Simulating an exploration of RNA conformation space with an appropriate parallel-updating strategy.
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Journal Article↗
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Results for “Space Simulation”
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Free-electron-laser simulations: Effects of beam quality and space charge.
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Journal Article↗
Simulation of pleural disease by disk space infection.
A young woman presented with the acute onset of pleuritic chest pain ahd pleural effusion which eventually proved to be secondary to an infected disk space. This complication most likely resulted from a paraspinal extension of the infection. Disk-space infection must be added to the differential diagnosis of acute pleural disease.
Acute Disease↗
Life sciences issues affecting space exploration.
The U.S. space program is undertaking a serious examination of new initiatives in human space exploration involving permanent colonies on the Moon and an outpost on Mars. Life scientists have major responsibilities to the crew, to assure their health, productivity, and safety throughout the mission and the postflight rehabilitation period; to the mission, to provide a productive working environment; and to the scientific community, to advance knowledge and understanding of human adaptation to the space environment. Critical areas essential to the support of human exploration include protection from the radiation hazards of the space environment, reduced gravity countermeasures, artificial gravity, medical care, life support systems, and behavior, performance, and human factors in an extraterrestrial environment. Developing solutions to these concerns is at the heart of the NASA Life Sciences ground-based and flight research programs. Facilities analogous to planetary outposts are being considered in Antarctica and other remote settings. Closed ecological life support systems will be tested on Earth and Space Station. For short-duration simulations and tests, the Space Shuttle and Spacelab will be used. Space Station Freedom will provide the essential scientific and technological research in areas that require long exposures to reduced gravity conditions. In preparation for Mars missions, research on the Moon will be vital. As the challenges of sustaining humans on space are resolved, advances in fundamental science, medicine and technology will follow.
Adaptation, Physiological↗
STUDY OF REQUIREMENTS FOR THE SIMULATION OF RENDEZVOUS AND DOCKING OF SPACE VEHICLES. TECHN DOCUM REP AMRL-TDR-63-100.
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Computers↗
[Muscle atrophy in microgravity and during its simulation].
Summarized are the results of comparative analysis of morphological changes in rat's skeletal muscles after microgravity and its simulation. On completion of space flight, hindlimb muscles of rats exhibited atrophy developed in space microgravity in consequence of the lack of weight-bearing loads and changes solely in the slow anti-g muscles due to the hemodynamic disorders appearing after space flight. Immobilization combined with clinostatting cannot be a veridical laboratory model of microgravity, as horizontally positioned animals still possess weight and, besides, experience severe chronic stress of immobilization. Tail suspension with the head-end permanently down and the hind limbs out of use appeared the most demonstrative model of the space microgravity effects. With this model, the hindlimb muscles underwent changes identical to what had been observed in space flown animals. Data of the simulation studies suggest stabilization of muscle atrophy at a certain level and an earlier and stronger reaction to the hindlimb unloading in young rats as compared to old animals. Skeletal muscles in females and males responded to suspension similarly in spite of difference in the hormonal status.
Animals↗
[Supernumerary (a 3rd) kidney simulating a tumor of the retroperitoneal space].
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Diagnosis, Differential↗
Simulated microgravity induced damage in human retinal pigment epithelial cells.
PURPOSE: The goal of this study was to determine the potential damage to the human retina that may occur from weightlessness during space flight using simulated microgravity. METHODS: Human retinal pigment epithelial (hRPE) cells were cultured for 24 h in a National Aeronautics and Space Administration-designed rotating wall bioreactor vessel to mimic the microgravity environment of space. Single-stranded breaks in hRPE DNA induced by simulated gravity were measured using the comet assay. In addition, the production of the inflammatory mediator prostaglandin E2 (PGE2) was measured in these cells 48 h after recovery from simulated microgravity exposure. RESULTS: Simulated microgravity induced single-stranded breaks in the hRPE DNA that were not repaired within 48 h. Furthermore, PG E2 production was dramatically increased 48 h after the initial microgravity-induced damage, indicating the induction of an inflammatory response. There was less DNA damage and no PGE2 release in hRPE cells pretreated with the antiinflammatory agent cysteine during their exposure to microgravity. CONCLUSIONS: We have demonstrated that the microgravity environment generated by a NASA-designed rotating wall bioreactor vessel induces an inflammatory response in hRPE cells. This system thus constitutes a new model system for the study of inflammation in the retina, a system that does not involve the introduction of an exogenous chemical agent or supplementary irradiation. This in vitro method may also be useful for testing novel therapeutic approaches for suppression of retinal inflammation. Furthermore, we suggest a safe prophylactic treatment for prevention of acute, transitory, or enhanced age-related permanent blindness in astronauts or flight personnel engaged in long-haul flights.
Anti-Inflammatory Agents↗
Phase behavior of colloidal hard tetragonal parallelepipeds (cuboids): a Monte Carlo simulation study.
The impact of particle geometry on the phase behavior of hard colloidal tetragonal parallelepipeds (TPs) was studied by using Monte Carlo simulations in continuum space. TPs or "cuboids" of aspect ratios varying from 0.25 to 8 were simulated by approximating their shapes with multisite objects, i.e., via rigid clusters of hard spheres. Using equation of state curves, order parameters, radial distribution functions, particle distribution functions along three directions, and visual analysis of configurations, an approximate phase diagram for the TPs was mapped out as a function of aspect ratio (r) and volume fraction. For r > 3 and intermediate concentrations, the behavior of the TPs was similar to that of spherocylinders, exhibiting similar liquid crystalline mesophases (e.g., nematic and smectic phases). For r = 1, a cubatic phase occurs with orientational order along the three axes but with little translational order. For 1 < r < 4, the TPs exhibit a cubatic-like mesophase with a high degree of order along three axes where the major axes of the particles are not all aligned in the same direction. For r < 1, the TPs exhibit a smectic-like phase where the particles have rotational freedom in each layer but form stacks with tetratic order. The equation of state for perfect hard cubes (r = 1) was also simulated and found to be consistent with that of the rounded-edge r = 1 TPs, except for its lack of discontinuity at the cubatic-solid transition.
Journal Article↗
Principles of carbopeptoid folding: a molecular dynamics simulation study.
The conformational spaces of five oligomers of tetrahydrofuran-based carbopeptoids in chloroform and dimethyl sulfoxide were investigated through nine molecular dynamics simulations. Prompted by nuclear magnetic resonance experiments that indicated various stable folds for some but not all of these carbopeptoids, their folding behaviour was investigated as a function of stereochemistry, chain length and solvent. The conformational distributions of these molecules were analysed in terms of occurrence of hydrogen bonds, backbone torsional-angle distributions, conformational clustering and solute configurational entropy. While a cis-linkage across the tetrahydrofuran ring favours right-handed helical structures, a trans-linkage results in a larger conformational variability. Intra-solute hydrogen bonding is reduced with increasing chain length and with increasing solvent polarity. Solute configurational entropies confirm the picture obtained: they are smaller for cis- than for trans-linked peptides, for chloroform than for dimethyl sulfoxide as solvent and for shorter peptide chains. The simulations provide an atomic picture of molecular conformational variability that is consistent with the available experimental data.
Computer Simulation↗
Extravehicular activity training and hardware design consideration.
Preparing astronauts to perform the many complex extravehicular activity (EVA) tasks required to assemble and maintain Space Station will be accomplished through training simulations in a variety of facilities. The adequacy of this training is dependent on a thorough understanding of the task to be performed, the environment in which the task will be performed, high-fidelity training hardware and an awareness of the limitations of each particular training facility. Designing hardware that can be successfully operated, or assembled, by EVA astronauts in an efficient manner, requires an acute understanding of human factors and the capabilities and limitations of the space-suited astronaut. Additionally, the significant effect the microgravity environment has on the crew members' capabilities has to be carefully considered not only for each particular task, but also for all the overhead related to the task and the general overhead associated with EVA. This paper will describe various training methods and facilities that will be used to train EVA astronauts for Space Station assembly and maintenance. User-friendly EVA hardware design considerations and recent EVA flight experience will also be presented.
Astronauts↗
Efficient photon beam dose calculations using DOSXYZnrc with BEAMnrc.
This study examines the efficiencies of doses calculated using DOSXYZnrc for 18 MV (10 X 10 cm2 field size) and 6 MV (10 X 10 cm2 and 20 X 20 cm2 field sizes) photon beams simulated using BEAMnrc. Both phase-space sources and full BEAMnrc simulation sources are used in the DOSXYZnrc calculations. BEAMnrc simulation sources consist of a BEAMnrc accelerator simulation compiled as a shared library and run by the user code (DOSXYZnrc in this case) to generate source particles. Their main advantage is in eliminating the need to store intermediate phase-space files. In addition, the efficiency improvements due to photon splitting and particle recycling in the DOSXYZnrc simulation are examined. It is found that photon splitting increases dose calculation efficiency by a factor of up to 6.5, depending on beam energy, field size, voxel size, and the type of secondary collimation used in the BEAMnrc simulation (multileaf collimator vs photon jaws). The optimum efficiency with photon splitting is approximately 55% higher than that with particle recycling, indicating that, while most of the gain is due to time saved by reusing source particle data, there is significant gain due to the uniform distribution of interaction sites and faster DOSXYZnrc simulation time when photon splitting is employed. Use of optimized directional bremsstrahlung splitting in the BEAMnrc simulation sources increases the efficiency of photon beam simulations sufficiently that the peak efficiencies (i.e., with optimum setting of the photon splitting number) of DOSXYZnrc simulations using these sources are only 3-13% lower than those with phase-space file sources. This points towards eliminating the need for storing intermediate phase-space files.
Body Burden↗
Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.
Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation techniques such as simulated annealing can capture these motions by comparing them to long-time molecular dynamics (MD) trajectories. The motions are analyzed by principal component analysis and compared using inner products of eigenvectors of the respective covariance matrices. Two very different systems are studied, the beta-spectrin PH domain and the single-stranded DNA binding protein (ssDBP) from the filamentous phage Pf3. A comparison of the ensembles from NMR and MD shows significant overlap of the essential spaces, which in the case of ssDBP is extraordinarily high. The influence of variations in the specifications of distance restraints is investigated. We also study the influence of the selection criterion for the final structure ensemble on the definition of mobility. The results suggest a modified criterion that improves conformational sampling in terms of amplitudes of correlated motion.
Computer Simulation↗
Simulation of the geomagnetic field experienced by the International Space Station in its revolution around the Earth: effects on psychophysiological responses to affective picture viewing.
There is evidence suggesting that exposure to an abnormal magnetic environment may produce psychophysiological effects related to abnormalities in responses to stress. This may be of relevance for space medicine where astronauts are exposed to a magnetic field different from that exerted by the Earth. Aim of this study was to assess how the exposure of the head to a magnetic field simulating the one encountered by the International Space Station (ISS) during a single orbit (90 min) around the Earth affects the cardiovascular and psychophysiological parameters. Twenty-four human volunteers were studied double blindly in random order under sham and magnetic exposure. During exposure, the persons were shown a set of pictures of different emotional content while subjective self-rating, skin conductance (SC), blood pressure (BP), and heart rate (HR) were measured. In addition, BP, HR, and tooth pain threshold were assessed before and after exposure. While subjects were under magnetic exposure, skin conductance was strongly differentiated (F(2,36)=22.927; p=0.0001), being high during emotionally involving (positive and negative) pictures and low during neutral pictures. Conversely, when subjects were under sham exposure, no significant differences were observed. There was, however, a trend for higher heart rate during picture viewing under magnetic exposure as compared to sham exposure. No effects were found for the other variables. These results suggest that an abnormal magnetic field that simulates the one encountered by ISS orbiting around the Earth may enhance autonomic response to emotional stimuli.
Adult↗
A population genetics model for multiple quantitative traits exhibiting pleiotropy and epistasis.
We study a population genetics model of an organism with a genome of L(tot)loci that determine the values of T quantitative traits. Each trait is controlled by a subset of L loci assigned randomly from the genome. There is an optimum value for each trait, and stabilizing selection acts on the phenotype as a whole to maintain actual trait values close to their optima. The model contains pleiotropic effects (loci can affect more than one trait) and epistasis in fitness. We use adaptive walk simulations to find high-fitness genotypes and to study the way these genotypes are distributed in sequence space. We then simulate the evolution of haploid and diploid populations on these fitness landscapes and show that the genotypes of populations are able to drift through sequence space despite stabilizing selection on the phenotype. We study the way the rate of drift and the extent of the accessible region of sequence space is affected by mutation rate, selection strength, population size, recombination rate, and the parameters L and T that control the landscape shape. There are three regimes of the model. If LT< >L(tot), there are many small peaks that can be spread over a wide region of sequence space. Compensatory neutral mutations are important in the population dynamics in this case.
Animals↗
Simulation of the gyroid phase in off-lattice models of pure diblock copolymer melts.
Particle-based molecular simulations of pure diblock copolymer (DBC) systems were performed in continuum space via dissipative particle dynamics and Monte Carlo methods for a bead-spring chain model. This model consisted of chains of soft repulsive particles often used with dissipative particle dynamics. The gyroid phase was successfully simulated in DBC melts at selected conditions provided that the simulation box size was commensurate with the gyroid lattice spacing. Simulations were concentrated at conditions where the gyroid phase is expected to be stable which allowed us to outline approximate phase boundaries. When more than one phase was observed by varying simulation box size, thermodynamic stability was discerned by comparing the Helmholtz free energy of the competing phases. For this purpose, chemical potentials were efficiently simulated via an expanded ensemble that gradually inserts/deletes a target chain to/from the system. These simulations employed a novel combination of Bennett's [J. Comput. Phys. 22, 245 (1976)] acceptance-ratio method to estimate free-energy differences and a recently proposed method to get biasing weights that maximize the number of times that the target chain is regrown. The analysis of the gyroid nodes revealed clear evidence of packing frustration in the form of an (entropically) unfavorably overstretching of chains, a phenomenon that has been suggested to provide the structural basis for the limited region of stability of the gyroid phase in the DBC phase diagram. Finally, the G phase and nodal chain stretching were also found in simulations with a completely different DBC particle-based model.
Journal Article↗
Responses to simulated echoes by neurons in the barn owl's auditory space map.
The natural acoustical environment contains many reflective surfaces that give rise to echoes, complicating the task of sound localization and identification. The barn owl (Tyto alba), as a nocturnal predator, relies heavily on its auditory system for tracking and capturing prey in this highly echoic environment. The external nucleus of the owl's inferior colliculus (ICx) contains a retina-like map of space composed of "space-specific" auditory neurons that have spatially limited receptive fields. We recorded extracellularly from individual space-specific neurons in an attempt to understand the pattern of activity across the ICx in response to a brief direct sound and a simulated echo. Space-specific neurons responded strongly to the direct sound, but their response to a simulated echo was suppressed, typically, if the echo arrived within 5 ms or less of the direct sound. Thus we expect there to be little or no representation within the ICx of echoes arriving within such short delays. Behavioral tests using the owl's natural tendency to turn their head toward a sound source suggested that owls, like their space-specific neurons, similarly localize only the first of two brief sounds. Naive, untrained owls were presented with a pair of sounds in rapid succession from two horizontally-separated speakers. With interstimulus delays of less than 10 ms, the owl consistently turned its head toward the leading speaker. Longer delays elicited head turns to either speaker with approximately equal frequency and in some cases to both speakers sequentially.
Acoustic Stimulation↗
A note on the relevance of human population genetic variation and molecular epidemiology to assessing radiation health risk for space travellers.
We discuss the relevance to space medicine of studies concerning human genetic variation and consequent variable disease susceptibility or sensitivity between individuals. The size of astronaut and cosmonaut populations is both presently and cumulatively small, and despite the launch of the International Space Station, unlikely to increase by orders of magnitude within the foreseeable future. In addition, astronauts-cosmonauts constitute unrepresentative samples of their national populations. While the context of exposure for the astronaut-cosmonaut group is one unlikely to be replicated elsewhere than in space, aspects of specific exposures may be simulated by events such as occupational radiation exposure or radiation therapy. Hence, population-based studies of genetic susceptibility or sensitivity to disease, especially where it is precipitated by events that may simulate consequences of the space environment, likely will prove of value in assessing long-term health risks.
Astronauts↗