Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Space Simulation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,477 records · Page 82Linked to original sources
PubMed2006

Molecular dynamics simulation of polymer electrolytes based on poly(ethylene oxide) and ionic liquids. I. Structural properties.

Molecular dynamics (MD) simulations have been performed for prototype models of polymer electrolytes in which the salt is an ionic liquid based on 1-alkyl-3-methylimidazolium cations and the polymer is poly(ethylene oxide), PEO. The MD simulations were performed by combining the previously proposed models for pure ionic liquids and polymer electrolytes containing simple inorganic ions. A systematic investigation of ionic liquid concentration, temperature, and the 1-alkyl- chain length, [1,3-dimethylimidazolium]PF6, and [1-butyl-3-methylimidazolium]PF6, effects on resulting equilibrium structure is provided. It is shown that the ionic liquid is dispersed in the polymeric matrix, but ionic pairs remain in the polymer electrolyte. Imidazolium cations are coordinated by both the anions and the oxygen atoms of PEO chains. Probability density maps of occurrences of nearest neighbors around imidazolium cations give a detailed physical picture of the environment experienced by cations. Conformational changes on PEO chains upon addition of the ionic liquid are identified. The equilibrium structure of simulated systems is also analyzed in reciprocal space by using the static structure factor, S(k). Calculated S(k) display a low wave-vector peak, indicating that spatial correlation in an extended-range order prevail in the ionic liquid polymer electrolytes. Long-range correlations are assigned to nonuniform distribution of ionic species within the simulation box.

Journal Article↗
PubMed1998

Nonlinear, three-dimensional finite-element model of skin biomechanics.

OBJECTIVE: The aim of this study was to expand the rigour and scope of soft-tissue finite-element modelling through the introduction of nonlinear biomechanics. The capability to simulate "tissue" movement in three-dimensional space was a priority. METHOD: A computer-based finite-element technique was used to approximate the exact solution to the governing differential equations. Common fusiform defects were "closed" in two- and three-dimensional space. Strains of approximately 17% were introduced. Skin was modelled as a nonlinear elastic anisotropic material in a laminated-composite structure undergoing large deformations and large strain. The finite-element software package for nonlinear biomechanical analysis was run on a university-based, multi-user workstation. Repeated simulations were performed. The key independent variables were the magnitude of the subcutaneous adhesion and the degree of undermining. The two dependent variables were the "closure" force and the distortion field. RESULTS: The absolute values computed for "closure" force, ranging from 4.4 N to 5.2 N, were consistent with previous animal studies. The periphery of the distortion field varied from 4.7 to 5.9 cm from the defect midline. The force of subcutaneous adhesion was varied from 2 to 20 kN/m (+900%) and led to a -19% and +16% change in the distortion field width and "closure" force, respectively. Undermining was progressively increased from 1 to 5 cm (+400%) and produced a +5% and -12% change in the width of the distortion field and the "closure" force, respectively. CONCLUSIONS: The application of nonlinear biomechanics to soft-tissue finite-element modelling has been rewarding. The results correlate well with surgical experience. With specific regard to undermining, additional insight has been gained. Undermining broad-based soft-tissue flaps has progressively limited benefits. The computational demonstration of this result, consistent with prior animal studies, has not been previously published. Future application of this technology may permit the development of more complex flaps. Animal experimentation may be reduced and/or deferred until postulated flap designs have been simulated and refined.

Biomechanical Phenomena↗
PubMed2002

Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies.

Prolines in transmembrane (TM) alpha-helices are believed to play an important structural and/or functional role in membrane proteins. At a structural level a proline residue distorts alpha-helical structure due to the loss of at least one stabilizing backbone hydrogen bond, and introduces flexibility in the helix that may result in substantial kink and swivel motions about the effective "hinge." At a functional level, for example in Kv channels, it is believed that proline-induced molecular hinges may have a direct role in gating, i.e., the conformational change linked to opening/closing the channel to movement of ions. In this article we study the conformational dynamics of the S6 TM helix from of the Kv channel Shaker, which possesses the motif PVP--a motif that is conserved in Kv channels. We perform multiple molecular dynamics simulations of single S6 helices in a membrane-mimetic environment in order to effectively map the kink-swivel conformational space of the protein, exploiting the ability of multiple simulations to achieve greater sampling. We show that the presence of proline locally perturbs the helix, disrupting local dihedral angles and producing local twist and unwinding in the region of the hinge--an effect that is relaxed with distance from the PVP motif. We furthermore show that motions about the hinge are highly anisotropic, reflecting a preferred region of kink-swivel conformation space that may have implications for the gating process.

Models, Molecular↗
PubMed2002

An investigation of air inlet velocity in simulating the dispersion of indoor contaminants via computational fluid dynamics.

Computational fluid dynamics (CFD) is potentially a valuable tool for simulating the dispersion of air contaminants in workrooms. However, CFD-estimated airflow and contaminant concentration patterns have not always shown good agreement with experimental results. Thus, understanding the factors affecting the accuracy of such simulations is critical for their successful application in occupational hygiene. The purposes of this study were to validate CFD approaches for simulating the dispersion of gases and vapors in an enclosed space at two air flow rates and to demonstrate the impact of one important determinant of simulation accuracy. The concentration of a tracer gas, isobutylene, was measured at 117 points in a rectangular chamber [1 (L) x 0.3 (H) x 0.7 m (W)] using a photoionization analyzer. Chamber air flow rates were scaled using geometric and kinematic similarity criteria to represent a full-sized room at two Reynolds numbers (Re = 5 x 10(2) and 5 x 10(3)). Also, CFD simulations were conducted to estimate tracer gas concentrations throughout the chamber. The simulation results for two treatments of air inlet velocity (profiled inlet velocity measured in traverses across the air inlet and the assumption that air velocity is uniform across the inlet) were compared with experimental observations. The CFD-simulated 3-dimensional distribution of tracer gas concentration using the profiled inlet velocity showed better agreement qualitatively and quantitatively with measured chamber concentration, while the concentration estimated using the uniform inlet velocity showed poor agreement for both comparisons. For estimating room air contaminant concentrations when inlet velocities can be determined, this study suggests that using the inlet velocity distribution to define inlet boundary conditions for CFD simulations can provide more reliable estimates. When the inlet velocity distribution is not known, for instance for prospective design of dilution ventilation systems, the trials of several velocity profiles with different source, air inlet and air outlet locations may be useful for determining the most efficient workroom layout.

Air Movements↗
PubMed2003

Damping of Crank-Nicolson error oscillations.

The Crank-Nicolson (CN) simulation method has an oscillatory response to sharp initial transients. The technique is convenient but the oscillations make it less popular. Several ways of damping the oscillations in two types of electrochemical computations are investigated. For a simple one-dimensional system with an initial singularity, subdivision of the first time interval into a number of equal subintervals (the Pearson method) works rather well, and so does division with exponentially increasing subintervals, where however an optimum expansion parameter must be found. This method can be computationally more expensive with some systems. The simple device of starting with one backward implicit (BI, or Laasonen) step does damp the oscillations, but not always sufficiently. For electrochemical microdisk simulations which are two-dimensional in space and using CN, the use of a first BI step is much more effective and is recommended. Division into subintervals is also effective, and again, both the Pearson method and exponentially increasing subintervals methods are effective here. Exponentially increasing subintervals are often considerably more expensive computationally. Expanding intervals over the whole simulation period, although capable of satisfactory results, for most systems will require more cpu time compared with subdivision of the first interval only.

Journal Article↗
PubMed2000

Nonlinear simulations of Jupiter's 5-micron hot spots.

Large-scale nonlinear simulations of Jupiter's 5-micron hot spots produce long-lived coherent structures that cause subsidence in local regions, explaining the low cloudiness and the dryness measured by the Galileo probe inside a hot spot. Like observed hot spots, the simulated coherent structures are equatorially confined, have periodic spacing, propagate west relative to the flow, are generally confined to one hemisphere, and have an anticyclonic gyre on their equatorward side. The southern edge of the simulated hot spots develops vertical shear of up to 70 meters per second in the eastward wind, which can explain the results of the Galileo probe Doppler wind experiment.

Ammonia↗
PubMed2004

An alternative subspace approach to EEG dipole source localization.

In the present study, we investigate a new approach to electroencephalography (EEG) three-dimensional (3D) dipole source localization by using a non-recursive subspace algorithm called FINES. In estimating source dipole locations, the present approach employs projections onto a subspace spanned by a small set of particular vectors (FINES vector set) in the estimated noise-only subspace instead of the entire estimated noise-only subspace in the case of classic MUSIC. The subspace spanned by this vector set is, in the sense of principal angle, closest to the subspace spanned by the array manifold associated with a particular brain region. By incorporating knowledge of the array manifold in identifying FINES vector sets in the estimated noise-only subspace for different brain regions, the present approach is able to estimate sources with enhanced accuracy and spatial resolution, thus enhancing the capability of resolving closely spaced sources and reducing estimation errors. The present computer simulations show, in EEG 3D dipole source localization, that compared to classic MUSIC, FINES has (1) better resolvability of two closely spaced dipolar sources and (2) better estimation accuracy of source locations. In comparison with RAP-MUSIC, FINES' performance is also better for the cases studied when the noise level is high and/or correlations among dipole sources exist.

Algorithms↗
PubMed2006

Spatio-temporal EEG source localization using a three-dimensional subspace FINE approach in a realistic geometry inhomogeneous head model.

The subspace source localization approach, i.e., first principle vectors (FINE), is able to enhance the spatial resolvability and localization accuracy for closely-spaced neural sources from EEG and MEG measurements. Computer simulations were conducted to evaluate the performance of the FINE algorithm in an inhomogeneous realistic geometry head model under a variety of conditions. The source localization abilities of FINE were examined at different cortical regions and at different depths. The present computer simulation results indicate that FINE has enhanced source localization capability, as compared with MUSIC and RAP-MUSIC, when sources are closely spaced, highly noise-contaminated, or inter-correlated. The source localization accuracy of FINE is better, for closely-spaced sources, than MUSIC at various noise levels, i.e., signal-to-noise ratio (SNR) from 6 dB to 16 dB, and RAP-MUSIC at relatively low noise levels, i.e., 6 dB to 12 dB. The FINE approach has been further applied to localize brain sources of motor potentials, obtained during the finger tapping tasks in a human subject. The experimental results suggest that the detailed neural activity distribution could be revealed by FINE. The present study suggests that FINE provides enhanced performance in localizing multiple closely spaced, and inter-correlated sources under low SNR, and may become an important alternative to brain source localization from EEG or MEG.

Algorithms↗
PubMed2001

[Monte Carlo simulation of a dynamic multileaf collimator:implementation and applications].

A model for the simulation of the accelerator heads of two identical linear accelerators was designed at the University Hospital of Tübingen, using the BEAM program developed at the National Research Council of Canada. Both linear accelerators are equipped with multileaf collimators (MLCs) and backup jaws (y-direction) with curved leaf-ends. The accelerator models were divided into two parts. The first part consisted of target, primary collimator, flattening filter, monitor chamber, and mirror. After the Monte Carlo simulation of these parts, the phase-space characteristics below the mirror were stored in a file and used as source for the second part of the accelerator head (jaw, MLC). The electron source was assumed to deliver a gaussian energy spectrum, with parallel direction to the beam axis. With this electron source, there was good agreement between the measured and simulated depth dose curves in water, with difference < 2%. A new module was created for the BEAM program to simulate backup jaws, while the standard MLCQ module from BEAM was used to simulate a MLC with curved leaf-ends. As a result, MLCs and backup jaws with curved leaf-ends make the shoulder of the y-profile higher than the straight-end MLCs.

Computer Simulation↗
PubMed1992

Effect on grating identification of sampling with degenerate arrays.

We have measured observer performance in identifying gratings that were sampled by degenerate-sampling arrays. Grating identification for high-spatial-frequency stimuli fell to threshold levels only after more than 88% of the sampling elements were subtracted. Although several studies with normal observers have shown that foveal visual acuity corresponds to estimates of interphotoreceptor spacing derived from anatomical photoreceptor density, a simple transformation of sampling-element density to mean spacing does not describe the results in our simulation of degenerate-sampling arrays. To the extent that our model simulates the anatomical changes of retinal pathology, our results suggest that grating acuity reflects the normal high-spatial-sampling rate of small regions of preserved anatomy in the degenerate retina rather than the mean density or spacing of foveal receptors after massive degeneration.

Adult↗
PubMed2005

Combining smart darting with parallel tempering using Eckart space: application to Lennard-Jones clusters.

The smart-darting algorithm is a Monte Carlo based simulation method used to overcome quasiergodicity problems associated with disconnected regions of configurations space separated by high energy barriers. As originally implemented, the smart-darting method works well for clusters at low temperatures with the angular momentum restricted to zero and where there are no transitions to permutational isomers. If the rotational motion of the clusters is unrestricted or if permutational isomerization becomes important, the acceptance probability of darting moves in the original implementation of the method becomes vanishingly small. In this work the smart-darting algorithm is combined with the parallel tempering method in a manner where both rotational motion and permutational isomerization events are important. To enable the combination of parallel tempering with smart darting so that the smart-darting moves have a reasonable acceptance probability, the original algorithm is modified by using a restricted space for the smart-darting moves. The restricted space uses a body-fixed coordinate system first introduced by Eckart, and moves in this Eckart space are coupled with local moves in the full 3N-dimensional space. The modified smart-darting method is applied to the calculation of the heat capacity of a seven-atom Lennard-Jones cluster. The smart-darting moves yield significant improvement in the statistical fluctuations of the calculated heat capacity in the region of temperatures where the system isomerizes. When the modified smart-darting algorithm is combined with parallel tempering, the statistical fluctuations of the heat capacity of a seven-atom Lennard-Jones cluster using the combined method are smaller than parallel tempering when used alone.

Journal Article↗
PubMed1986

Effects of gravity perturbation on developing animal systems.

Developing systems provide unique opportunities for analyzing the effects of microgravity on animals. Several unusual types of cells as well as various extraordinary cellular behavior patterns characterize the embryos of most animals. Those features have been exploited as test systems for space flight. The data from previous experiments are reviewed, and considerations for the design of future experiments are presented.

Animals↗
PubMed2004

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.

The parsimony method of Suzuki and Gojobori (1999) and the maximum likelihood method developed from the work of Nielsen and Yang (1998) are two widely used methods for detecting positive selection in homologous protein coding sequences. Both methods consider an excess of nonsynonymous (replacement) substitutions as evidence for positive selection. Previously published simulation studies comparing the performance of the two methods show contradictory results. Here we conduct a more thorough simulation study to cover and extend the parameter space used in previous studies. We also reanalyzed an HLA data set that was previously proposed to cause problems when analyzed using the maximum likelihood method. Our new simulations and a reanalysis of the HLA data demonstrate that the maximum likelihood method has good power and accuracy in detecting positive selection over a wide range of parameter values. Previous studies reporting poor performance of the method appear to be due to numerical problems in the optimization algorithms and did not reflect the true performance of the method. The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites.

Algorithms↗
PubMed1997

An algorithm for numerical calculation of the k-space data-weighting for polarly sampled trajectories: application to spiral imaging.

Image reconstruction of data sampled into a non-uniform k-space grid requires appropriate data weighting and, for spiral-scan raw data, this weighting is usually calculated analytically under the assumption of uniform radial k-space sampling. This paper presents a simple and efficient algorithm for explicit numerical calculation of the data weighting for generalised polarly sampled k-space trajectories. The algorithm has been tested against both simulated data and data from experimental spiral-scan imaging and clearly provides significant improvements in image reconstruction when the radial uniformity of the k-space trajectory is poor.

Algorithms↗
PubMed2000

[Changes of learning and memory function under weightlessness or simulated weightlessness].

The work efficiency of astronauts has an intimate connection with the brain function state during space flight. The research results of the learning and memory mechanism of the brain in recent years were introduced. The effects of weightlessness or simulated weightlessness on brain's learning, memory, focused attention and many other higher neural activities and on the relative neural transmitters were summarized. Several research aspects were put forward in the future.

Aerospace Medicine↗
PubMed2004

A fourth-order accurate, Numerov-type, three-point finite-difference discretization of electrochemical reaction-diffusion equations on nonuniform (exponentially expanding) spatial grids in one-dimensional space geometry.

The validity for finite-difference electrochemical kinetic simulations, of the extension of the Numerov discretization designed by Chawla and Katti [J Comput Appl Math 1980, 6, 189-196] for the solution of two-point boundary value problems in ordinary differential equations, is examined. The discretization is adapted to systems of time-dependent reaction-diffusion partial differential equations in one-dimensional space geometry, on nonuniform space grids resulting from coordinate transformations. The equations must not involve first spatial derivatives of the unknowns. Relevant discrete formulae are outlined and tested in calculations on two example kinetic models. The models describe potential step chronoamperometry under limiting current conditions, for the catalytic EC, and Reinert-Berg CE reaction mechanisms. Exponentially expanding space grid is used. The discretization considered proves the most accurate and efficient, out of all the three-point finite-difference discretizations on such grids, that have been used thus far in electrochemical kinetics. Therefore, it can be recommended as a method of choice.

Journal Article↗
PubMed2003

Segmental dynamics of polymers in nanoscopic confinements, as probed by simulations of polymer/layered-silicate nanocomposites.

In this paper we review molecular modeling investigations of polymer/layered-silicate intercalates, as model systems to explore polymers in nanoscopically confined spaces. The atomic-scale picture, as revealed by computer simulations, is presented in the context of salient results from a wide range of experimental techniques. This approach provides insights into how polymeric segmental dynamics are affected by severe geometric constraints. Focusing on intercalated systems, i.e. polystyrene (PS) in 2 nm wide slit-pores and polyethylene-oxide (PEO) in 1 nm wide slit-pores, a very rich picture for the segmental dynamics is unveiled, despite the topological constraints imposed by the confining solid surfaces. On a local scale, intercalated polymers exhibit a very wide distribution of segmental relaxation times (ranging from ultra-fast to ultra-slow, over a wide range of temperatures). In both cases (PS and PEO), the segmental relaxations originate from the confinement-induced local density variations. Additionally, where there exist special interactions between the polymer and the confining surfaces ( e.g., PEO) more molecular mechanisms are identified.

Computer Simulation↗