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At least 1,639 records · Page 91Linked to original sources
PubMed2006

Multibaric-multithermal ensemble molecular dynamics simulations.

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.

Journal Article↗
PubMed2002

[Effects of weightlessness on baroreflex function].

The declination of baroreceptor reflex function is one of the important factor causing orthostatic intolerance after space flight. The change of baroreceptor reflex function during weightlessness and simulated weightlessness is introduced, and the influence of elevatory upper body blood pressure and electrolyte changes caused by weightlessness on baroreflex function are analyzed.

Baroreflex↗
PubMed2000

Finite-precision stationary states at and away from equilibrium

We study the precision dependence of equilibrium and nonequilibrium phase-space distribution functions for time-reversible dynamical systems simulated with finite, computational precision. The conservative and dissipative cases show different behavior, with substantially reduced period lengths in the dissipative case. The main effect of finite precision is to change the phase-space fraction occupied by the distributions. The convergence of thermodynamic averages is only slightly affected. We introduce and discuss a simple stochastic model which is nicely consistent with all of our numerical results. This model links the length of periodic orbits to the strange attractor's correlation dimension.

Journal Article↗
PubMed2005

Simulating nonequilibrium quantum fields with stochastic quantization techniques.

We present lattice simulations of nonequilibrium quantum fields in Minkowskian space-time. Starting from a nonthermal initial state, the real-time quantum ensemble in (3 + 1) dimensions is constructed by a stochastic process in an additional (5th) "Langevin-time." For the example of a self-interacting scalar field, we show how to resolve apparent unstable Langevin dynamics and compare our quantum results with those obtained in classical field theory. Such a direct simulation method is crucial for our understanding of collision experiments of heavy nuclei or other nonequilibrium phenomena in strongly coupled quantum many-body systems.

Journal Article↗
PubMed2001

Bed-rest studies for the International Space Station.

The microgravity experienced during space flight induces physiological changes that affect astronauts' health and performance. Simulations such as prolonged bed rest can mimic some of these changes and provide study conditions that are more accessible than during space flight itself. Previous studies, including several long and short-term bed-rest campaigns supported by ESA, have yielded significant medical data on the physiological changes induced by space flight. These data are being used extensively to study the effects of various countermeasures on those physiological changes.

Bed Rest↗
PubMed2001

Modelling space perception in human early vision: a computational approach.

A computational approach in studying vision is important for understanding the biological mechanisms, as well as for integrating the known cortical architecture of primary visual area (V1) and the physiological functions (some of them experimentally proved, some only presumed). We present, in parallel, two models for early vision mechanisms: one for obtaining the disparity map in stereo vision, and the other for edges enhancement in contour integration, both of them seen from such a computational perspective. We implemented the two models and the results of the simulation were consistent with the biological data. They also account for the importance of interactions between parallel channels of visual information processing.

Computer Simulation↗
PubMed1983

Classification of scattering objects by regular arrays of scatterers using Fourier analysis.

For a class of scattering objects the mean separation between the scatterers is determined. Over a range of frequencies, ultrasonic back-scattered pressure signals are recorded. It is suggested to derive the mean spacing of an unknown scattering object by employing Fourier analysis and comparing the signal with signals from known regular arrays of scatterers. In a computer simulation it is shown that this approach determines the mean spacing very well for random arrays consisting of three-dimensional spherical scatterers.

Fourier Analysis↗
PubMed2004

The spatial-temporal distribution of drought, wetting, and human cases of St. Louis encephalitis in southcentral Florida.

Using a dynamic hydrology model, we simulated land surface wetness conditions at 42 sites in 28 counties in southcentral Florida from 1990 to 1998 and compared these simulations with the incidence of human cases of St. Louis encephalitis (SLE) within these counties. Within counties, drought four months prior and wetting one-half month prior were significantly associated with human cases of SLE. Simulated land surface wetness conditions resolved transmission loci in both space and time, and May drought was significantly associated with the subsequent occurrence of human SLE cases. These findings are consistent with previous results associating simulated land surface wetness conditions with the transmission of SLE virus as measured in sentinel chickens, and support our working hypothesis that springtime drought facilitates SLE virus amplification in mosquito and wild bird populations.

Demography↗
PubMed2001

Monte Carlo simulation of electron beams from an accelerator head using PENELOPE.

The Monte Carlo code PENELOPE has been used to simulate electron beams from a Siemens Mevatron KDS linac with nominal energies of 6, 12 and 18 MeV. Owing to its accuracy, which stems from that of the underlying physical interaction models, PENELOPE is suitable for simulating problems of interest to the medical physics community. It includes a geometry package that allows the definition of complex quadric geometries, such as those of irradiation instruments, in a straightforward manner. Dose distributions in water simulated with PENELOPE agree well with experimental measurements using a silicon detector and a monitoring ionization chamber. Insertion of a lead slab in the incident beam at the surface of the water phantom produces sharp variations in the dose distributions, which are correctly reproduced by the simulation code. Results from PENELOPE are also compared with those of equivalent simulations with the EGS4-based user codes BEAM and DOSXYZ. Angular and energy distributions of electrons and photons in the phase-space plane (at the downstream end of the applicator) obtained from both simulation codes are similar, although significant differences do appear in some cases. These differences, however, are shown to have a negligible effect on the calculated dose distributions. Various practical aspects of the simulations, such as the calculation of statistical uncertainties and the effect of the 'latent' variance in the phase-space file, are discussed in detail.

Dose-Response Relationship, Radiation↗
PubMed2000

Laboratory evaluation of two bi-level toothbrush products for subgingival access and gingival margin cleaning.

Recent technological advances have enabled the production of split or feathered endings of individual toothbrush filaments. The purpose of this laboratory study was to compare a bi-level manual toothbrush containing standard end-rounded bristles with the same shaped toothbrush containing feathered filaments, 3 mm deep, on the outer raised bi-level rows to achieve subgingival access (SA) and remove artificial plaque at the gingival margin, or gingival margin cleaning (GMC). Simulated gingivae were prepared with a 0.2 mm space between the gingivae and tooth surface. The toothbrushes were aligned with the papillae at the gingival margin, and were tested using wet brushing conditions for 60 seconds at two strokes per second with a 15 mm stroke. Four toothbrushes of each type were evaluated four times, for a total of 16 assays per design. The SA maximum depth was recorded on pressure-sensitive paper under the simulated gingivae, and the length of gingival margin cleaning was recorded as the GMC efficacy. Readings were performed with 3x magnification by one investigator. In these laboratory assays, the bi-level toothbrush with feathered outer-row bristles significantly (p < 0.001) increased the ability of the bristles to achieve SA by 35.7% and GMC efficacy by 54.5% compared to an identical bi-level toothbrush with end-rounded bristles.

Dental Plaque↗
PubMedDate not supplied

A cell-based molecular transport simulator for pharmacokinetic prediction and cheminformatic exploration.

In the body, cell monolayers serve as permeability barriers, determining transport of molecules from one organ or tissue compartment to another. After oral drug administration, for example, transport across the epithelial cell monolayer lining the lumen of the intestine determines the fraction of drug in the gut that is absorbed by the body. By modeling passive transcellular transport properties in the presence of an apical to basolateral concentration gradient, we demonstrate how a computational, cell-based molecular transport simulator can be used to define a physicochemical property space occupied by molecules with desirable permeability and intracellular retention characteristics. Considering extracellular domains of cell surface receptors located on the opposite side of a cell monolayer as a drug's desired site of action, simulation of transcellular transport can be used to define the physicochemical properties of molecules with maximal transcellular permeability but minimal intracellular retention. Arguably, these molecules would possess very desirable features: least likely to exhibit nonspecific toxicity, metabolism, and side effects associated with high (undesirable) intracellular accumulation; and most likely to exhibit favorable bioavailability and efficacy associated with maximal rates of transport across cells and minimal intracellular retention, resulting in (desirable) accumulation at the extracellular site of action. Simulated permeability values showed good correlations with PAMPA, Caco-2, and intestinal permeability measurements, without "training" the model and without resorting to statistical regression techniques to "fit" the data. Therefore, cell-based molecular transport simulators could be useful in silico screening tools for chemical genomics and drug discovery.

Biological Availability↗
PubMed1998

In vitro comparison of beclomethasone and salbutamol metered-dose inhaler aerosols inhaled during pediatric tidal breathing from four valved holding chambers.

STUDY OBJECTIVES: To determine the amount of salbutamol or beclomethasone delivered from metered-dose inhalers (MDIs) in particle sizes appropriate for inhalational treatment with four common holding chambers (AeroChamber, OptiChamber, Space Chamber, E-Z Spacer) when used under simulated pediatric tidal breathing conditions. DESIGN: Five devices of each type were tested with salbutamol (100 microg, Glaxo-Wellcome) and beclomethasone (50 microg, Glaxo-Wellcome) MDIs. Each device was connected to face replicas representative of 7-month-old (infant), 2-year-old (toddler), and 4-year-old (child) children and aerosol inhaled into a cascade impactor (Anderson) using a valve system and simulated tidal breathing patterns representative of children of these ages. MEASUREMENTS AND RESULTS: Amounts of drug inhaled in fine particles varied significantly between devices and ages (p < 0.01), eg, for beclomethasone, from 4 microg (infant, Space Chamber) to 8 microg (toddler, OptiChamber), and for salbutamol, from 18 to 36 microg. The AeroChamber and OptiChamber behaved quite similarly, delivering more drug in the fine particles than the other two devices, and having insignificant variations in these amounts with age (p > 0.05). CONCLUSIONS: Amounts of drug inhaled in fine particles during pediatric tidal breathing from valved holding chambers are dependent on the holding chamber model, the drug used, and the breathing pattern, although dependence on the breathing pattern is relatively small for some of the devices tested.

Administration, Inhalation↗
PubMedDate not supplied

Human thermohomeostasis onboard "Mir" and in simulated microgravity studies.

Significant changes of thermogomeostatic parameters was obtained by thermotopometric method using the techniques simulate of microgravity effects: bed rest, pressurized isolation, suit immersion (SI). However, each of ground models made rectal temperature (T) trend downward. The autothermometric study (24 and 12 sessions, 2-13th and 6-174th flight days) was carried out onboard "Mir" by two flight engineers who had preliminary tested at SI (1-2 days). Studies of German investigators onboard "Mir" confirmed: rectal T must be higher in space flight as compared to the normal environment (n=4). Comparative studies suggest that microgravity is a key factor for the human body surface T raise and abolishment of the external/internal T-gradient. T-homeostasis was not really changing during missions and could be regarded as acute effect of microgravity. After delineation of changes in body surface T--by Carnot's thermodynamic law--rectal T raise should have been anticipated. Facts pointing to the excess entropy of human body must not be passed over.

Adaptation, Physiological↗
PubMedDate not supplied

A k nearest neighbour test for space-time interaction.

This paper describes a k nearest neighbour statistic sensitive to the pattern of cases expected of space-time clusters of health events. The Knox and Mantel tests are frequently used for space-time clustering but have two disadvantages. First, the selection of critical space-time distances for the Knox test and of a data transformation for the Mantel test is subjective. Second, the Mantel statistic is the sum of the products of space and time distances, is linear in form, and is not sensitive to non-linear associations between small space and time distances expected of contagious processes. The k nearest neighbour statistic is the number of case pairs that are k nearest neighbours in both space and time, and is evaluated under the null hypothesis of independent space and time nearest neighbour relationships. The test was applied to simulated and real data and compared to the Knox and Mantel tests using statistical power comparisons. The k nearest neighbour test proved sensitive to the space-time interaction pattern expected of disease clusters, does not require parameters (such as critical distances) to be estimated from the data, and may be used to test hypotheses about the spatial and temporal scale of the cluster process. The method addresses significant weaknesses in existing space-time cluster tests and should prove useful in the quantification and evaluation of clusters of human health events. Additional research is needed to further document the power of the test under different cluster processes.

Censuses↗
PubMed2005

Elastically coupled two-dimensional Brownian motors.

Many workers have theoretically and numerically studied Brownian motors (ratchet models) as models for molecular motors for many years. Their studies have been mainly concerned about one-dimensional motion of a particle or coupled particles experiencing spatially asymmetric interaction force. In this paper, we introduce a coupled flashing ratchet model, that is, elastically coupled Brownian particles with their own easily advancing directions under the on-and-off (or occasional) influence of two-dimensional interaction force asymmetric in the easily advancing direction of each particle. The dynamics of the model is investigated by computer simulation and characteristic motion of the particles in the two-dimensional space is observed. Our model is also studied as that for molecular motors in muscle contraction and the simulation results are compared with those of in vitro biological experiments in motility assays of the molecular motors. We succeed in reproducing the experimental results qualitatively with our model.

Colloids↗
PubMedDate not supplied

Comparison of local grid refinement methods for MODFLOW.

Many ground water modeling efforts use a finite-difference method to solve the ground water flow equation, and many of these models require a relatively fine-grid discretization to accurately represent the selected process in limited areas of interest. Use of a fine grid over the entire domain can be computationally prohibitive; using a variably spaced grid can lead to cells with a large aspect ratio and refinement in areas where detail is not needed. One solution is to use local-grid refinement (LGR) whereby the grid is only refined in the area of interest. This work reviews some LGR methods and identifies advantages and drawbacks in test cases using MODFLOW-2000. The first test case is two dimensional and heterogeneous; the second is three dimensional and includes interaction with a meandering river. Results include simulations using a uniform fine grid, a variably spaced grid, a traditional method of LGR without feedback, and a new shared node method with feedback. Discrepancies from the solution obtained with the uniform fine grid are investigated. For the models tested, the traditional one-way coupled approaches produced discrepancies in head up to 6.8% and discrepancies in cell-to-cell fluxes up to 7.1%, while the new method has head and cell-to-cell flux discrepancies of 0.089% and 0.14%, respectively. Additional results highlight the accuracy, flexibility, and CPU time trade-off of these methods and demonstrate how the new method can be successfully implemented to model surface water-ground water interactions.

Computer Simulation↗
PubMed2005

Molecular simulations for the conformational assessment of a porphyrin-fullerene dyad in different environments.

Conformational space of a porphyrin-fullerene dyad with the donor and acceptor connected by a relatively flexible linker is studied by molecular dynamics simulations in both non-polar and polar solvents, as well as in vacuum. The most probable conformations obtained from the vacuum MD simulations were optimized with semi-empirical (SE) and density functional theory (DFT) methods and the extent of the structural changes is assessed. The computational results indicate the co-existence of different conformers in both polar and nonpolar solvents showing agreement with experimental results. The most probable vacuum conformations at 300 K are similar to the ones at 0 K, while the structures most often observed in the solvents show less compact conformations. Optimization with SE and DFT calculations leads to structures, which represent relatively well the folded conformations in solvent, which validates the electronic structure calculations relevant to describing photoinduced electron-transfer in H2P-O34-C60.

Computer Simulation↗