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Ab initio methods for polariton chemistry

Polariton chemistry exploits the strong interaction between quantized excitations in molecules and quantized photon states in optical cavities to affect chemical reactivity. Molecular polaritons have been experimentally realized by the coupling of electronic, vibrational, and rovibrational transitions to photon modes, which has spurred a tremendous theoretical effort to model and explain how polariton formation can influence chemistry. This tutorial review focuses on computational approaches for the electronic strong coupling problem through the combination of familiar techniques from ab initio electronic structure theory and cavity quantum electrodynamics, toward the goal of supplying predictive theories for polariton chemistry. Our aim is to emphasize the relevant theoretical details with enough clarity for newcomers to the field to follow, and to present simple and practical code examples to catalyze further development work.

Chemistry↗

Quantum simulation of boson-related Hamiltonians: techniques, effective Hamiltonian construction, and error analysis

Elementary quantum mechanics proposes that a closed physical system consistently evolves in a reversible manner. However, control and readout necessitate the coupling of the quantum system to the external environment, subjecting it to relaxation and decoherence. Consequently, system-environment interactions are indispensable for simulating physically significant theories. A broad spectrum of physical systems in condensed-matter and high-energy physics, vibrational spectroscopy, and circuit and cavity QED necessitates the incorporation of bosonic degrees of freedom, such as phonons, photons, and gluons, into optimized fermion algorithms for near-future quantum simulations. In particular, when a quantum system is surrounded by an external environment, its basic physics can usually be simplified to a spin or fermionic system interacting with bosonic modes. Nevertheless, troublesome factors such as the magnitude of the bosonic degrees of freedom typically complicate the direct quantum simulation of these interacting models, necessitating the consideration of a comprehensive plan. This strategy should specifically include a suitable fermion/boson-to-qubit mapping scheme to encode sufficiently large yet manageable bosonic modes, and a method for truncating and/or downfolding the Hamiltonian to the defined subspace for performing an approximate but highly accurate simulation, guided by rigorous error analysis. In this pedagogical tutorial review, we aim to provide such an exhaustive strategy, focusing on encoding and simulating certain bosonic-related model Hamiltonians, inclusive of their static properties and time evolutions. Specifically, we emphasize two aspects: (1) the discussion of recently developed quantum algorithms for these interacting models and the construction of effective Hamiltonians, and (2) a detailed analysis regarding a tightened error bound for truncating the bosonic modes for a class of fermion-boson interacting Hamiltonians.

bosonic Hamiltonian↗

Quantitative elemental imaging in eukaryotic algae

Abstract All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.

59 BASIC BIOLOGICAL SCIENCES↗

Considerations in upconversion: A practical guide to sum-frequency generation spectrometer design and implementation

Here, in this tutorial review, we discuss how the choice of upconversion pulse shape in broadband vibrational sum-frequency generation (SFG) spectrometer design impacts the chemical or physical insights one can obtain from a set of measurements. A time-domain picture of a vibrational coherence being mapped by a second optical field is described and the implications of how this mapping, or upconversion process, takes place are given in the context of several popular and emerging approaches found in the literature. Emphasis is placed on broadband frequency-domain measurements, where the choice of upconversion pulse enhances or limits the information contained in the SFG spectrum. We conclude with an outline for a flexible approach to SFG upconversion using pulse-shaping methods and a simple guide to design and optimize the associated instrumentation.

47 OTHER INSTRUMENTATION↗

Precision dispersive approaches versus unitarized chiral perturbation theory for the lightest scalar resonances $\sigma /f_0(500) $ and $\kappa /K_0^*(700) $

For several decades, the $\sigma /f_0(500) $ and $\kappa /K_0^*(700) $ resonances have been subject to long-standing debate. Both their existence and properties were controversial until very recently. In this tutorial review, we compare model-independent dispersive and analytic techniques versus unitarized Chiral Perturbation Theory, when applied to the lightest scalar mesons $\sigma /f_0(500) $ and $\kappa /K_0^*(700) $. Here, the former have settled the long-standing controversy about the existence of these states, providing a precise determination of their parameters, whereas unitarization of chiral effective theories allows us to understand their nature, spectroscopic classification and dependence on QCD parameters. Here we review in a pedagogical way their uses, advantages and caveats.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Method—Using Microelectrodes to Explore Solid Polymer Electrolytes

Solid polymer electrolytes are an emerging technology in electrochemistry driven by their use in energy applications such as fuel cells, electrolyzers, and solid-state batteries. Compared to traditional liquid electrolytes, solid polymer electrolytes provide safer, cheaper, and potentially improved device performance. However, there is a lack of standard experimental methods for studying solid electrolytes. Microelectrodes have inherent benefits capable of filling this experimental gap due primarily to their integration into model electrochemical cells with solid electrolytes that represent complex interfaces, enabling additional insight into reaction processes. In this tutorial review, we explore the use of microelectrodes to study solid polymer electrolytes, beginning with a brief history of the field including common experimental cell designs and their benefits and drawbacks. Methods of evaluating essential kinetic and mass-transport parameters are then examined. In addition, the key studies of the past 30 years utilizing microelectrode cells and solid polymer electrolytes are summarized, with important results highlighted and compared. Finally, future studies of solid polymer electrolytes with microelectrodes and potential new avenues of research are commented on.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Studying Turbulence Using Numerical Simulation Databases: Proceedings of the Summer Program - No. 7

The Seventh Summer Program of the Center for Turbulence Research took place in the four-week period, July 5 to July 31, 1998. This was the largest CTR Summer Program to date, involving thirty-six participants from the U. S. and nine other countries. Thirty-one Stanford and NASA-Ames staff members facilitated and contributed to most of the Summer projects. A new feature, and perhaps a preview of the future programs, was that many of the projects were executed on non-NASA computers. These included supercomputers located in Europe as well as those operated by the Departments of Defense and Energy in the United States. In addition, several simulation programs developed by the visiting participants at their home institutions were used. Another new feature was the prevalence of lap-top personal computers which were used by several participants to carry out some of the work that in the past were performed on desk-top workstations. We expect these trends to continue as computing power is enhanced and as more researchers (many of whom CTR alumni) use numerical simulations to study turbulent flows. CTR's main role continues to be in providing a forum for the study of turbulence for engineering analysis and in facilitating intellectual exchange among the leading researchers in the field. Once again the combustion group was the largest. Turbulent combustion has enjoyed remarkable progress in using simulations to address increasingly complex and practically more relevant questions. The combustion group's studies included such challenging topics as fuel evaporation, soot chemistry, and thermonuclear reactions. The latter study was one of three projects related to the Department of Energy's ASCI Program (www.llnl.gov/asci); the other two (rocket propulsion and fire safety) were carried out in the turbulence modeling group. The flow control and acoustics group demonstrated a successful application of the so-called evolution algorithms which actually led to a previously unknown forcing strategy for jets yielding increased spreading rate. A very efficient algorithm for flow in complex geometries with moving boundaries based on the immersed boundary forcing technique was tested with very encouraging results. Also a new strategy for the destruction of aircraft trailing vortices was introduced and tested. The Reynolds Averaged Modeling (RANS) group demonstrated that the elliptic relaxation concept for RANS calculations is also applicable to transonic flows with shocks; however, prediction of laminar/turbulent transition remains an important pacing item. A large fraction of the LES effort was devoted to the development and testing of a new algorithmic procedure (as opposed to phenomenological model) for subgrid scale modeling based on regularized de-filtering of the flow variables. This appears to be a very promising approach, and a significant effort is currently underway to assess its robustness in high Reynolds number flows and in conjunction with numerical methods for complex flows. As part of the Summer Program two review tutorials were given on Turbulent structures in hydrocarbon pool fires (Sheldon Tieszen), and Turbulent combustion modeling: from RANS to LES via DNS (Luc Vervisch); and two seminars entitled Assessment of turbulence models for engineering applications (Paul Durbin) and Subgrid-scale modeling for non-premixed, turbulent reacting flows (James Riley) were presented. A number of colleagues from universities, government agencies, and industry attended the final presentations of the participants on July 31 and participated in the discussions. There are twenty-six papers in this volume grouped in five areas. Each group is preceded with an overview by its coordinator.

Source record↗

Role of genetic background in induced instability

Genomic instability is effectively induced by ionizing radiation. Recently, evidence has accumulated supporting a relationship between genetic background and the radiation-induced genomic instability phenotype. This is possibly due to alterations in proteins responsible for maintenance of genomic integrity or altered oxidative metabolism. Studies in human cell lines, human primary cells, and mouse models have been performed predominantly using high linear energy transfer (LET) radiation, or high doses of low LET radiation. The interplay between genetics, radiation response, and genomic instability has not been fully determined at low doses of low LET radiation. However, recent studies using low doses of low LET radiation suggest that the relationship between genetic background and radiation-induced genomic instability may be more complicated than these same relationships at high LET or high doses of low LET radiation. The complexity of this relationship at low doses of low LET radiation suggests that more of the population may be at risk than previously recognized and may have implications for radiation risk assessment.

NASA Discipline Radiation Health↗

Sensorimotor aspects of high-speed artificial gravity: III. Sensorimotor adaptation

As a countermeasure to the debilitating physiological effects of weightlessness, astronauts could live continuously in an artificial gravity environment created by slow rotation of an entire spacecraft or be exposed to brief daily "doses" in a short radius centrifuge housed within a non-rotating spacecraft. A potential drawback to both approaches is that head movements made during rotation may be disorienting and nauseogenic. These side effects are more severe at higher rotation rates, especially upon first exposure. Head movements during rotation generate aberrant vestibular stimulation and Coriolis force perturbations of the head-neck motor system. This article reviews our progress toward distinguishing vestibular and motor factors in side effects of rotation, and presents new data concerning the rates of rotation up to which adaptation is possible. We have studied subjects pointing to targets during constant velocity rotation, because these movements generate Coriolis motor perturbations of the arm but do not involve unusual vestibular stimulation. Initially, reaching paths and endpoints are deviated in the direction of the transient lateral Coriolis forces generated. With practice, subjects soon move in straighter paths and land on target once more. If sight of the arm is permitted, adaptation is more rapid than in darkness. Initial arm movement trajectory and endpoint deviations are proportional to Coriolis force magnitude over a range of rotation speeds from 5 to 20 rpm, and there is rapid, complete motor adaptation at all speeds. These new results indicate that motor adaptation to high rotation rates is possible. Coriolis force perturbations of head movements also occur in a rotating environment but adaptation gradually develops over the course of many head movements.

Non-NASA Center↗

Fundamental space radiobiology

The unique feature of the space radiation environment is the dominance of high-energy charged particles (HZE or high LET radiation) emitted by the Sun and galactic sources, or trapped in the Van Allen radiation belts. These charged particles present a significant hazard to space flight crews, and accelerator-based experiments are underway to quantify the health risks due to unavoidable radiation exposure. There are three principal properties of charged particles that distinguish them from conventional radiation, i.e. gamma rays and x-rays. First, they have a defined range in matter rather than an exponential absorption profile. Second, they undergo nuclear reactions to produce secondary particles. Third, and most important, they deposit their energy along well-defined linear paths or tracks rather than diffuse fields. The structured energy deposition pattern interacts on multiple scales with the biological structures of DNA, cells and tissues to produce correlated patterns of damage that evade repair systems. Traditional concepts of dose and its associated normalization parameter, RBE (relative biological effectiveness), break down under experimental scrutiny, and probabilistic models of risk based on the number of particle traversals per cell may be more appropriate. Unique patterns of DNA damage, gene expression, mobilization of repair proteins, activation of cytokines and remodeling of cellular microenvironment are observed following exposure to high LET radiation. At low levels of exposure the communication of bioactive substances from irradiated to unirradiated "bystander" cells can amplify the damage and cause a significant deviation from linearity in dose vs. response relations. Under some circumstances, there is even a multigenerational delay in the expression of radiation-induced genetic damage (genomic instability) which is not strictly dose dependent. These issues and the experimental evidence derived from ground based experiments at particle accelerators are presented along with speculation about how modified inertial conditions might perturb homeostatic responses to radiation to further complicate risk assessment for space flight.

NASA Discipline Radiation Health↗

Neuroprotection trek--the next generation: neuromodulation I. Techniques--deep brain stimulation, vagus nerve stimulation, and transcranial magnetic stimulation

Neuromodulation denotes controlled electrical stimulation of the central or peripheral nervous system. The three forms of neuromodulation described in this paper-deep brain stimulation, vagus nerve stimulation, and transcranial magnetic stimulation-were chosen primarily for their demonstrated or potential clinical usefulness. Deep brain stimulation is a completely implanted technique for improving movement disorders, such as Parkinson's disease, by very focal electrical stimulation of the brain-a technique that employs well-established hardware (electrode and pulse generator/battery). Vagus nerve stimulation is similar to deep brain stimulation in being well-established (for the treatment of refractory epilepsy), completely implanted, and having hardware that can be considered standard at the present time. Vagus nerve stimulation differs from deep brain stimulation, however, in that afferent stimulation of the vagus nerve results in diffuse effects on many regions throughout the brain. Although use of deep brain stimulation for applications beyond movement disorders will no doubt involve placing the stimulating electrode(s) in regions other than the thalamus, subthalamus, or globus pallidus, the use of vagus nerve stimulation for applications beyond epilepsy-for example, depression and eating disorders-is unlikely to require altering the hardware significantly (although stimulation protocols may differ). Transcranial magnetic stimulation is an example of an external or non-implanted, intermittent (at least given the current state of the hardware) stimulation technique, the clinical value of which for neuromodulation and neuroprotection remains to be determined.

Review, Tutorial↗

How do we get from cell and animal data to risks for humans from space radiations?

After four decades of human exploration in space, many scientists consider the medical consequences from radiation exposures to be the major biological risk associated with long-term missions. This conclusion is based upon results from a research program that has evolved over the past thirty years. Despite the diversity in both opinions and approaches that necessarily arise in research endeavors such as this, a commonality has emerged from our community. We need epidemiological data for humans, animal data in areas where no human data exist, and data on mechanisms to get from animal to humans. We need a programmatic infrastructure that addresses specific goals as well as basic research. These concepts might be deemed overly simplistic and even tautologous were it not for the fact that they are frequently underutilized and even ignored. This article examines the goals, premises, and infrastructures proposed by expert panels and agencies to address radiation risks in space. It is proposed that the required level of effort and the resources available demand a unified, focused international effort that is, at the same time, subjected to rigorous peer review if it is to be successful. There is a plan; let us implement it.

Non-NASA Center↗

Adsorption processes in spacecraft environmental control and life support systems

The environmental control and life support system on a spacecraft maintains a safe and comfortable environment in which the crew can live and work by supplying oxygen and water and by removing carbon dioxide, water vapor, and trace contaminants from cabin air. Although open-loop systems have been used successfully in the past for short-duration missions, the economics of current and future long-duration missions in space will make nearly complete recycling of air and water imperative. A variety of operations will be necessary to achieve the goal of nearly complete recycling. These include separation and reduction of carbon dioxide, removal of trace gas-phase contaminants, recovery and purification of humidity condensate, purification and polishing of wastewater streams, and others. Several of these can be performed totally or in part by adsorption processes. These processes are good candidates to perform separations and purifications in space due to their gravity independence, high reliability, relative high energy efficiency, design flexibility, technological maturity, and regenerative nature. For these reasons, adsorption has historically played a key role in life support on U.S. and Russian piloted spacecraft. Among the life support applications that can be achieved through use of adsorption technology are removal of trace contaminants and carbon dioxide from cabin air and recovery of potable water from waste streams. In each of these cases adsorption technology has been selected for use onboard the International Space Station. The requirements, science, and hardware for these applications are discussed. Human space exploration may eventually lead to construction of planetary habitats. These habitats may provide additional opportunities for use of adsorption processes, such as control of greenhouse gas composition, and may have different resources available to them, such as gases present in the planetary atmosphere. Separation and purification processes based on adsorption can be expected to continue to fulfill environmental control and life support needs on future missions.

Review, Tutorial↗

Cardiac myofilaments: mechanics and regulation

The mechanical properties of the cardiac myofilament are an important determinant of pump function of the heart. This report is focused on the regulation of myofilament function in cardiac muscle. Calcium ions form the trigger that induces activation of the thin filament which, in turn, allows for cross-bridge formation, ATP hydrolysis, and force development. The structure and protein-protein interactions of the cardiac sarcomere that are responsible for these processes will be reviewed. The molecular mechanism that underlies myofilament activation is incompletely understood. Recent experimental approaches have been employed to unravel the mechanism and regulation of myofilament mechanics and energetics by activator calcium and sarcomere length, as well as contractile protein phosphorylation mediated by protein kinase A. Central to these studies is the question whether such factors impact on muscle function simply by altering thin filament activation state, or whether modulation of cross-bridge cycling also plays a part in the responses of muscle to these stimuli.

Review, Tutorial↗

Radiation-induced second cancers: the impact of 3D-CRT and IMRT

Information concerning radiation-induced malignancies comes from the A-bomb survivors and from medically exposed individuals, including second cancers in radiation therapy patients. The A-bomb survivors show an excess incidence of carcinomas in tissues such as the gastrointestinal tract, breast, thyroid, and bladder, which is linear with dose up to about 2.5 Sv. There is great uncertainty concerning the dose-response relationship for radiation-induced carcinogenesis at higher doses. Some animal and human data suggest a decrease at higher doses, usually attributed to cell killing; other data suggest a plateau in dose. Radiotherapy patients also show an excess incidence of carcinomas, often in sites remote from the treatment fields; in addition there is an excess incidence of sarcomas in the heavily irradiated in-field tissues. The transition from conventional radiotherapy to three-dimensional conformal radiation therapy (3D-CRT) involves a reduction in the volume of normal tissues receiving a high dose, with an increase in dose to the target volume that includes the tumor and a limited amount of normal tissue. One might expect a decrease in the number of sarcomas induced and also (less certain) a small decrease in the number of carcinomas. All around, a good thing. By contrast, the move from 3D-CRT to intensity-modulated radiation therapy (IMRT) involves more fields, and the dose-volume histograms show that, as a consequence, a larger volume of normal tissue is exposed to lower doses. In addition, the number of monitor units is increased by a factor of 2 to 3, increasing the total body exposure, due to leakage radiation. Both factors will tend to increase the risk of second cancers. Altogether, IMRT is likely to almost double the incidence of second malignancies compared with conventional radiotherapy from about 1% to 1.75% for patients surviving 10 years. The numbers may be larger for longer survival (or for younger patients), but the ratio should remain the same.

Review, Tutorial↗

On the nature and evolution of the neural bases of human language

The traditional theory equating the brain bases of language with Broca's and Wernicke's neocortical areas is wrong. Neural circuits linking activity in anatomically segregated populations of neurons in subcortical structures and the neocortex throughout the human brain regulate complex behaviors such as walking, talking, and comprehending the meaning of sentences. When we hear or read a word, neural structures involved in the perception or real-world associations of the word are activated as well as posterior cortical regions adjacent to Wernicke's area. Many areas of the neocortex and subcortical structures support the cortical-striatal-cortical circuits that confer complex syntactic ability, speech production, and a large vocabulary. However, many of these structures also form part of the neural circuits regulating other aspects of behavior. For example, the basal ganglia, which regulate motor control, are also crucial elements in the circuits that confer human linguistic ability and abstract reasoning. The cerebellum, traditionally associated with motor control, is active in motor learning. The basal ganglia are also key elements in reward-based learning. Data from studies of Broca's aphasia, Parkinson's disease, hypoxia, focal brain damage, and a genetically transmitted brain anomaly (the putative "language gene," family KE), and from comparative studies of the brains and behavior of other species, demonstrate that the basal ganglia sequence the discrete elements that constitute a complete motor act, syntactic process, or thought process. Imaging studies of intact human subjects and electrophysiologic and tracer studies of the brains and behavior of other species confirm these findings. As Dobzansky put it, "Nothing in biology makes sense except in the light of evolution" (cited in Mayr, 1982). That applies with as much force to the human brain and the neural bases of language as it does to the human foot or jaw. The converse follows: the mark of evolution on the brains of human beings and other species provides insight into the evolution of the brain bases of human language. The neural substrate that regulated motor control in the common ancestor of apes and humans most likely was modified to enhance cognitive and linguistic ability. Speech communication played a central role in this process. However, the process that ultimately resulted in the human brain may have started when our earliest hominid ancestors began to walk.

Review, Tutorial↗

Photic and circadian regulation of retinal melatonin in mammals

Several studies have established that melatonin synthesis occurs in the retina of vertebrates, including mammals. In mammals, a subpopulation of photoreceptors (probably the cones) synthesize melatonin. Melatonin synthesis in the retina is elevated at night and reduced during the day in a fashion similar to events in the pineal gland. Both the MT1 and MT2 melatonin receptors are present in the retina and retinal melatonin does not contribute to circulating levels, suggesting that retinal melatonin acts locally as a neurohormone and/or neuromodulator. Melatonin synthesis in the retina of mammals is under the control of a circadian oscillator, and circadian rhythms in melatonin synthesis and/or release have been described for several species of mammals. These rhythms are present in vivo, persist in vitro, are entrained by light and are temperature compensated. The cloning of the gene responsible for the synthesis of the enzyme arylalkylamine N-acetyltransferase (the key enzyme in the melatonin biosynthetic pathway) has allowed studies of the molecular mechanisms responsible for the generation of retinal melatonin rhythmicity. The present review focuses on the cellular and molecular mechanisms that regulate melatonin synthesis. In particular, we discuss how the photic environment and the circadian clock interact in determining melatonin levels, in addition to the role that melatonin plays in retinal physiology.

NASA Discipline Space Human Factors↗

Electrochemical approaches for chemical and biological analysis on Mars

Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and with the correct methodology provide unamibiguous detection of such life forms.

Non-NASA Center↗