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PubMed1991

Solution conformations of the gamma-carboxyglutamic acid domain of bovine prothrombin fragment 1, residues 1-65.

Molecular dynamics simulations have been performed (AMBER version 3.1) on solvated residues 1-65 of bovine prothrombin fragment 1 (BF1) by using the 2.8-A resolution crystallographic coordinates as the starting conformation for understanding calcium ion-induced conformational changes that precede experimentally observable phospholipid binding. Simulations were performed on the non-metal-bound crystal structure, the form resulting from addition of eight calcium ions to the 1-65 region of the crystal structure, the form resulting from removal of calcium ions after 107 ps and continuing the simulation, and an isolated hexapeptide loop (residues 18-23). In all cases, the 100-ps time scale seemed adequate to sample an ensemble of solution conformers within a particular region of conformation space. The non-metal-containing BF1 did not unfold appreciably during a 106-ps simulation starting from the crystallographic geometry. The calcium ion-containing structure (Ca-BF1) underwent an interesting conformational reorganization during its evolution from the crystal structure: during the time course of a 107-ps simulation, Ca-BF1 experienced a trans----cis isomerization of the gamma-carboxyglutamic acid-21 (Gla-21)-Pro-22 peptide bond. Removal of the calcium ions from this structure followed by 114 ps of additional molecular dynamics showed significant unfolding relative to the final 20-ps average structure of the 107-ps simulation; however, the Gla-21-Pro-22 peptide bond remained cis. A 265-ps simulation on the termini-protected hexapeptide loop (Cys-18 to Cys-23) containing two calcium ions also did not undergo a trans----cis isomerization. It is believed that the necessary activation energy for the transitional event observed in the Ca-BF1 simulation was largely supplied by global conformational events with a possible assist from relief of intermolecular crystal packing forces. The presence of a Gla preceding Pro-22, the inclusion of Pro-22 in a highly strained loop structure, and the formation of two long-lived salt bridges prior to isomerization may all contribute to this finding.

1-Carboxyglutamic Acid↗
PubMed1999

Competition and dispersal in predator-prey waves.

Dispersing predators and prey can exhibit complex spatio-temporal wave-like patterns if the interactions between them cause oscillatory dynamics. We study the effect of these predator-prey density waves on the competition between prey populations and between predator populations with different dispersal strategies. We first describe 1- and 2-dimensional simulations of both discrete and continuous predator-prey models. The results suggest that any population that diffuses faster, disperses farther, or is more likely to disperse will exclude slower diffusing, shorter dispersing, or less likely dispersing populations, everything else being equal. It also appears that it does not matter whether time, space, or state are discrete or continuous, nor what the exact interactions between the predators and prey are. So long as waves exist the competition between populations occurs in a similar fashion. We derive a theory that qualitatively explains the observed behaviour and calculate approximate analytical solutions that describe, to a reasonable extent, these behaviours. Predictions about the cost of dispersal are tested. If strong enough, cost can reverse the populations' relative competitive strengths or lead to coexistence because of the effect of spiral wave cores. The theory is also able to explain previous results of simulations of coexistence in host-parasitoid models (Comins, H. N., and Massell, M. P., 1996, J. Theor. Biol. 183, 19-28).

Animals↗
PubMed1999

What are the conditions for exponential time-cubed echo decays?

Diffusion of precessing spins through a constant field gradient is well-known to produce two distinctive features: an exp(-bt(3)) decay of the echo amplitude in response to two pulses and a much slower decay of the Carr-Purcell echo train. These features will appear whenever the spin frequency is described by a continuous random-walk. The present work shows that this may also occur in the presence of motions with long correlation times tau(c)-continuous Gaussian frequency noise with an exponential autocorrelation has the correct properties over time durations smaller than tau(c). Thus, time-cubed echo decays will occur in situations other than physical diffusion. The decay rate of the Carr-Purcell echo train is shown to vary with the pulse spacing tau whenever the correlation time tau(c) is long; the slower Carr-Purcell decay compared to the two-pulse echo decay is not unique to diffusion. Simulations are presented that display time-cubed decays. The simulations confirm two important criteria: the echo time must be less than tau(c) and the frequency noise must consist of nearly continuous variations, as opposed to step-like changes. These criteria define the range of physical parameters for which time-cubed decays will be observable.

Computer Simulation↗
PubMed1993

Evolutionary games and computer simulations.

The Prisoner's Dilemma has long been considered the paradigm for studying the emergence of cooperation among selfish individuals. Because of its importance, it has been studied through computer experiments as well as in the laboratory and by analytical means. However, there are important differences between the way a system composed of many interacting elements is simulated by a digital machine and the manner in which it behaves when studied in real experiments. In some instances, these disparities can be marked enough so as to cast doubt on the implications of cellular automata-type simulations for the study of cooperation in social systems. In particular, if such a simulation imposes space-time granularity, then its ability to describe the real world may be compromised. Indeed, we show that the results of digital simulations regarding territoriality and cooperation differ greatly when time is discrete as opposed to continuous.

Animals↗
PubMed1996

Computational fluid mechanical study of the convective heat transfer in a closed space simulating an infant incubator.

The uneven distribution of the ambient temperature in a model of an infant incubator was demonstrated using the computational fluid mechanical (CFM) simulation of the air flow. A finite volume method of CFM calculation was performed on a three-dimensional (3D) model of an infant incubator including a model baby. The time course of the temperature distribution was computed solving the heat transfer equations simultaneously with the momentum equations. An uneven temperature distribution was observed for a long period (60 s) after the warm inflow was introduced into the incubator chamber. The temperature distribution was complex in 3D space and unsteady even after a long time, suggesting that it may take a considerable time to settle and may continue to be unsteady even if the inflow velocity is steady.

Computer Simulation↗
PubMed2006

Configurational-bias sampling technique for predicting side-chain conformations in proteins.

Prediction of side-chain conformations is an important component of several biological modeling applications. In this work, we have developed and tested an advanced Monte Carlo sampling strategy for predicting side-chain conformations. Our method is based on a cooperative rearrangement of atoms that belong to a group of neighboring side-chains. This rearrangement is accomplished by deleting groups of atoms from the side-chains in a particular region, and regrowing them with the generation of trial positions that depends on both a rotamer library and a molecular mechanics potential function. This method allows us to incorporate flexibility about the rotamers in the library and explore phase space in a continuous fashion about the primary rotamers. We have tested our algorithm on a set of 76 proteins using the all-atom AMBER99 force field and electrostatics that are governed by a distance-dependent dielectric function. When the tolerance for correct prediction of the dihedral angles is a <20 degrees deviation from the native state, our prediction accuracies for chi1 are 83.3% and for chi1 and chi2 are 65.4%. The accuracies of our predictions are comparable to the best results in the literature that often used Hamiltonians that have been specifically optimized for side-chain packing. We believe that the continuous exploration of phase space enables our method to overcome limitations inherent with using discrete rotamers as trials.

Bias↗
PubMed1999

[Electron microscopic analysis of particles from surgical gloves and their possible introduction into the epidural space during epidural anesthesia].

OBJECTIVE: Many publications have linked surgical glove powder to inflammatory reactions of the peritoneum, pleura, pericardium and meninges. Accidental contamination may also increase the likelihood of complications after spinal and epidural anesthesia. We aimed to analyze the morphological characteristics of microscopic particles adhering to surgical gloves and to analyze how likely such particles are to enter the epidural space during catheterization. MATERIAL AND METHOD: One hundred epidural catheters were studied in two groups (A and B) of 50. Group A catheters contained stylettes and the distal ends were open (Vygon). Group B catheters contained no stylettes and had closed distal ends and three side openings (Becton Dickinson). Continuous epidural anesthesia was simulated with half the catheters in each group (25) by touching the distal end of each line with the gloves and later inserting the catheter through a Tuohy needle. All catheters--those used in the simulation as well as the untouched ones--were then examined under a scanning electron microscope. The particles on the internal and external surfaces of the gloves had previously been identified under a microscope and analyzed by X-ray diffraction. RESULTS: Gloves: external glove surfaces carried particles measuring between 3 and 4 mu; their morphology was consistent with calcium carbonate. On internal surfaces we found larger particles, between 11 and 14 mu in diameter, shaped differently and of smooth appearance. Analysis of the latter showed them to contain traces of magnesium and to have characteristics consistent with organic molecules. The particles of one surface were never observed on the other. Catheters: the non-manipulated catheters in both groups contained no free particles matching those described above, whereas the outside surfaces of the catheters in contact with gloves contained particles consistent with those of external glove surfaces. The number of particles per square millimeter of surface was 2,598 (95% CI 2,200 to 2,900) in group A catheters and 2,340 (95% CI 2,000 to 2,600) in the group B catheters (p = NS). The differences in the number of particles adhering to catheters touched by gloves and those that had not been manipulated were statistically significant (p < 0.001). CONCLUSIONS: Particles adhering to gloves can be drawn into the epidural space during continuous epidural anesthesia. All unnecessary manipulation should therefore be avoided, and the portion of the catheter to be inserted into the epidural space should not be touched in order to prevent possible nonspecific meningeal inflammatory responses.

Anesthesia, Epidural↗
PubMed2001

Elastic properties of Sierpinski-like carpets: finite-element-based simulation.

The elastic properties of two-dimensional continuous composites of fractal structures are studied with the set of Sierpinski-like carpets filled by voids or rigid inclusions. The effective elastic moduli of these carpets are calculated numerically using the finite-element and position-space renormalization group techniques. The fixed-point problem is analyzed by flow diagrams in the plane of the current Poisson ratios and coefficients of anisotropy of the composites. It is found that in the general case the effective elastic moduli asymptotically approach a power-law behavior. Moreover, the common exponent characterizes the scaling behavior of each component of the elastic modulus tensor of a definite carpet. The values of the scaling exponents and positions of the fixed points are shown to be independent of the elastic properties of the host and depend significantly on the fractal dimension of the composite.

Journal Article↗
PubMed2001

[Development of food rations for humans in extreme environments].

Adequacy of food rations to the human body demands was assessed in three series of investigations with 73 volunteers. The first series (n = 31) was arranged in various climatic-geographic areas (the Arctic, desert, high altitude, and the moderate climate of Russia). Each test continued for 12 days. Energy value of the food ration made up 3560 kilocalories. The second and third series (n = 12 and n = 30, respectively) were performed in a pressurized module with simulation of some extreme factors of space flight. Energy value of the food ration balanced in the content of staple nutrients varied between 2800 and 3500 kcal. Results of physical-hygienic studies suggest adequacy of the proposed food rations to volunteers' physiological demands for nutrients and energy in various extreme conditions.

Altitude↗
PubMed2000

Modeling contact networks and infection transmission in geographic and social space using GERMS.

BACKGROUND: Stochastic models of discrete individuals and deterministic models of continuous populations may give different answers to questions about infectious diseases. GOAL: Discrete individual model formulations are sought that extend deterministic models of infection transmission systems so that both model forms contribute cooperatively to model-based decision making. STUDY DESIGN: GERMS models are defined as stochastic processes in continuous time with parameters analogous to those in deterministic models. A GERMS model simulator was developed that insured that the rate of events depended only on the current state of model. RESULTS: The confidence intervals of long-term averages of infection level in simulated GERMS models were shown to contain the deterministic model means. CONCLUSION: GERMS models provide a convenient framework for testing the sensitivity of model-based decisions to a variety of unrealistic assumptions that are characteristic of differential equation models. GERMS especially facilitates making more realistic assumptions about contact patterns in geographic and social space.

Humans↗
PubMed1993

Mathematical analysis and computer simulation of the respiratory system in the newborn infant.

A mathematical model of neonatal respiratory control is proposed which can be used to stimulate the system under different physiological conditions. The model consists of a continuous plant and a discrete controller. Included in the plant are lungs, body tissue, brain tissue, a cerebrospinal fluid compartment, and central and peripheral receptors. The effect of shunt in the lungs is included in the model and the lung volume and the dead space are time varying. The controller utilizes outputs from peripheral and central receptors to adjust the depth and rate of breathing and the effects of prematurity of peripheral receptors are included in the system. Hering-Breuer type reflexes are embodied in the controller to accomplish respiratory synchronization. The model is examined and its simulation results under test conditions in hypoxia and hypercapnia are presented.

Blood Gas Analysis↗
PubMed2002

Does oxygen deficit to the cerebral blood flow caused by subdural hematoma and/or increased intracranial pressure affect the variations in auditory evoked potentials in white New Zealand rabbits?

The experiment entails surgically placing two subarachnoid bolts and a subdural balloon through the skull of white New Zealand rabbits. One bolt is used to raise the intracranial pressure (ICP) by continuously infusing lactated Ringer's solution (LRS) into the subarachnoid space to maintain the desired level of ICPs, and the second bolt is to monitor the ICP. A subdural balloon is inflated with a known volume of LRS to simulate a subdural hematoma condition. Using various levels of ICP and/or different sizes of balloons, auditory evoked potentials (AEPs) were recorded from a rabbit. The results indicate that a major correlation of changes in AEP peak latencies is due to mechanical forces of a mass (inflated balloon simulating a hematoma) on the brain matter rather than increased ICP. The AEP peak latencies are relatively insensitive to an increase in ICP without the simulated intracranial hematoma. This study provides evidence that oxygen deficit to the cerebral blood flow caused by deformation of certain parts of the brain could be identified using AEPs.

Animals↗
PubMed2002

Controlled breaks as a fatigue countermeasure on the flight deck.

BACKGROUND: A major challenge for flight crews is the need to maintain vigilance during long, highly automated nighttime flights. No system currently exists to assist in managing alertness, and countermeasure options are limited. Surveys reveal many pilots use breaks as an in-flight countermeasure, but there have been no controlled studies of their effectiveness. HYPOTHESIS: We hypothesized that brief, regular breaks could improve alertness and performance during an overnight flight. METHOD: A 6-h, uneventful, nighttime flight in a Boeing 747-400 flight simulator was flown by fourteen two-man crews. The 14 subjects in the treatment group received 5 short breaks spaced hourly during cruise; the 14 subjects in the control group received 1 break in the middle of cruise. Continuous EEG/EOG, subjective sleepiness, and psychomotor vigilance performance data were collected. RESULTS: During the latter part of the night, the treatment group showed significant reductions for 15 min post-break in slow eye movements, theta-band activity, and unintended sleep episodes compared with the control group. The treatment group reported significantly greater subjective alertness for up to 25 min post-break, with strongest effects near the time of the circadian trough. There was no evidence of objective vigilance performance improvement at 15-25 min post-break, with expected performance deterioration occurring due to elevated sleep drive and circadian time. CONCLUSIONS: The physiological and subjective data indicate the breaks reduced nighttime sleepiness for at least 15 min post-break and may have masked sleepiness for up to 25 min, suggesting the potential usefulness of short-duration breaks as an in-flight fatigue countermeasure.

Adult↗
PubMed1993

[Role of radiology in the diagnosis of joint chondrocalcinosis. Calcium pseudogout].

Chondrocalcinosis is a really frequent clinicopathologic entity, which is caused by the penetration of calcium pyrophosphate dihydrate microcrystals into the structures of the joint, including hyaline cartilages and fibrocartilages--hense its name--as well as the synovial fluid and membrane. Calcium gout, which preferentially appears in the knees, is the most spectacular and characteristic symptom of chondrocalcinosis, expressing a crisis of acute microcrystal synovitis, of which it has all the usual clinical features, and thus simulating uratic gout. The positive diagnosis is based on: a) the radiologic demonstration of articular calcifications in the lining cartilages, forming a continuous or fragmented opaque border on the subchondral bone, from which it is separated by a light space, and/or in the fibrocartilaginous structures (most often the menisci, the symphysis pubis, the disk of the inferior radioulnar joint) where they appear as small, irregular clusters with blurred or cloudy margins. The knee is the most frequent site of calcium impregnation images, both in hyaline cartilages and in fibrocartilages. b) the presence of calcium pyrophosphate microcrystals in the synovial fluid; their nature is usually demonstrated convincingly enough with a conventional light microscope; c) needle biopsy findings of microcrystalline clusters embedded in the synovial membrane, that can be easily identified with routine staining. In practice, demonstrating radiologic signs, when these are characteristic and can be detected in their preferred sites, allows recognizing diffuse chondrocalcinosis in satisfactory safety conditions after a calcium gout crisis, as well as in the presence of the many atypical or misleading symptomatic aspects of this microcystal arthropathy, that will be the subject of a further paper.

Calcium↗
PubMed1990

Theoretical analysis of factors influencing recovery of ventilation distributions from inert gas washout data.

A method is presented that allows to calculate distributions of ventilation from measured time courses of inert gas washout. In the mathematical description of the washout process a discontinuous algorithm is applied: For each individual breath inspiratory and expiratory tidal volumes, endexpiratory alveolar volume, and dead space inspiration are taken into account. Furthermore, volume reduction of the alveolar gas according to the gas exchange ratio is considered. Commonly in ventilation analysis, the specific ventilation serves as abscissa of the density of the ventilation distribution. As at a given location the specific ventilation changes with varying tidal volumes even if the distribution pattern of the ventilation amongst the lung remains unchanged, the normalized specific ventilation is newly introduced instead. This quantity is defined to be the ratio of regional alveolar ventilation and regional endexpiratory alveolar volume divided by the total alveolar ventilation. The normalized specific ventilation reflects the distribution of the ventilation independently of variations in tidal volume and respiratory frequency. Furthermore, it allows direct comparison of ventilation distributions that are determined at varying alveolar ventilations. Ventilation distributions are approximated by the transformed beta distribution which is parameterized by its mean, variance, and skewness. In order to evaluate simplifications introduced in former studies and to quantify their effects on the resulting ventilation distributions, washout time courses are generated in a computer simulation from the comprehensive discontinuous algorithm and are used to recover ventilation distributions by means of accordingly simplified algorithms. Furthermore, the influence of errors that may occur in the measurement of tidal volumes are assessed. The results of these studies are summarized as follows: Serious errors are introduced in the recovered distributions if ventilation is modelled as a continuous process and if physiological variations in tidal volumes or endexpiratory alveolar volumes or dead space inspiration are neglected. Modelling the entire dead space as common dead space or as local dead space only, entails significant errors as well. Statistical errors of 2% in the measured volumes practically do not have any impacts on the recovered distributions whereas systematic errors significantly deteriorate the results. In conclusion, in ventilation analysis it is essential to apply a discontinuous description of the inert gas washout process that accounts for dead space inspiration and variations in the above mentioned quantities. In addition it is important to obtain all measured values with the highest achievable precision.

Computer Simulation↗
PubMed2000

Spontaneous secondary spiking in excitable cells.

Kepler & Marder (1993, Biol. Cybern.68, 209-214) proposed a model describing the electrical activity of a crab neuron in which a train of directly induced action potentials is sometimes followed by one or more spontaneous action potentials, referred to as spontaneous secondary spikes. We reduce their five-dimensional model to three dimensions in two different ways in order to gain insight into the mechanism underlying the spontaneous spikes. We then treat a slowly varying current as a parameter in order to give a qualitative explanation of the phenomenon using phase-plane and bifurcation analysis. We demonstrate that a three-dimensional model, consisting of a two-dimensional excitable system plus a slow inward current, is sufficient to produce the behaviour observed in the original model. The exact dynamics of the excitable system are not important, but the relative time constant and amplitude of the slow inward current are crucial. Using the numerical bifurcation analysis package AUTO (Doedel & Kernevez, 1986, AUTO: Software for Continuation and Bifurcation Problems in Ordinary Differential Equations. California Institute of Technology), we compute bifurcation diagrams using the maximum amplitude of the slow inward current as the bifurcation parameter. The full and reduced models have a stable resting potential for all values of the bifurcation parameter. At a critical value of the bifurcation parameter, a stable tonic firing mode arises via a saddle-node of periodics bifurcation. Whether or not the models can exhibit transient or continuous spontaneous spiking depends on their position in parameter space relative to this saddle-node of periodics.

Action Potentials↗
PubMed1998

Form and function of mammalian lung: analysis by scientific computing.

This study approaches the investigation of airway morphology of the lung with a new set of imaging and computer graphical methods, including confocal imaging, computer-guided image acquisition, visualization and fractal graphics. The key result is that, in contrast to the belief that the design of the conductive part of lung of smaller mammals can be described with a trumpet model, the findings reported here document a strongly monopodial branching pattern with the functional consequence of a variation of dead space between the trachea and the acini. This non-dichotomic structural design finds its continuation within the respiratory units as the necessary requirement for an optimal space filling and dense packing which cannot be achieved by a dichotomic branching only. Based on a computer model, computational physics tightly coupled with computer visualistics enables functional simulation of the lung model regarding gas transport. The predicted variance in the ventilation of acini gives rise to an explanation of the well-known difference between the morphologically predicted and physiologically required diffusion capacity.

Bronchi↗