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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Parallel algorithms for hyperdynamics and local hyperdynamics

Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In [Kim, Perez, Voter, J Chem Phys, 139:144110, 2013)1, a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. In this paper, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost 3-5x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of Pt(100) surface for 80 and 160 μs.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1983

Sleep-wake responses of squirrel monkeys exposed to hyperdynamic environments

This study examines the sleep responses of primates to acute 3 Gz environments. To investigate this question, loosely-restrained squirrel monkeys were exposed to 70 minutes of 3 Gz during the day. The animals' behavioral state was polygraphically monitored (EEG, EMG, EOG) along with video and deep body temperature. During the control period, animals exhibited slow wave sleep (SWS) napping behavior. SWS occurred during approximately 20 percent of the control period. Body temperature was maintained at 38.7 C. At 3 Gz, SWS was inhibited for 5 minutes, after which SWS occurred at levels 50 percent lower than in the control period. During the post-centrifugation period, SWS was elevated above the control (50 percent) and hyperdynamic (100 percent) levels. Body temperature was depressed 1.5 C when the animals were at 3 Gz. Thus, hyperdynamic environments are capable of modifying primate sleep behavior, at least as a result of acute exposure. Further, the increased arousal in the hyperdynamic environment is correlated with a lower body temperature. This negative correlation differs from the normal positive correlation of arousal and body temperature.

Fuller, C. A.↗
NASA NTRS1982

Short hyperdynamic profiles influence primate temperature regulation

Primates have been shown to be sensitive to hyperdynamic fields. That is, when exposed to + 2Gz, body temperature falls. The purpose of this study was to examine the relative sensitivity of these animals to short centrifugation profiles which mimic the gravitational envelope seen on the Space Shuttle during launch (8 minutes, 2.9 Gz max) and re-entry (19 min, 1.7 Gz max). Four loosely restrained squirrel monkeys, isolated from additional external stimuli, were exposed to these profiles. During launch simulation, the temperatures never fell markedly below control levels. However, subsequent to return to 1G, the recovery phase showed decreases in body temperature in all four animals averaging 0.4 C over the next 10 to 15 minutes. The two animals exposed to the reentry profile showed decreases in body temperature within five minutes of the onset of centrifugation. Maximum fall in body temperature was reached by the end of the centrifugation phase and averaged 0.7 C. Thus, the temperature regulation system of this primate is sensitive to short hyperdynamic field exposures.

Fuller, C. A.↗
NASA NTRS1984

Acute physiological responses of squirrel monkeys exposed to hyperdynamic environments

Physiological and behavioral responses to a hyperdynamic environment were examined in four adult male squirrel monkeys. After baseline monitoring at 1 G, monkeys were exposed to one of three conditions: (1) +2 Gz for 60 minutes, (2) +2.9 Gz max for 8 minutes (simulating Space Shuttle launch), or (3) +1.7 Gz max for 19 minutes (simulating Space Shuttle reentry). During all experimental conditions, heart rate rose, and colonic temperature began to decline within the first ten minutes of centrifugation and decreased by as much as 2 C in some instances. Behaviorally, during centrifugation, the monkeys seemed to exhibit drowsiness and fall asleep, an observation not made during the control period. It is concluded that primates are susceptible to acute hyperdynamic field exposure.

Fuller, C. A.↗
NASA NTRS1985

Homeostasis in Primates in the Hyperdynamic Environment

The influence of chronic centrifugation upon the homestatic regulation of the circadian timekeeping system was examined. The interactions of body temperature regulation and the behavioral state of arousal were studied by evaluating the influence of cephalic fluid shifts induced by lower body positive air pressure (LBPP), upon these systems. The small diurnal squirrel monkey (Saimiri sciureus) was used as the non-human primate model. Results show that the circadian timekeeping system of these primates is functional in the hyperdynamic environment, however, some of its components appear to be regulated at different homeostatic levels. The LBPP resulted in an approximate 0.7 C decrease in DBT (p 0.01). However, although on video some animals appeared drowsy during LBPP, sleep recording revealed no significant changes in state of arousal. Thus, the physiological mechanisms underlying this lowering of body temperature can be independent of the arousal state.

Fuller, C. A.↗
NASA NTRS1984

The primate circadian timekeeping system in a hyperdynamic environment

The effect of hyperdynamic field (12 d at 1.5 G and 35 d at 2.0 G phases, preceded and followed by 1.0 G phases of 15 and 18 days, respectively) on the circadian rhythm in the feeding and drinking of the squirrel monkey was studied. Two lighting regimens were employed: (1) the 24-hr light-dark cycle (LD 12:12) at all G phases and (2) constant light (LL) during the two 1.0 G phases and a 2.0 G phase. In the LD regimen, both feeding and drinking rhythms were entrained with the 24-hr periods at all G levels, but a phase delay occurred in high G environment. In the LL regimen, the rhythm persisted with a free-running period greater than 24 hours and an increase at 2.0 G, compared to the 1.0 G phases. Thus, although the circadian rhythm is functional at high G, some of its components appear to be regulated at different homeostatic levels.

Fuller, C. A.↗
NASA NTRS1990

The effect of hyperdynamic fields on the oxidative metabolism of the paraventricular nucleus

An important issue in space biology and medicine is understanding the effect of gravitational changes on the mechanisms that regulate fluid homeostasis. The results of this study show that, following 7-d exposure to a 2 G or 3 G hyperdynamic field, rats exhibited a linear increase in the cytochrome oxidase staining of neurons in the paraventricular nucleus (PVN). The elevated oxidative metabolism in the PVN suggests that there was an increase in the manufacturing and release of vasopressin into the plasma in response to a perceived hypovolemic condition caused by increased hydrostatic pressure and redistribution of fluid to the periphery. Since vasopressin also has widespread cardiovascular effects, it will be important to understand the relationship between vasopressin and altered gravitational fields.

Murakami, Dean M.↗
NASA NTRS1993

The regulation of rat activity following exposure to hyperdynamic fields

The microgravity of space flight and the hyperdynamic fields produced via centrifugation have allowed researchers to examine the effect of altered gravitational environments on the regulation of physiological systems. In this study, a high frequency light/dark cycle was provided for 24 hours as an environmental challenge to assess the recovery of homeostatic and circadian components of physiological regulation in rats. For example, the nocturnal rat exhibited a homeostatic increase in body temperature during the dark periods and a decrease during the light periods. In addition, the magnitude of the body temperature response exhibits a time of day variation demonstrating the effect on circadian regulation.

Fuller, Charles A.↗
NASA NTRS1983

Avian embryonic development in hyperdynamic environments

Embryos which developed for 24 hours in the oviduct of hens maintained at 2 G and which were subsequently incubated at Earth gravity had a 14% reduction in hatchability. Increased mortality during the first 4 days, and an increase in embryonic abnormalities were of the types usually found during the first mortality peak (2-3 days). Embryos in eggs that were produced at Earth gravity and continued their development on the centrifuge at fields of 2 G or less did not appear to be greatly affected by the treatment. At 4 G, 91% of the embryos died, mostly on the first and second days of incubation. Abnormalities prominent in the centrifuged eggs include: (a) a failure of the primitive streak to develop; (b) interference with the development of the axial skeleton; (c) multiple hemorrhages, mostly petechial which is consistent with capillary fragility; and (d) retardation of embryo growth, possibly caused by an interference with gaseous diffusion, the result of an acceleration-induced increase in gas density in the centrifuging incubator.

Abbott, U. K.↗
NASA NTRS1985

Influence of exposure to a prolonged hyperdynamic field on body temperature in the squirrel monkey

The effect of gravitational loading on the regulation of body temperature is examined. Five adult male squirrel monkeys were exposed to a 2-G environment twice for 48 hours, once beginning in the middle of their light cycle and the second time in the middle of their dark cycle. It is observed that a reduction in body temperature occurs during the light cycle phase and at night there is an insignificant change in body temperature. The rhythmic characteristics of the light and dark cycles are analyzed. The data reveal that the body temperature in animals at 2 G is influenced more during the active phase of the animals 24-hour cycle.

Fuller, C. A.↗
NASA NTRS1985

The effect of a hyperdynamic environment on the development of the rat retina

The effects of a 2 G field on the retinal development of the layers in the rat and central visual system nuclei are investigated. The thickness of the retinal layers, ganglion cells, and brains of male and female Wistar rats suspended from an 18 foot diameter centrifuge creating a 2 G field are evaluated and compared with a control group. A decrease in the thickness of the outer nuclear layer (ONL) of 37.1 percent, of 58.5 percent in the inner nuclear layer (INL), and of 28.8 percent in the inner plexiform layer (IPL), and a reduction in body weight are observed in the 2-G rats. The data reveal that the ganglion cells and visual system nuclei activity correspond well with the control data; however, the medial terminal nucleus (MTN) activity is inhibited in the 2-G rats. It is concluded that the differences in ONL and IPL are attributed to body weight reduction, but the INL and MTN are affected by the 2-G conditions.

Murakami, D. M.↗
NASA NTRS1996

Squirrel Monkey Requirements for Chronic Acceleration

This study examined: (1) the ability of a small non-human primate to tolerate chronic centrifugation on a centrifuge with a radius of 0.9 m, and (2) the influence of centrifuge radius on the response of primates to hyperdynamic fields. Eight adult male squirrel monkeys were exposed to 1.5 g via centrifugation at two different radii (0.9 m and 3.0 m). Body temperature, activity, feeding and drinking were monitored. These primates did tolerate and adapt to 1.5G via centrifugation on either radius centrifuge. The results show, however, that centrifuge radius does have an effect on the responses of the primate to the hyperdynamic environment. Adaptation to the hyperdynamic environment occurred more quickly on the larger centrifuge. This study demonstrates that a small, non-human primate model, such as the squirrel monkey, could be used on a 0.9 m radius centrifuge such as is being considered by the NASA Space Station Program.

Fuller, Charles A.↗
NASA NTRS1975

Gravitational effects on body composition in birds

Gallinaceous birds, presenting a wide range of body size, were adapted physiologically to hyperdynamic environments, provided by chronic centrifugation. Chemical composition was measured directly on prepared carcasses, which were anatomically comparable, and more amenable to analysis than the intact body. Body mass and body fat decreased arithmetically with increasing field strength and also with increasing body mass. Water content of lean tissue increased in hyperdynamic environments, but irrespectively of body size.

Smith, A. H.↗
NASA NTRS1989

Temperature regulation in rats exposed to a 2 G field

The regulation of body temperature involves both homeostatic and circadian control systems. Both systems are influenced by exposure to hyperdynamic fields and demonstrate acute responses that eventually recover to an adapted level. This experiment examined both the homeostatic and circadian responses of body temperature to a separate environmental challenge (high frequency light/dark cycles) during exposure to a 2 G hyperdynamic field.

Ishihama, Linda M.↗
NASA NTRS1994

Changes in hypothalamic staining for c-Fos following 2G exposure in rats

The static gravitational field of the earth has been an important selective pressure that has shaped the evolution of biological organisms. This is illustrated by the evolution of tetrapods from a water environment where gravitational force was partially negated to a terrestrial environment where gravity is of greater consequence. Terrestrial invasion resulted in a series of new structural, physiological, and behavioral features. Therefore, it is not surprising that alterations in the gravitational field can cause widespread effects in many physiological systems and behaviors. Our previous studies have demonstrated that both exposure to hyperdynamic fields and the microgravity condition of space flight have significant effects on body temperature, heartrate, activity, feeding, drinking, and circadian rhythms. However, it has not been determined whether these physiological adaptations are associated with changes in neural activity within the hypothalamic nuclei that regulate these functions. This study examined the changes in body temperature, activity, body weight and food and water intake in rats caused by exposure to a hyperdynamic field. In addition, the immediate early gene activation marker, c-Fos, was used to examine potential protein synthesis changes in the hypothalamic nuclei that regulate these functions.

NASA Discipline Regulatory Physiology↗
DOE OSTI2024

Evolution of dislocation loops in irradiated α-Uranium: An atomistically-informed cluster dynamics investigation

An atomistically-informed mean field cluster dynamics model has been developed to investigate the nucleation and growth of prismatic loops in irradiated a-Uranium. TEM analysis of neutron irradiated a-Uranium shows the evolution of self-interstitial atom and vacancy loops on (010) and (100) crystallographic planes, respectively, resulting in an anisotropic lattice swelling of its face-centered orthorhombic crystal. To provide model parameters, the crystallography of loops and the binding energy of point defects to these loops were studied using an angular dependent EAM potential and classical molecular dynamics (MD) simulations. Furthermore, using the bond-boost hyperdynamics method, the anisotropic diffusion of interstitials and vacancies in a-Uranium was investigated. Here, the mechanisms of point defect diffusion and the associated migration energies were reported and compared with previous DFT studies. The energetics and kinetic quantities mentioned above were used in the cluster dynamics model to predict the cluster density as a function of dose rate, dose and temperature and the results were compared to the reported neutron irradiation experiments. The model predictions reveal an accumulation of small sized vacancy loops along with a population of large and growing self-interstitial loops, which closely corresponds to the TEM observations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

A Joint Modeling/Experimental Approach to Characterize Ionization and Fragmentation of SOA Molecules with CIMS

The Molecular Dynamics technique Collective variable hyperdynamics (CVHD) interfaced with density functional tight-binding at the GFN1-xTB and GFN2-xTB levels of electronic structure theory has been applied to the H + GAG positively charged peptide system to explore the fragmentation of this simple tripeptide under relatively low temperature/energy conditions. Unlike conventional chemical dynamics simulations which can only be performed up to hundreds of picoseconds when coupled with semi-empirical Hamiltonians, CVHD is able to capture the long-time dynamics of multiple proton hopping, the formation of reversible ring structures, and ester rearrangement of the H + GAG system prior to fragmentation. The CVHD method applied to H + GAG is also able to uncover alternative fragmentation pathways not considered previously such as glycine fragmentation on the N-terminal side of the charged peptide and new cyclic cationic species. These findings in the H + GAG case have implications for other peptide systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1982

Chronic acceleration and brain density

Tests carried out on rabbits show that the effect of chronic acceleration is not uniform among the various tissues studied. Although body mass is reduced by the treatment, as expected, no change is apparent in brain mass or in the density of cerebrospinal fluid. Acceleration-induced changes are encountered in tissue density, the myocardium exhibiting a transient increase followed by an exponential decrease toward a limit and the brain showing an arithmetic increase in density with continued exposure to 2.5 G. The data are seen as suggesting that a specific brain load is not a regulated phenomenon and that no physiological processes occur to attenuate the increased load imposed by the hyperdynamic environment. An equation is derived indicating that the stimulus potential per unit of brain load increases with body size, even though brain density decreases and cerebrospinal fluid density increases.

Hoffman, L. F.↗