary heart
disease that occurred between 1980 and 1990, the reduction was
due largely to secondary prevention and other improvements in
treatment, with primary prevention accounting for only one
quarter of the decline.

4) Still, one might question whether we have enjoyed the maximal
return on the more than $250 billion that this country has
invested in the NIH since 1950. Consider that in 2000 the life
expectancy at birth for men and women in the United States lagged
be-hind that of 22 other countries, ranging from Japan to Israel
and including Canada and most of western Europe. If we view the
longevity of citizens in our sister nations as an indication of
what is possible in the modern world, then we must question why
our reality is falling short.

5) Some may believe that the difference between life expectancy
in the United States and that in other economically developed
countries is largely a manifestation of societal differences. The
author, however, believes the answer is this: we in the United
States, both health providers and members of the public, are not
applying what we know. Indeed, medical researchers and public and
political leaders are increasingly talking about the lack of
success we have had in translating research findings into medical
practice and personal behavior. Regardless of the reasons cited
for this phenomenon -- structural, economic, or motivational --
the result is the same: we are not reaping the full public health
benefits of our investment in research. Given the ever-growing
sophistication of our scientific knowledge and the additional new
discoveries that are likely in the future, many of us harbor an
uneasy, but quite realistic, suspicion that this gap between what
we know about diseases and what we do to prevent and treat them
will become ever wider. And it is not just recent research
results that are not finding their way into clinical practice and
public health behaviors; there is plenty of evidence that "old"
research outcomes have been lost in translation as well.

New Engl. J. Med. http://www.nejm.org

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CONTROL OF INFECTIOUS DISEASES 1900-1999

The first US civilian whose life was saved by penicillin died in
June 1999 at the age of 90 years. The story is as follows: In
March 1942, a 33-year-old woman was hospitalized for a month with
a life-threatening streptococcal infection at a New Haven,
Connecticut hospital. She was delirious, and her temperature
reached almost 107 degrees Fahrenheit (41 degrees centigrade).
Treatments with sulfa drugs, blood transfusions, and surgery had
no effect. As a last resort, her doctors injected her with a
minuscule amount of an obscure experimental drug called
penicillin. Her hospital chart, now at the Smithsonian
Institution, indicates a sharp overnight drop in temperature, and
apparently by the next day she was no longer delirious. The woman
survived to marry, raise a family, and meet Alexander Fleming
(1881-1955), the scientist who discovered penicillin [*Note #1].
In 1945, Fleming was awarded the Nobel Prize for Physiology and
Medicine, along with Ernst Chain and Howard Florey, who helped
develop penicillin into a widely available medical product.

The US Centers for Disease Control and Prevention, in a recent
review of the control of infectious diseases in the 20th century
(Morb. Mort. Weekly Rep 1999 48:621), makes the following points:

1) Deaths from infectious diseases have declined markedly in the
US during the 20th century. This decline contributed to a sharp
drop in infant and child mortality, and to the 29.2-year increase
in life expectancy.

2) In 1900, 30.4 percent of all deaths occurred among children
less than 5 years of age; in 1997, deaths in this group were only
1.4 percent of the total.

3) In 1900, the 3 leading causes of death were a) pneumonia, b)
tuberculosis, c) diarrhea and inflammation of the intestinal
tract (enteritis). These 3 causes, together with diphtheria,
caused one-third of all deaths. Of these deaths, 40 percent were
among children less than 5 years of age. In 1997, heart disease
and cancers accounted for 54.7 percent of all deaths, with 4.5
percent attributable to pneumonia, influenza, and human immune
deficiency virus (HIV) infection.

4) Despite this overall progress, one of the most devastating
epidemics in human history occurred during the 20th century: the
1918 influenza epidemic that resulted in 20 million deaths,
including 500,000 in the US, in less than 1 year -- more than
have died in as short a time during any war or famine in the
world. HIV infection, first recognized in 1981, has caused a
pandemic that is still in progress, affecting 33 million people
and causing an estimated 13.9 million deaths. These epidemics
illustrate the volatility of infectious diseases death rates and
unpredictability of disease emergence.

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Notes:

*Note #1: The story of Fleming's discovery of penicillin is a
classic tale of serendipity. In 1928, shortly after he was
appointed professor of bacteriology at the University of London,
Fleming left a culture of staphylococcus germs uncovered for some
days. He was finished working with the culture, and he was about
to discard the culture dish when he noticed that several specks
of mold had fallen into it, and that around every mold speck the
bacterial colony had dissolved away for a short distance. The
clear space surrounding each speck indicated that bacteria had
died and no new growth had invaded the area. The physicist John
Tyndall (1820-1893), who among other things did much research
with ordinary dust, had briefly noted a similar observation 50
years earlier. Fleming isolated the mold and eventually
identified it as Penicillium notatum, a mold closely related to
the common variety often found growing on stale bread. Fleming
decided that the mold liberated some compound that inhibited
bacterial growth, and he labelled the substance "penicillin". In
a lecture many years later, Fleming spoke of his accidental
discovery of penicillin: "I have been trying to point out that in
our lives chance may have an astonishing influence and, if I may
offer advice to the young laboratory worker, it would be this --
never to neglect an extraordinary appearance or happening. It may
be -- usually is, in fact -- a false alarm that leads to nothing,
but it may on the other hand be the clue provided by fate to lead
you to some important advance."

ScienceWeek http://www.scienceweek.com

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3. ENVIRONMENTAL STRESS AND THE EFFECTS OF MUTATION

The following points are made by S.F. Elena and J.A. de Visser
(J. Biol. 2003 2:12):

1) When considering how individual organisms and populations
evolve, key issues are the genotype of the organism(s), how the
genotype is manifest as phenotype and how it contributes to the
fitness of the organism(s) under different environmental
conditions. One of the basic genetic concepts learned by
undergraduate students in evolutionary biology is the "reaction
norm", a mathematical function -- usually presented as a graph --
that describes the range of phenotypes that can arise from a
given genotype in response to variation in the environment.
Especially interesting from an evolutionary standpoint is the
"fitness reaction norm" -- the range of possible fitnesses in
different environments -- since it describes the evolutionary
potential of an individual in alternative environments. The range
of fitnesses seen among different mutant genotypes in a given
environment is termed the "mutational variance"

2) It is generally thought that the deleterious effects of
mutations on fitness will be exacerbated in stressful
environments. But recent observations suggest that in fact the
negative fitness effects of deleterious mutations can be reduced
in stressful environments. The dependence of the fitness of a
particular genotype on the environment may be classified into one
of three categories. In the first category, mutations are
unconditionally deleterious across alternative environments
because they impair an essential function of the organism. The
relative effect of each of these mutations can change and usually
increases with the degree of environmental harshness, but they
remain deleterious. In the second category, mutations are
conditionally neutral; that is, they are deleterious in some
environments but neutral in others, because they affect the
organism's match with specific environmental factors. In the
third category, mutations are conditionally beneficial --
deleterious in some environments but beneficial in others.

3) Unconditionally deleterious mutations are invariably purged
from populations by natural selection, under any environmental
conditions, so their long-term impact is limited. But
conditionally beneficial variation is of great evolutionary
significance because it drives ecological specialization in
marginal habitats and, eventually, leads to speciation. Together,
the form of the interaction between genotype and environment, the
underlying genetic architecture, and the pattern of exposure to
the relevant environments direct the outcome of evolution. For
example, if the fitness reaction norms for a given set of
genotypes decrease monotonically with increasing stress, the
mutational variance will increase. But, if the rank order of the
fitness of different genotypes alters across environments in such
a way that the slopes of reaction norms are of different sign --
for example with some mutations being unconditionally deleterious
but others conditionally beneficial -- changes in mutational
variance across environments are unpredictable. In this case, not
all reaction norms go in the same direction and if the
environment fluctuates spatially or temporally different
genotypes may be optimal in each alternative environment,
supporting the situation of a balanced polymorphism.

4) In summary: Mutations are the ultimate fuel for evolution, but
most mutations have a negative effect on fitness. It has been
widely accepted that these deleterious fitness effects are, on
average, magnified in stressful environments. Recent observations
suggest that the effects of deleterious mutations can, instead,
sometimes be ameliorated in stressful environments.

J. Biol. http://jbiol.com

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ON GLOBAL CLIMATE CHANGE AND HEALTH

The following points are made by J.A. Patz and M. Khaliq (J. Am.
Med. Assoc. 2002 287:2283):

1) Global climate change is expected to have broad health
impacts.[1] If current warming trends continue, heat waves,
floods, and droughts and their attendant physical effects are
likely to become more frequent and severe. Warmer air
temperatures can influence the concentration of regional air
pollutants and aeroallergens. Less direct health impacts may
result from the disruption of ecosystems and of water and food
supplies, which in turn could affect infectious disease incidence
and nutritional status. Finally, sea-level rise could lead to
major population displacement and economic disruption.

2) Human activities related primarily to the burning of fossil
fuels and changes in land cover such as deforestation are
changing the concentration of atmospheric constituents or
properties of the earth's surface that help to absorb or scatter
radiant energy.[2] Since the preindustrial mid-1800s, increases
in concentrations of three major greenhouse gases, carbon
dioxide, methane, and nitrous oxide, have exceeded past changes
that occurred over the last 10 000 years; carbon dioxide alone
has increased by 30% since the late 1800s.[1] Warmer air, such as
that resulting from the greenhouse effect, can hold more moisture
and more quickly evaporate surface water, thereby increasing the
frequency of severe storms, floods, and droughts.[1]

3) According to the United Nations Intergovernmental Panel on
Climate Change (IPCC), "An increasing body of observations gives
a collective picture of a warming world and other changes in the
climate system.[3] During the 20th century, global average
surface temperature increased about 0.6 degrees C, global average
sea level rose 10 cm to 20 cm, and snow and ice cover
decreased.[2] The latest IPCC report predicts that if current
trends continue, sea level rise will rise 45 cm and global
temperatures will increase by 3 degrees C by the year 2100.[3]

4) Small changes in global mean temperatures can produce
relatively large changes in the frequency of extreme
temperatures.[2] Mortality rates increase at both hot and cold
extremes of temperature.[4] Increases in temperature have a
direct and substantial impact on excess mortality for elderly
individuals and individuals with pre-existing illnesses. Much of
the mortality attributable to heat waves is a result of
cardiovascular, cerebrovascular, and respiratory disease.[5] A
1995 heat wave in Chicago that caused 514 heat-related deaths (12
per 100 000 population) may be part of a recent trend of longer,
more frequent heat waves and record-setting temperatures. Long-
term global warming trends are further exacerbated by the "heat
island" effect, whereby high concentrations of heat-retaining
surfaces such as asphalt and tar roofs sustain higher
temperatures through the night. Heat waves also have the
secondary effect of worsening urban air pollution. Ozone, which
forms chemically from precursor pollutants, is the most
temperature-dependent air pollutant and may contribute to the
development of asthma in children.

References (abridged):

1. Patz JA, Engelberg D, Last J. The effects of changing weather
on public health. Ann Rev Public Health. 2000;21:271-307.

2. Intergovernmental Panel on Climate Change (IPCC). Climate
Change 2001: The Scientific Basis: Contribution of Working Group
I to the Third Assessment Report of the IPCC. Houghton J, Ding Y,
Griggs M, et al, eds. Cambridge, England: Cambridge University
Press; 2001.

3. McMichael A. Human health. In: IPCC Working Group II, ed.
Climate Change 2001: Impacts, Adaptation, and Vulnerability.
Cambridge, England: Cambridge University Press; 2001:453-485.

4. Curriero FC, Heiner KS, Samet JM, et al. Temperature and
mortality in 11 cities of the eastern United States. Am J
Epidemiol. 2002;155:80-87.

5. Kilbourne E. Heat waves. In: Noji E, ed. The Public Health
Consequences of Disasters. New York, NY: Oxford University Press;
1997:51-61.

J. Am. Med. Assoc. http://www.jama.com

ScienceWeek http://www.scienceweek.com

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4. PALEOCLIMATE: MECHANISMS OF ABRUPT CLIMATE CHANGE

The following points are made by G. Clarke et al (Science 2003
301:922):

1) As concern about the magnitude and rate of future climate
change looms, it becomes increasingly important to understand the
mechanisms underlying past abrupt climate change events. A cold
event that occurred 8200 years ago, although much less extreme
than some events during the Ice Ages, is probably most amenable
to detailed examination because it is the most recent such event.

2) According to the ice-core record from Greenland, the abrupt
cooling 8200 years ago was the largest climate excursion of the
past 10,000 years: The mean temperature dropped by about 5
degrees C for about 200 years, snow accumulation decreased
sharply, precipitation of chemical impurities increased, and
forest fires became more frequent. The event, which affected much
of the Northern Hemisphere, appears to have been triggered by the
sudden release of fresh water from a huge, glacier-dammed lake
that had formed during the deglaciation of North America.

3) Changes in the volume and extent of the ice sheets that once
covered much of North America directly influenced the freshwater
balance of the North Atlantic and are implicated in many abrupt
climate events of the past 100,000 years. During the last Ice
Age, when a kilometers-thick ice sheet covered most of Canada and
parts of the northern United States, armadas of icebergs were
episodically launched into the North Atlantic. The melting of
this freshwater ice and the associated freshening of ocean
surface waters are believed to have changed the strength of the
oceanic thermohaline circulation, thereby causing abrupt climate
changes.

4) The deglaciation of North America produced large volumes of
glacial meltwater, which also appears to have influenced the
circulation of the North Atlantic. The "Younger Dryas" cooling
event, which began about 12,700 years ago, is thought to have
been triggered by an outburst of waters from a large ice-dammed
lake and sustained by the redirection of meltwater from the
Mississippi to the St. Lawrence Valley. To explain the 8200-year
cold event, a search for large sources of fresh water is thus a
good starting point.

Science http://www.sciencemag.org

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ON GLOBAL CLIMATE CHANGE

Environmental change involves jumps, fluctuations, and trends,
the environment changing through the operation of the internal
machinery of the *ecosphere (biosphere), and through the external
agencies of cosmic and geological forces. Evidence of past
environmental change, almost always incomplete, derives from
geochemical, physical, biological, historical, and instrumental
sources. In recent years, high-speed computers have allowed
researchers to manipulate complicated and reasonably realistic
models of environmental change, with modeling particularly useful
for studying changes in *sedimentary basins, biogeochemical
cycles, and climate. General circulation models, run with
appropriate boundary conditions, predict climates of the past,
and these predicted climates can be compared with paleoclimatic
indicators.

The following points are made by R.B. Alley et al (Proc. Nat.
Acad. Sci. 1999 96:9987):

1) Prediction of climate change requires observational
constraints on the current climate state, knowledge of the way
the coupled air-ocean-ice-earth-life system behaves, and
information on changing forcings such as solar variability.
Studies of past climate are also required to focus model-building
efforts on climate components that are likely to change, and to
allow testing of the ability of models to predict time-evolution
of the system.

2) The last few million years have been generally cold and icy
compared with the previous hundred million years but have
alternated between warmer and colder conditions. These
alternations have been linked to changes over tens of thousands
of years in the seasonal and latitudinal distribution of sunlight
on Earth caused by features of Earth's orbit. Globally
synchronous climate change despite some hemispheric asynchrony of
the forcing is explained at least in part by lowering carbon
dioxide during colder times in response to changes in ocean
chemistry. We live in one of the warmer times of these orbital
cycles; the coolest times brought glaciation to nearly one-third
of the modern land area.

3) Studies of past climate changes indicate that the Earth system
has experienced greater and more rapid changes over larger areas
that was generally believed possible, with jumping between
fundamentally different modes of operation in as little as a few
years. Most of the last 100,000 years or longer has been
characterized by large and abrupt regional-to-global climate
changes, and agriculture and industry have developed during
anomalously stable climatic conditions. New high-resolution
analysis of sediment cores indicates these past changes have been
caused by "*band jumps" between modes of operation of the climate
system. Recurrence of such band jumps is possible and might be
affected by human activities.

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Notes:

ecosphere (biosphere): In general, the term "biosphere" refers to
the portion of the planet capable of supporting life. It ranges
from elevations of approximately 10,000 meters above sea level to
the deep ocean, and a few hundred meters below the surface of the
soil. The biosphere consists of the hydrosphere, the lower
atmosphere (troposphere), and the surface of the *lithosphere,
all three regions inhabited by metabolically active organisms.

lithosphere: In current geology, the lithosphere is the
approximately 100 kilometer rigid upper layer of the crust and
upper mantle of the Earth.

sedimentary basins: The term "sedimentary basin" refers to a
subsiding area of the Earth's crust, which permits the net
accumulation of sediment, i.e., material derived from pre-
existing rock, from biogenic sources, or precipitated by chemical
processes.

band jumps: In this context, the term "band jump" refers to an
abrupt change from one range of variation to another.

Proc. Nat. Acad. Sci. http://www.pnas.org

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5. CONDENSED MATTER: SUPERCONDUCTIVITY AND COOPER PAIRS

The following points are made by Piers Coleman (Nature 2003
424:625):

1) One of the outstanding mysteries in condensed-matter physics
is that the most perfect conductors so far discovered -- the
high-temperature superconductors -- are more like insulators than
metals. Superconductivity, the flow without resistance of current
through some materials, usually only occurs at very low
temperatures. Conventional superconductivity develops in metals,
but high-temperature superconductivity (at about 90 K) occurs in
insulating copper oxide ceramics when small amounts of charge are
injected by chemical doping.

2) The quantum physicist Paul Dirac (1902-1984) once remarked
that the equations needed to understand most of physics are
known, but are far too complicated to solve. Lurking in this
complexity lies the astounding ability of matter to develop new
types of collective behavior, such as superconductivity and
magnetism. The equation that accurately describes all of this
behavior is the many-body Schröedinger equation. This involves
two essential elements: the wavefunction, which is related to the
probability of finding the electrons (or other particles) of a
system in a given spatial configuration; and the Hamiltonian, a
function that determines the energy of a system from its
wavefunction. In a typical material, the number of particles
tracked by the wavefunction is of the order of Avogadro's number
-- 6 x 10^(23). This level of complexity means that understanding
collective behavior, such as that of electrons in a
superconductor, depends on the creative abstraction of both the
Hamiltonian and the wavefunction into a much simpler model that
captures the essence of the physics.

3) Conventionally, superconductivity develops in a conducting
metal when the electrons bind together to form "Cooper pairs".
Each electron spins like a tiny top, and in a Cooper pair the
electron spins are aligned in an antiparallel configuration. Soon
after high-temperature superconductivity was discovered, it was
noted that the insulating state from which high-temperature
superconductivity arises is a special kind of insulator, called a
"Mott insulator". The mobile electrons in a high-temperature
superconductor hop from one copper atom to the next, but repel
one another because of their negative charges. When these
repulsive forces are large enough, the electrons are prevented
from ever doubly occupying a given copper atom.

4) In undoped copper oxide superconductors, there is precisely
one mobile electron per copper atom, so the restriction on double
occupancy causes the electrons to remain localized, at one
electron per site. Strong magnetic forces between the localized
electrons at different sites cause their spins to orient together
in oppositely aligned pairs. According to the "resonating valence
bond" (RVB) model of high-temperature superconductivity, these
pairs form a fluid that resonates between the sites in a fashion
reminiscent of the Cooper pairs inside a superconductor. When
charge is introduced into this insulating background of pairs
(through doping with impurity atoms), the RVB state evolves
directly from insulator to superconductor.

Nature http://www.nature.com/nature

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MATERIALS SCIENCE: ON HIGH-TEMPERATURE SUPERCONDUCTORS

At temperatures close to absolute zero (-273.15 degrees Celsius),
the thermal, electric, and magnetic properties of many substances
undergo dramatic changes. One such phenomenon is
superconductivity, which occurs below a critical temperature
specific for each substance that exhibits the effect.

Superconductivity was discovered in 1911 by Heike Kamerlingh
Onnes (1853-1926), who was awarded the Nobel Prize for Physics in
1913 for his low temperature research. Kamerlingh Onnes found
that the electrical resistance of a mercury wire suddenly
disappears when the wire is cooled below a temperature of
approximately 4 degrees kelvin. Similar behavior (but at widely
varying critical temperatures) has been found in approximately 25
other chemical elements, including lead and tin, and in thousands
of alloys and chemical compounds. Apart from these known
superconducting materials, all other substances investigated to
within fractions of a degree of absolute zero show normal (non-
superconducting) resistance to the flow of electric currents.

For almost 50 years after the discovery of superconductivity by
Kamerlingh Onnes, there was no successful fundamental theory that
could explain the phenomenon. Finally, in 1957, an apparently
satisfactory theory of superconductivity was presented by John
Bardeen (1908-1991), Leon N. Cooper, and John R. Schrieffer, who
all shared the Nobel Prize for Physics in 1972. The theory is now
called the BCS theory of superconductivity.

The essential aspect of BCS theory is the grouping of electrons
in superconductors in pairs ("Cooper pairs"), with the motions of
all the Cooper pairs within a single superconductor correlated,
i.e., the population of Cooper-pair electrons constituting a
system that functions essentially as a single entity. (In quantum
mechanical terms, each Cooper pair consists of electrons of
opposite spins, thus forming a spin-zero single *boson, and the
population of bosons form a *Bose-Einstein condensate described
by a single wave function.) Application of an electric voltage to
the superconductor causes all Cooper pairs to move, the movement
constituting a current. When the voltage is removed, current
continues to flow indefinitely because the Cooper pairs (as
members of a coherent condensate) are not scattered by the atomic
lattice. As a superconductor is warmed, its Cooper pairs separate
into individual electrons, and the material becomes non-
superconducting.

Such was the theory of superconductivity for nearly 30 years, the
theory successfully predicting the behavior of superconducting
materials with critical temperatures close to absolute zero. In
1986, Karl A. Mueller and J. Georg Bednorz discovered that
certain materials exhibit superconductivity at temperatures as
high as 35 degrees kelvin, and compounds retaining
superconductivity at temperatures as high as 160 degrees kelvin
have since been found. Mueller and Bednorz were awarded the Nobel
Prize in Physics in 1987 for their work with high-temperature
superconductors. Such high-temperature superconductors all
contain copper and oxygen atoms that form planes or chains of
atoms in the crystal, and it is believed that anisotropy is an
important factor in their superconducting behavior. These
materials are ceramic oxides, and because they are
superconducting at temperatures easily obtainable with liquid
nitrogen, great effort has been expended to find applications for
these substances. But problems of brittleness, instabilities, and
the aggregation of impurities at surfaces have slowed progress.
Nevertheless, in contrast to superconducting ceramics,
superconducting metals and their alloys must be cooled to near
absolute zero with liquid helium, a process much more expensive
than cooling with liquid nitrogen. Superconducting ceramics thus
remain an important frontier of research in materials science.

In terms of theory, what is significant is that BCS theory
apparently cannot provide a complete explanation of the behavior
of high-temperature ceramic superconductors. A version of BCS
theory may explain how superconductivity occurs in certain
ceramic materials, but no complete theory of high-temperature
superconductivity in ceramic materials has yet been proposed.

Recently, researchers in superconductivity were startled when J.
Nagamatsu et al (5 authors at 2 installations, JP) (Nature 1 Mar
01 410:63) (in a paper consisting of only 3 short paragraphs)
reported the discovery of bulk superconductivity in the simple
and readily available compound magnesium diboride [MgB(sub2)],
with magnetization and resistivity measurements establishing a
transition temperature of 39 degrees kelvin, the highest known
critical temperature for a non-copper-oxide (non-ceramic) bulk
superconductor. [Editor's note: The surprise of condensed-matter
physicists at this new discovery is reminiscent of the surprise
of the same community at the discovery by Mueller and Bednorz in
1986 of high-temperature ceramic superconductors. See related
background material below.]

The following points are made by Robert J. Cava (Nature 2001
410:23):

1) The author points out that in the ideal case of
superconductivity, the zero-resistance state is absolute:
electrons flowing in a continuous loop of superconducting wire
below the critical temperature could theoretically flow for the
age of the Universe and never lose any energy. But in the real
world there are losses, e.g., from microscopic inhomogeneities,
and the ideal is never obtained. Nevertheless, devices made with
superconducting materials have resistances orders of magnitude
lower than those of devices made with conventional conductors.
This low resistance to current means that large currents (on the
order of 10^(6) amperes per square centimeter of wire cross-
section) can be passed without significant heating. For example,
the magnets in magnetic resonance imaging instruments now in
common use are made from metal-alloy superconducting wires, and
these magnets are cooled below the critical temperature of the
metal-alloy by immersion in liquid helium at 4.2 degrees kelvin.

2) The author points out there are two reasons for the current
excitement concerning the discovery of superconductivity in
magnesium diboride: a) Early indications are that magnesium
diboride becomes superconducting by the BCS mechanism, so that
unlike high-temperature copper-oxide superconductors, magnesium
diboride appears to be a "conventional" superconductor. Magnesium
diboride has the highest critical temperature known for a
chemically stable, bulk compound of this type, and this suggests
the possible existence of even higher superconducting critical
temperatures in conventional and readily available materials yet
to be investigated. b) The second reason for excitement is that
it has proved so difficult to make useful wires of
superconducting ceramics. This new report by J. Nagamatsu et al
raises the possibility that superconducting materials based on
magnesium diboride may eventually be able to carry more current
than copper oxide superconductors. With a critical temperature of
39 degrees kelvin, there is also the possibility that magnesium
diboride superconductors would not need to be cooled by liquid
helium, but could be cooled by electrical refrigerators. The
author concludes: "How much this discovery changes the path of
materials physics depends on whether magnesium diboride is a
solitary example of a new way of making high-temperature
superconductors or whether it represents only the tip of an
iceberg."

--------------------------------

Notes:

boson: According to current physics, all particles in nature are
either fermions or bosons, with fermions (always elementary
particles) having half-integer spin (spin-states characterized by
half-integer multiples of Planck's constant divided by 2pi), and
bosons (all other particles) having integer spin (spin-states
characterized by integer multiples of Planck's constant divided
by 2pi). In general, bosons are particles that obey *Bose-
Einstein statistics, and they include photons, *pi mesons, all
nuclei having an even number of particles, and all particles with
integer or zero spin.

Bose-Einstein statistics: Bose-Einstein statistics is the
statistical mechanics of a system of indistinguishable particles
for which there is no restriction on the number of particles that
may simultaneously exist in the same quantum energy state.
Particles that obey Bose-Einstein statistics are called "bosons".

Bose-Einstein condensate: In general, "Bose-Einstein
condensation" is a phenomenon occurring in a macroscopic system
consisting of a relatively large number of bosons at a
sufficiently low temperature (microkelvins down to nanokelvins)
in which a significant fraction of the particles occupy a single
quantum state of lowest energy (the ground state). In an atomic
Bose-Einstein condensate, several thousand atoms essentially
become a single atom, a "superatom", and this effect has been
observed experimentally with atoms of rubidium and lithium, the
atoms trapped and cooled by special methods.

Nature http://www.nature.com/nature

ScienceWeek http://www.scienceweek.com

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6. QUANTUM PHYSICS: CONTROL OF QUANTUM SYSTEMS

The following points are made by I. Walmsley and H. Rabitz
(Physics Today 2003 August):

1) The term "quantum control" refers to active intervention in a
system's dynamics to maximize the probability that the system
evolves toward a desired target state. For example, quantum
control might be used to redirect a chemical reaction along a
specific pathway, or to precisely operate a quantum logic gate in
the presence of environmental noise. In addition to producing the
desired evolution, control of quantum systems promises to provide
a refined means for learning about the behavior of the systems
themselves.

2) The preparation, controlled evolution, and measurement of
specific quantum states are fundamental activities in physics.
The study of new states of matter and the new perspectives on
quantum physics that are provided by processing the information
are but two of the important reasons for pursuing such research.
The numerous potential applications range from performing
precision measurements to manipulating molecular nanoscale
devices. Optimally designing the control and measurement
strategies is important for extracting the most information about
the state of the system from a given set of measurements. Tools
based on control theory have been developed for such purposes for
systems that obey the laws of classical physics. But for quantum
systems, redirecting those tools -- and possibly introducing new
ones as needed -- is a challenge.

3) That control concepts may be useful for robustly creating
particular quantum states has long been recognized. The
development of complex pulse sequences in nuclear magnetic
resonance is a widely exploited example. Since the invention of
lasers some 40 years ago, a goal has been to achieve laser-
selective molecular transformations based on the controlled
deposition of energy within molecules. These applications and
others rely on the coherent evolution of quantum systems to
achieve the desired manipulations.

4) Being able to use tailored external fields to freely
manipulate quantum systems has significant implications for
physics, and concepts of control can lead to practical
realizations of that goal in the laboratory. The number of
successful quantum control experiments is rising rapidly,
although the research area is still in its infancy. Many issues
remain, including the degree to which quantum systems may be
controlled, the identification of the best tools for their
manipulation, and the nature of new physics that may be
discovered from applying quantum control concepts. Such ideas
have had a long gestation period in the physics community.

5) Quantum systems subjected to control range from a single atom
or molecule to the collective degrees of freedom, such as
excitons and phonons, in solids. A common tool for exercising
control is the optical field from a laser. Shaped ultrashort
laser pulses are proving to be very versatile, because the time-
dependent amplitudes and phases of the pulsed fields can be tuned
to match the multiple frequencies of the electronic and
vibrational degrees of freedom of atoms, molecules, and
excitations in solids.

Physics Today http://www.physicstoday.org

--------------------------------

QUANTUM DECOHERENCE AND QUANTUM INFORMATION PROCESSING

The following points are made by D. Bacon et al (Phys. Rev. Lett.
2001 87:247902):

1) One of the most severe experimental difficulties in quantum
information processing is the fragile nature of quantum
information. Every real quantum system is an open system which
readily couples to its environment, and this coupling causes
quantum information in the system to become entangled with its
environment, which in turn results in the system information
losing its intrinsic quantum nature. This process is known as
"decoherence". Circumvention of this "decoherence problem" has
been shown to be theoretically possible with the development of
the theory of fault-tolerant quantum error correction. However,
the set of requirements to reach the threshold for such fault-
tolerant quantum computation is extremely daunting.

2) In the absence of coupling between a system and its
environment, the system and environment have separate temporal
evolutions determined by their individual energy spectra. When a
small interaction (relative to these energy scales) is switched
on between the two, the resulting evolution is dominated by
pathways that conserve the energy of the unperturbed system-plus-
environment. Under the assumption of such a perturbative
interaction, energetics play a key role in determining the rate
of decoherence processes. Such energy-conserving decoherence has
three possible forms: a) energy is supplied from the system to
the environment (cooling); b) energy is supplied from the
environment to the system (heating); c) or no energy is exchanged
at all (non-dissipative). Thus, even when the environment is a
heat bath at zero temperature, cooling, and especially non-
dissipative interactions, can be a major source of decoherence.

3) The authors present a quantum informatics method for
suppressing the detrimental effects of decoherence, while at the
same time allowing for robust manipulation of the quantum
information, the objective to aid in breaching the threshold for
robust quantum computation.

Phys. Rev. Lett. http://prl.aps.org

ScienceWeek http://www.scienceweek.com

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