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At least 1,153 records · Page 64Linked to original sources
PubMed2006

Finding a picture's station point: reconstructing virtual space when the usual way will not work.

To reconstruct the space represented in a photograph or other picture made in perspective, its vantage point, or station point, must first be found, and the usual way to find this point requires that the picture show a rectilinear grid or at least one grid element. The station points of the many pictures that lack any such grid may be found by a new method presented here, on two conditions: The line of sight, from the original observer to the scene, must be determinable, and, within the scene, there must be at least one quantitative spatial relation involving both a depth extent and an extent laterally (breadth or height), the 3-D value of which is known. Researchers may use either the graphic (projective) or the computational (algebraic) procedures of this new "sightline" method, in reconstructing the spaces of pictures used as stimuli.

Art↗
PubMed2006

Effectiveness of iterative algorithms in recovering phase in the presence of noise.

Inversion of coherent X-ray diffraction patterns allows the imaging of three-dimensional density distributions. The recovery of such shapes often requires application of iterative algorithms, such as Fienup's error reduction or hybrid input/output. Since the measurement of such a pattern records the intensity in reciprocal space, any errors due to noise will probably not have a straightforward impact on the final real-space result. In this paper, the effect of the types of noise common in coherent X-ray diffraction (CXD) experiments, counting statistics, scatter from alien particles and detector noise, on the recovered real-space density projection is explored by simulating a two-dimensional CXD pattern and adding noise. It is found that an R factor measuring the reproducibility between the best and second-best real-space result is a leading indicator of performance.

Algorithms↗
PubMed2005

Stochastic discrete event simulation of germinal center reactions.

We introduce a generic reaction-diffusion model for germinal center reactions and perform numerical simulations within a stochastic discrete event approach. In contrast to the frequently used deterministic continuum approach, each single reaction event is monitored in space and time in order to simulate the correct time evolution of this complex biological system. Germinal centers play an important role in the immune system by performing a reaction that aims at improving the affinity between antibodies and antigens. Our model captures experimentally observed features of this reaction, such as the development of the remarkable germinal center morphology and the maturation of antibody-antigen affinity in the course of time. We model affinity maturation within a simple affinity class picture and study it as a function of the distance between the initial antibody-antigen affinity and the highest possible affinity. The model reveals that this mutation distance may be responsible for the experimentally observed all-or-none behavior of germinal centers; i.e., they generate either mainly output cells of high affinity or no high-affinity output cells at all. Furthermore, the exact simulation of the system dynamics allows us to study the hypothesis of cell recycling in germinal centers as a mechanism for affinity optimization. A comparison of three possible recycling pathways indicates that affinity maturation is optimized by a recycling pathway that has previously not been taken into account in deterministic continuum models.

Animals↗
PubMed2001

A virtual environment for simulated rat dissection.

Animal dissection for the scientific examination of organ subsystems is a delicate procedure. Performing this procedure under the complex environment of microgravity presents additional challenges because of the limited training opportunities available that can recreate the altered gravity environment. Traditional crew training often occurs several months in advance of experimentation, provides limited realism, and involves complicated logistics. We have developed an interactive virtual environment that can simulate several common tasks performed during animal dissection. In this paper, we describe the imaging modality used to reconstruct the rat in virtual space, provide an overview of the simulation environment and briefly discuss some of the techniques used to manipulate the virtual rat.

Animals↗
PubMed2004

Modeling intra-crown and intra-canopy interactions in red maple: assessment of light transfer on carbon dioxide and water vapor exchange.

Daily and seasonal net photosynthesis (Anet), transpiration (E), absorbed photosynthetically active radiation (Qa) and light-use efficiency (epsilonc) in a red maple container nursery were simulated with MAESTRA, a three-dimensional canopy model. Effects of canopy heterogeneity were simulated by imposing changes in crown spacing. The light transfer sub-model, a distribution model of incident, direct, diffuse and scattered radiation within MAESTRA, was validated against field measurements of light interception on an intra-crown scale. In the container nursery, we found that a fiber-optic-based method of integrating photosynthetically active radiation (Q) was more suitable for crown-layer light transfer measurements and adjustments than either orthogonal line or individual quantum sensor measurements. The model underestimated intercepted Q by 9.3, 18 and 11.1% for crown layers 1, 2 and 3, respectively; however, there were linear relationships between model estimates and observations made with each of the three measurement methods. We used the validated and parameterized light transfer model to assess intra-crown and intra-canopy light transfer on a layer, crown and canopy basis, and investigated effects of tree size ratio and tree spacing interactions on Anet, E, Qa and epsilonc in the container nursery. Heterogeneous crown and canopy photosynthesis were predicted to exceed values for a uniform canopy under space-limiting conditions. Tree size ratio had large effects on Anet, E, Qa and epsilonc when light to lower-canopy layers was limited by inadequate space between crowns. Increasing Qa at lower-crown layers had the largest impact on whole-crown and whole-canopy Anet, E, Qa and epsilonc. Increases in canopy productivity led to increased water use. Simulations of heterogeneous stands with adequate soil water indicated that light absorption is maximized under space-limiting conditions as a canopy crown moves toward heterogeneity. Nursery and plantation productivity per unit land area was optimized by tactical placement of trees of several sizes, but this was accompanied by increased canopy water use.

Acer↗
PubMed2005

Coexistence of 1,3-butadiene conformers in ionization energies and Dyson orbitals.

The minimum-energy structures on the torsional potential-energy surface of 1,3-butadiene have been studied quantum mechanically using a range of models including ab initio Hartree-Fock and second-order Møller-Plesset theories, outer valence Green's function, and density-functional theory with a hybrid functional and statistical average orbital potential model in order to understand the binding-energy (ionization energy) spectra and orbital cross sections observed by experiments. The unique full geometry optimization process locates the s-trans-1,3-butadiene as the global minimum structure and the s-gauche-1,3-butadiene as the local minimum structure. The latter possesses the dihedral angle of the central carbon bond of 32.81 degrees in agreement with the range of 30 degrees-41 degrees obtained by other theoretical models. Ionization energies in the outer valence space of the conformer pair have been obtained using Hartree-Fock, outer valence Green's function, and density-functional (statistical average orbital potentials) models, respectively. The Hartree-Fock results indicate that electron correlation (and orbital relaxation) effects become more significant towards the inner shell. The spectroscopic pole strengths calculated in the Green's function model are in the range of 0.85-0.91, suggesting that the independent particle picture is a good approximation in the present study. The binding energies from the density-functional (statisticaly averaged orbital potential) model are in good agreement with photoelectron spectroscopy, and the simulated Dyson orbitals in momentum space approximated by the density-functional orbitals using plane-wave impulse approximation agree well with those from experimental electron momentum spectroscopy. The coexistence of the conformer pair under the experimental conditions is supported by the approximated experimental binding-energy spectra due to the split conformer orbital energies, as well as the orbital momentum distributions of the mixed conformer pair observed in the orbital cross sections of electron momentum spectroscopy.

Butadienes↗
PubMed1992

A model of radiation conditions during spacecraft flights in the interplanetary space and in the Earth's magnetosphere.

Based on the available measurement data, simulations of radiation conditions during spacecraft flights in the interplanetary space and in the Earth's and Jupiter's radiation belts has been carried out. The > or = 10 MeV and > or = 30 MeV solar flare proton fluence forecast has been proposed for Cycle 22. Radiation conditions due to both magnetospheric electrons and protons and to solar flare protons, magnetic rigidity cutoff being taken into account, have been evaluated on spacecraft trajectories in the Earth's and Jupiter's magnetospheres.

Cosmic Radiation↗
PubMed1985

[Circulatory and hormonal changes induced by microgravity].

The absence (or decrease) of the hydrostatic pressure during space flights (microgravity state) or simulations of weightlessness (by immersion, bed rest or head-down tilt) result in a body fluid shift and an engorgement of the central circulation where mechanoreceptors involved in plasma volume regulation are located. Their activation induces the initial (first hours) hormonal response with a decrease in plasma vasopressin, renin and aldosterone and probably an increase in a natriuretic factor (Gauer reflex). Prolonged exposure to microgravity leads to more complex and often hypothetical responses: cardiovascular deconditioning, modifications in secretion and circadian rhythms of above cited hormones. After 24 years of studies on approximately 200 astronauts our knowledge of cardiovascular and hormonal adaptation to space flight is still at the beginning.

Adaptation, Physiological↗
PubMed2001

Excluded volume in protein side-chain packing.

The excluded volume occupied by protein side-chains and the requirement of high packing density in the protein interior should severely limit the number of side-chain conformations compatible with a given native backbone. To examine the relationship between side-chain geometry and side-chain packing, we use an all-atom Monte Carlo simulation to sample the large space of side-chain conformations. We study three models of excluded volume and use umbrella sampling to effectively explore the entire space. We find that while excluded volume constraints reduce the size of conformational space by many orders of magnitude, the number of allowed conformations is still large. An average repacked conformation has 20 % of its chi angles in a non-native state, a marked reduction from the expected 67 % in the absence of excluded volume. Interestingly, well-packed conformations with up to 50 % non-native chi angles exist. The repacked conformations have native packing density as measured by a standard Voronoi procedure. Entropy is distributed non-uniformly over positions, and we partially explain the observed distribution using rotamer probabilities derived from the Protein Data Bank database. In several cases, native rotamers that occur infrequently in the database are seen with high probability in our simulation, indicating that sequence-specific excluded volume interactions can stabilize rotamers that are rare for a given backbone. In spite of our finding that 65 % of the native rotamers and 85 % of chi(1) angles can be predicted correctly on the basis of excluded volume only, 95 % of positions can accommodate more than one rotamer in simulation. We estimate that, in order to quench the side-chain entropy observed in the presence of excluded volume interactions, other interactions (hydrophobic, polar, electrostatic) must provide an additional stabilization of at least 0.6 kT per residue in order to single out the native state.

Algorithms↗
PubMed2002

Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations.

The free energy landscapes of peptide conformations were calibrated by ab initio quantum chemical calculations, after the enhanced conformational diversity search using the multicanonical molecular dynamics simulations. Three different potentials of mean force for an isolated dipeptide were individually obtained by the multicanonical molecular dynamics simulations using the conventional force fields, AMBER parm94, AMBER parm96, and CHARMm22. Each potential of mean force was then calibrated based upon the umbrella sampling algorithm from the adiabatic energy map that was calculated separately by the ab initio molecular orbital method, and all of the calibrated potentials of mean force coincided well. The calibration method was also applied to the simulations of a peptide dimer in explicit water models, and it was shown that the calibrated free energy landscapes did not depend on the force field used in the classical simulations, as far as the conformational space was sampled well. The current calibration method fuses the classical free energy calculation with the quantum chemical calculation, and it should generally make simulations for biomolecular systems much more reliable when combining with enhanced conformational sampling.

Models, Molecular↗
PubMed1988

Software systems to control sensitivity studies of Monte Carlo simulation models.

Studies of the sensitivity of Monte Carlo models to changes in the values of their features involve repetitive simulations. Subsequent displays and analyses express variation in simulated outcomes as a function of change in location in multidimensional feature space and provide feedback via inputs for future simulations. A software system has been designed to control execution of the interacting programs required, reducing the need for human intervention. Assumptions about the goals and operation of the system as a whole are isolated within a program which executes component packages using interprogram control and communication mechanisms. The latter allow component programs to operate independently of the sources of data or the execution environment: they may be used separately, or in software systems, such as for sensitivity analysis of a Monte Carlo epidemic model. The methodology contributes to modularity at the level of executable programs and to the plausibility and efficiency of sensitivity studies.

Computer Simulation↗
PubMed1994

Effect of interseed spacing, tissue perfusion, thermoseed temperatures and catheters in ferromagnetic hyperthermia: results from simulations using finite element models of thermoseeds and catheters.

Finite element heat-transfer models of ferromagnetic thermoseeds and catheters are developed for simulating ferromagnetic hyperthermia. These models are implemented into a general purpose, finite element computer program to solve the bioheat transfer equation. The seed and catheter models are unique in that they have fewer modeling constraints than other previously developed thermal models. Simulations are conducted with a 4 x 4 array of seeds in a multicompartment tissue model. The heat transfer model predicts that fractions of tumor greater than 43 degrees C are between 8 and 40% lower when seed temperatures depend on power versus models which assume a constant seed temperature. Fractions of tumor greater than 42 degrees C, in simulations using seed and catheter models, are between 3.3 and 25% lower than in simulations with bare seeds. It is demonstrated that an array of seeds with Curie points of 62.6 degrees C heats the tumor very well over nearly all blood perfusion cases studied. In summary, results herein suggest that thermal models simulating ferromagnetic hyperthermia should consider the power-temperature dependence of seeds and include explicit models of catheters.

Catheterization↗
PubMedDate not supplied

Simulations of a fox-rabies epidemic on an island using space-time finite elements.

The two-dimensional reaction diffusion equations for the spread of rabies in a logistically growing fox population are solved numerically. The method, based upon Galerkin's approach, uses space-time finite elements. The numerical model is shown, quantitatively, to possess the essential features of earlier one and two-dimensional models and to reproduce the values of field data accurately. A more realistic illustration of the use of the model, a study of the spread of rabies over the Isle of Anglesey, is then discussed.

Animals↗
PubMed1999

Visualizing integrated bioprocess designs through "windows of operation".

This paper demonstrates a simple graphical approach for the design and analysis of a bioprocess flowsheet in which process interactions are significant. Results are presented showing how the feasible space for operation can be simulated and used both to address key design and operating decisions and to identify suitable trade-offs between operating variables, such as fermentation growth rate and disruption conditions, in order to achieve prespecified levels of process performance. Using verified models to describe the production and isolation of an intracellular protein alcohol dehydrogenase (ADH) in yeast as a test bed, a series of so-called "windows of operation" are developed at growth rates in the range of 0.06-0.28 h(-1) and for a range of overall process specifications. The effects of altering the process design performance specification as defined by the level of cell debris removal and the overall process productivity on the size and position of the feasible space were investigated to demonstrate the sensitivity of the flowsheet to changes in process objectives. Using the approach it has been possible to visualise the processing trade-offs required to increase performance in terms of the level of cell debris removal by 50% and the overall process productivity by 400% from a defined base level. The approach provides a convenient tool when designing integrated bioprocesses by enabling process options to be compared visually and can help in achieving better process designs and accelerating process development for the biological process industry.

Alcohol Dehydrogenase↗
PubMed1998

Launch conditions might affect the formation of blood vessels in the quail chorioallantoic membrane.

As a part of the first joint USA-Russian MIR/Shuttle program, fertilized quail eggs were flown on the MIR 18 mission. Post-flight examination indicated impaired survival of both the embryos in space and also of control embryo exposed to vibrational and g-forces simulating the condition experienced during the launch of Progress 227. We hypothesized that excess mechanical forces and/or other conditions during the launch might cause abnormal development or the blood supply in the chorioallantoic membrane (CAM) leading to the impaired survival of the embryos. The CAM, a highly vascularized extraembryonic organ, provides for the oxygen exchange across the egg shell and is thus pivotal for proper embryonic development. To test our hypothesis, we compared angiogenesis in CAMs of eggs which were either exposed to the vibration and g-force profile simulating the conditions at launch of Progress 227 (synchronous controls), or kept under routine conditions in a laboratory incubator (laboratory controls). At various time points during incubation, the eggs were fixed in paraformaldehyde for subsequent dissection. At the time of dissection, the CAM was carefully lifted from the egg shell and examined as whole mounts by bright-field and fluorescent microscopy. The development of the vasculature (angiogenesis) was assessed from the density of blood vessels per viewing field and evaluated by computer aided image analysis. We observed a significant decrease in blood-vessel density in the synchronous controls versus "normal" laboratory controls beginning from day 10 of incubation. The decrease in vascular density was restricted to the smallest vessels only, suggesting that conditions during the launch and/or during the subsequent incubation of the eggs may affect the normal progress of angiogenesis in the CAM. Abnormal angiogensis in the CAM might contribute to the impaired survival of the embryos observed in synchronous controls as well as in space.

Allantois↗
PubMed1994

Postural reactions of circulation and its regulation during simulated weightlessness.

The extention and intensification of space exploration the influence of weightlessness on human organism and the formation of a new level of adaptation. The studies of blood circulation is very important because of frequent occurrence of cardiovascular disorders in the middle age subjects. In connection with extension and intensification of space exploration the influence of weightlessness on human organism and the formation of a new level of adaptation mechanisms acquires a special significance. The data obtained in recently undertaken model experiments and also during space flights indicate that weightlessness in many ways affects various physiological systems of organism, and first of all cardiovascular system with the development of reflex, humeral and metabolic reactions. It also indicates, that the changes in functioning of cardiovascular system brings about the disruption of its regular responses, which is foremost expressed in decreased antigravitational response, which manifests itself in lowered orthostatic stability. It is worth mentioning, that the changes during previous investigations of haemodynamics were mainly carried out with the subjects under forty, therefore age related specific features of blood circulation system response are described in a few articles. The studies of the kind are especially important because of frequent occurrence of cardiovascular disorders such as heart and brain vessels atherosclerosis, hypertension in the middle age, which can to a great extent complicate and affect the "acute" period of adaptation to weightlessness and readaptation process.

Adaptation, Physiological↗
PubMed1986

Simulation of the metabolism and enterohepatic circulation of endogenous chenodeoxycholic acid in man using a physiological pharmacokinetic model.

The metabolism and enterohepatic circulation of chenodeoxycholic acid (CDC), a major primary bile acid in man, has been stimulated using a multicompartmental physiological pharmacokinetic model which was previously reported and used to simulate the metabolism of cholic acid. The model features compartments and linear transfer coefficients. Compartments, which are defined as the pools of single chemical species in well defined anatomical volumes, are aggregated into nine 'spaces' based on anatomical and physiological considerations (liver, gall-bladder, bile ducts, duodeno-jejunum, ileum, colon, portal blood, sinusoidal blood, and general circulation). Each space contains several compartments which correspond to the compounds present in that space, for example, the compound in question and its biotransformation products. For CDC (as for cholic acid in the previous simulation) each space contains three compartments corresponding to the unconjugated bile acid, its glycine amidate, and its taurine amidate. Transfer coefficients, which denote the fractional amount of the compartment's contents exiting per unit time, are categorized according to function: flow, for example gall-bladder contraction (which involves transfer of all substances contained in the space at the same fractional rate); biotransformation (which transfers the substrate from one compartment to another within the same space); or transport (which denotes movements between contiguous compartments, belonging to different spaces across a diffusion membrane or a cellular barrier). The model is made time-dependent by incorporating meals which trigger gall-bladder emptying and modify intestinal flow. The transfer coefficients in the cholic acid model were modified for the CDC model since there is indirect evidence that CDC amidates (probably chenodeoxycholylglycine) are absorbed from the duodeno-jejunum and the first pass hepatic clearance of CDC species differs from that of cholyl species. The model was then used with all existing experimental data to simulate CDC metabolism in healthy humans over a 24-h period during which three meals were ingested. Satisfactory agreement was obtained between simulated and experimental data indicating that this model continues to be useful for describing the metabolism of bile acids and may also be of value for describing the metabolism of drugs whose metabolism is similar to that of bile acids.

Bile Acids and Salts↗
PubMed1997

Simulation of the conformation and dynamics of a double-helical model for DNA.

We propose a partially flexible, double-helical model for describing the conformational and dynamic properties of DNA. In this model, each nucleotide is represented by one element (bead), and the known geometrical features of the double helix are incorporated in the equilibrium conformation. Each bead is connected to a few neighbor beads in both strands by means of stiff springs that maintain the connectivity but still allow for some extent of flexibility and internal motion. We have used Brownian dynamics simulation to sample the conformational space and monitor the overall and internal dynamics of short DNA pieces, with up to 20 basepairs. From Brownian trajectories, we calculate the dimensions of the helix and estimate its persistence length. We obtain translational diffusion coefficient and various rotational relaxation times, including both overall rotation and internal motion. Although we have not carried out a detailed parameterization of the model, the calculated properties agree rather well with experimental data available for those oligomers.

Biophysical Phenomena↗