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PubMed1992

Cardiovascular simulation using a multiple modeling method on a digital computer--simulation of interaction between the cardiovascular system and angiotensin II.

A cardiovascular system model that simulates interactive responses to drugs has been developed on a small digital computer. The overall model basically consists of three models. The first is a momentum transport model that represents relations between blood pressure and flow in the cardiovascular system. In this model, the cardiovascular system is divided into 14 components and modeled by using equivalent electrical circuits. The second is a mass transport model comprising 14 compartments corresponding to the respective components of the cardiovascular system. This model represents the distribution of the administered drug in the various cardiovascular components. The third is an interaction model that represents the relationships between the momentum and mass transport models. This model causes variations in the resistance and capacitance parameters of the momentum transport model as a function of the current drug concentrations in the appropriate compartments of the mass transport model. The capacitances representing the ventricles are varied in a time-dependent fashion to simulate the beat of the heart. Simulation is performed by using the Euler method to solve a system of 28 ordinary differential equations governing the momentum and mass transport models on a 32-bit microcomputer, a Macintosh II. The model was assessed by performing two demonstrations of the cardiovascular response to the vasopressor angiotensin II (AT II). They first examined the interaction between the cardiovascular system and AT II. The effect of AT II on the cardiovascular system was incorporated into the interaction model. Administration of AT II as a constant infusion (200 micrograms/hr) resulted in an elevation of mean arterial pressure from approximately 100 to 150 mm Hg.(ABSTRACT TRUNCATED AT 250 WORDS)

Angiotensin II↗
PubMed1991

Computer simulations of cell-target encounter including biased cell motion toward targets: single and multiple cell-target simulations in two dimensions.

In order for immune cells to carry out many of their functions, including clearance of infectious agents from tissue, they must first encounter their targets in the tissue. This encounter process is often the rate-limiting step in the overall function. Most immune cells exhibit chemotactic ability, and previous continuum models for encounter rates and dynamics have shown that chemotaxis can be a great advantage to cells by greatly increasing encounter rates relative to those for randomly moving cells. This paper describes computer simulations of discrete cell-target encounter events in two dimensions, for the two cases considered by the continuum models: where only a single cell and a single target are present, and where many cells and targets are present. The results of these simulations verify our previous model predictions that a small amount of chemotactic bias dramatically decreases the encounter time, while further increases in the amount of bias have a much smaller effect. Chemotactic ability is shown to be an important determinant of the kinetics of target clearance, and its effects depend on the initial cell-target ratio and the initial distributions of cells and targets. To the best of our knowledge, this work provides the first computer simulations of particle-target encounter in which there is biased motion of particles toward their targets, and is therefore of general interest beyond specific application to immune cell function.

Animals↗
PubMed1992

A method for computer simulation of ultrasound Doppler color flow images--II. Simulation results.

A computational method of simulating Doppler color flow images has been developed. It is based on a point-scattering model of moving blood and surrounding tissue and is capable of treating the entire flow image generation process. Simulated images of parabolic flow dynamics in a cylindrical vessel are presented to show the statistical nature of the map of velocity estimates and to demonstrate the effects of wall filters and different display schemes. Quantitative results of extracted velocity profiles are included and indicate the usefulness of the simulation method for studying the quantitative capabilities of flow imaging.

Blood Flow Velocity↗
PubMed2006

The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment.

We present an experimental and computational analysis of the folding pathway of the 17th domain of chicken brain alpha-spectrin, R17. Wild-type R17 folds in a two-state manner and the chevron plot (plot of the logarithm of the observed rate constant against concentration of urea) shows essentially linear folding and unfolding arms. A number of mutant proteins, however, show a change in slope of the unfolding arm at high concentration of denaturant, hinting at complexity in the folding landscape. Through a combination of mutational studies and high temperature molecular dynamics simulations we show that the folding of R17 can be described by a model with two sequential transition states separated by an intermediate species. The rate limiting transition state for folding in water has been characterized both through experimental Phi-value analysis and by simulation. In contrast, a detailed analysis of the transition state predicted to dominate under highly denaturing conditions is only possible by simulation.

Amino Acid Sequence↗
PubMed2001

A new approach for the real-time simulation of tissue deformations in surgery simulation.

Simulation of the behaviour of elastic objects in real time is one of the present objectives of computer graphics. One of its fields of application lies in virtual reality, mainly in surgery simulation systems. Models used for the construction of objects with deformable behaviour in computer graphics are known as deformable models. These have two conflicting characteristics: interactivity and movement realism. The deformable models developed up till now have promoted one characteristic to the detriment of the other. In this paper, a new approach is proposed based on boundary element methods (BEM). This is characterised by a positive equilibrium between speed and realism and great robustness. These properties along with the experimental results described in this paper permit one to assert that establishing deformable models with BEM is a reliable method to model objects in virtual reality environments for surgery simulation. In addition to that, the required elasticity parameters could be obtained experimentally through the use of a pig's liver.

Algorithms↗
PubMed1998

The influence of experience with a set of simulated patients on diagnosis of simulated patients not previously diagnosed.

BACKGROUND AND PURPOSE: Diagnoses, to be useful, should be accurate. The purpose of this study using fictitious patients and student judges was to test the theory that diagnostic errors would occur when students saw simulated patients who were similar to previously seen simulated patients. SUBJECTS: Sixty physical therapist (PT) students and 60 non-physical therapist (NPT) students were studied. Subjects were assigned randomly to one of three groups. METHODS: Instructions to the three groups differed in terms of rules provided for diagnoses and instructions to remember the patients. Students first diagnosed the same eight fictitious patients five times. The students then diagnosed eight new patients with similar characteristics interspersed with the original eight patients. Half of the new patients had a diagnosis different from that of the most similar old patient. RESULTS: Students who were given a rule for diagnosis made fewer errors than students who were not given a rule. Students in the PT group took longer but made fewer errors on the critical opposite-diagnosis new cases than did students in the NPT group. CONCLUSION AND DISCUSSION: The results do not provide support for the theory that diagnostic errors would occur when students saw patients who were similar to previously seen patients. Students in the PT group appeared to emphasize accuracy at the expense of speed in making their diagnoses. Given the nature of the simulated patient information and the mode of presentation used in the experiment, however, the conclusion that therapists in actual practice do not make errors because of the similarity between new and previously seen patients is not yet warranted.

Adult↗
PubMed2002

Model intestinal microflora in computer simulation: a simulation and modeling package for host-microflora interactions.

The ecology of the human intestinal microflora and its interaction with the host are poorly understood. Though more and more data are being acquired, in part using modern molecular methods, development of a quantitative theory has not kept pace with this increase in observing power. This is in part due to the complexity of the system and to the lack of simulation environments in which to test what the ecological effect of a hypothetical mechanism of interaction would be, before resorting to laboratory experiments. The MIMICS project attempts to address this through the development of a cellular automaton for simulation of the intestinal microflora. In this paper, the design and evaluation of this simulator is discussed.

Bacteria, Aerobic↗
PubMedDate not supplied

The Anesthesia Simulator Consultant: simulation plus expert system.

The Anesthesia Simulator Consultant was designed to provide anesthesiologists the opportunity to practice the management of anesthesia-critical incidents. The program simulates the operating room environment in a graphic display on the screen of a personal computer. Physiologic models predict the patient responses and an automated record-keeping system produces a detailed summary of the case. An expert system provides interpretations of patient information, differential diagnosis, and treatment for abnormal patient conditions. The coupling of the simulator, recorder, and expert system creates a unique self-study and evaluation environment.

Anesthesiology↗
PubMed2000

Changes in myocardial contractility and contractile proteins after four weeks of simulated [correction of simulate] weightlessness in rats.

The interaction between the gravitational field, the position of the body, and the functional characteristics of the blood vessels determines the distribution of intravascular volume. In turn, this distribution determines cardiac pump function. One of the most profound circulatory changes that occurs in man during exposure to weightlessness is a cephalad redistribution of fluid caused by the lack of hydrostatic pressure in this microgravitative environment. The cephalad redistribution of fluid results in a loss of blood volume and then induces a decrease in preload. Recently, a decrease in sensitivity of arteriole to catecholamine has reported in rats of simulated weightlessness. This change in arteriole may reduce afterload. As a result, cardiovascular system may be shifted to a hypokinetic state during weightlessness condition for long-term. Echocardiographic data from astronauts during space flight showed an increase in heart rate, a 12 % decrease in stroke volume, and a 16 % decrease in left end diastolic volume. Electron-microscopic studies have shown changes in cardiac morphology in rats after exposure to microgravity for 7-12.5 days. After the COSMOS 2044 flight for 14 days, the light-microscopic studies have shown an atrophy of papillary muscles in rats left cardiac ventricle. It is not clear whether the function of atrophic myocardium is impaired. The data in three aspects as mentioned above suggest that weightlessness or simulated weightlessness may decrease the myocardial function. However, definite changes in cardiac performance have been hard to prove due to many limits. This studies were to answer two questions: Is the myocardial contractility depressed in rats subjected to simulated weightlessness for four weeks? What are the underlying mechanisms of the changing contractility?

Animals↗
PubMed2006

Physically accurate mesh simulation in a laparoscopic hernia surgery simulator.

In this paper we use the 2D angular spring based mass-spring-damper (AMSD) model to simulate the plastic mesh in a laparoscopic hernia surgery simulator. We propose a physically based method to systematically derive the optimal parameters of the 2D AMSD model. While the traditional 2D MSD model lacks resistance against bending, the 2D AMSD model with optimized parameters can provide correct bending resistance as well as stretching resistance. The simulated mesh is demonstrated to be much more realistic.

Algorithms↗
PubMedDate not supplied

A comprehensive simulator of the human respiratory system: validation with experimental and simulated data.

A comprehensive model of oxygen (O2) and carbon dioxide (CO2) exchange, transport, and storage in the adult human is presented, and its ability to provide realistic responses under different physiological conditions is evaluated. The model comprises three compartments (i.e., lung, body tissue, and brain tissue) and incorporates a controller that adjusts alveolar ventilation and cardiac output dynamically integrating stimuli coming from peripheral and central chemoreceptors. A new realistic CO2 dissociation curve based on a two-buffer model of acid-base chemical regulation is included. In addition, the model explicitly considers relevant physiological factors such as buffer base, the nonlinear interaction between the O2 and CO2 chemoreceptor responses, pulmonary shunt, dead space, variable time delays, and Bohr and Haldane effects. Model simulations provide results consistent with both dynamic and steady-state responses measured in subjects undergoing inhalation of high CO2 (hypercapnia) or low O2 (hypoxia) and subsequent recovery. An analysis of the results indicates that the proposed model fits the experimental data of ventilation and gas partial pressures as some meaningful simulators now available and in a very large range of gas intake fractions. Moreover, it also provides values of blood concentrations of CO2, HCO3-, and hydrogen ions in good agreement with more complex simulators characterized by an implicit formulation of the CO2 dissociation curve. In the experimental conditions analyzed, the model seems to represent a single theoretical framework able to appropriately describe the different phenomena involved in the control of respiration.

Acid-Base Equilibrium↗
PubMed2001

Knowledge representation and qualitative simulation of salmon redd functioning. Part I: qualitative modeling and simulation.

This work aims at representing empirical knowledge of freshwater ecologists on the functioning of salmon redds (spawning areas of salmon) and its impact on mortality of early stages. For this, we use Qsim, a qualitative simulator. In this first part, we provide unfamiliar readers with the underlying qualitative differential equation (QDE) ontology of Qsim: representing quantities, qualitative variables, qualitative constraints, QDE structure. Based on a very simple example taken of the salmon redd application, we show how informal biological knowledge may be represented and simulated using an approach that was first intended to analyze qualitatively ordinary differential equations systems. A companion paper (Part II) gives the full description and simulation of the salmon redd qualitative model. This work was part of a project aimed at assessing the impact of the environment on salmon populations dynamics by the use of models of processes acting at different levels: catchment, river, and redds. Only the latter level is dealt with in this paper.

Animals↗
PubMedDate not supplied

Declarative simulation of dynamicals systems: the 812 programming language and its application to the simulation of genetic networks.

A major part of biological processes can be modeled as dynamical systems (DS), that is, as a time-varying state. In this article, we advocate a declarative approach for prototyping the simulation of DS. We introduce the concepts of collection, stream and fabric. A fabric is a multi-dimensional object that represents the successive values of a structured set of variables. A declarative programming language, called 8 1/2 has been developed to support the concept of fabrics. Several examples of working 8 1/2 programs are given to illustrate the relevance of the fabric data structure for simulation applications and to show how recursive fabric definitions can be easily used to model various biological phenomena in a natural way (a resolution of PDE, a simulation in artificial life, the Turing diffusion-reaction process and various examples of genetic networks). In the conclusion, we recapitulate several lessons we have learned from the 8 1/2 project.

Programming Languages↗
PubMed2001

Chemistry-structure-simulation or chemistry-simulation-structure sequences? The case of MIL-34, a new porous aluminophosphate.

A new aluminophosphate, MIL-34, is investigated from its as-synthesized structure to its calcined microporous form. Single-crystal X-ray diffraction measurements on the as-synthesized MIL-34 (Al(4)(PO(4))(4)OH x C(4)H(10)N, space group P-1, a = 8.701(3) A, b = 9.210(3) A, c = 12.385(3) A, alpha = 111.11(2) degrees, beta = 101.42(2) degrees, gamma = 102.08(2) degrees, V = 863.8(4) A(3), Z = 2, R = 3.8%) reveal a 3-D open framework where Al atoms are in both tetrahedral and trigonal bipyramidal coordinations. It contains a 2-D pore system defined by eight rings where channels along [100] cross channels running along [010] and [110]. CBuA molecules are trapped at their intersection. (27)Al, (31)P, and (1)H MAS NMR spectroscopies corroborate these structural features. Calcination treatments of a powder sample of the as-synthesized MIL-34 indicate its transformation into the related template-free structure that is stable up to 1000 degrees C. Lattice energy minimizations are then used in order to anticipate the crystal structure of the calcined MIL-34, starting with the knowledge of the as-synthesized structure exclusively. Energy minimizations predict a new regular zeotype structure (AlPO(4), space group P-1, a = 8.706 A, b = 8.749 A, c = 12.768 A, alpha = 111.17 degrees, beta = 97.70 degrees, gamma = 105.14 degrees, V = 846.75 A(3), Z = 2) together with a thermodynamic stability similar to that of existing zeotype AlPOs. Excellent agreement is observed between the diffraction pattern calculated from the predicted calcined MIL-34 and the experimental X-ray powder diffraction pattern of the calcined sample. Finally, the atomic coordinates and cell parameters of the calcined MIL-34 predicted from the simulations are used to perform the Rietveld refinement of the calcined sample powder pattern, further corroborated by (27)Al and (31)P NMR measurements. This unique combination of experiment and simulation approaches is an interesting and innovative strategy in materials sciences, where simulations articulate the prediction of a possible template-free framework from its as-synthesized templated form. This is especially valuable when straightforward characterizations of the solid of interest with conventional techniques are not easy to carry out.

Journal Article↗
PubMed2000

Matching simulation and experiment: a new simplified model for simulating protein folding.

Simulations of simplified protein folding models have provided much insight into solving the protein folding problem. We propose here a new off-lattice bead model, capable of simulating several different fold classes of small proteins. We present the sequence for an alpha/beta protein resembling the IgG-binding proteins L and G. The thermodynamics of the folding process for this model are characterized using the multiple multihistogram method combined with constant-temperature Langevin simulations. The folding is shown to be highly cooperative, with chain collapse nearly accompanying folding. Two parallel folding pathways are shown to exist on the folding free energy landscape. One pathway contains an intermediate--similar to experiments on protein G, and one pathway contains no intermediates-similar to experiments on protein L. The folding kinetics are characterized by tabulating mean-first passage times, and we show that the onset of glasslike kinetics occurs at much lower temperatures than the folding temperature. This model is expected to be useful in many future contexts: investigating questions of the role of local versus nonlocal interactions in various fold classes, addressing the effect of sequence mutations affecting secondary structure propensities, and providing a computationally feasible model for studying the role of solvation forces in protein folding.

Computational Biology↗
PubMed1993

Development of simulation models for protein folding in a thermal annealing process--I: A simulation of BPTI folding by the pearl necklace model.

A model system is proposed to simulate the folding processes of proteins during thermal annealing. This system consists of four subsystems: (i) the pearl necklace model with isotropic inter-residue interactions; (ii) the extended pearl necklace model with anisotropic interaction potentials; (iii) molten globule phase dynamics; and (iv) final generation of the three-dimensional structure of a given protein. In this paper results obtained with the pearl necklace model are reported. This model consists of spherical elements and virtual bonds of 3.8 A in length and is intended to simulate dynamical processes at relatively high temperature where entropic terms play a dominant role. Inter-residue interactions are composed of spherical soft repulsive potentials and hydrophobic interactions inherent to respective residues. A simulation of folding processes of BPTI starting from the fully extended conformation indicated that intermediates, even at early stages of folding, are not randomly coiled but assume organized structures that resemble, to some extent, the native conformation.

Aprotinin↗
PubMed1992

Application of restrained minimization, simulated annealing and molecular dynamics simulations for the conformational analysis of oligosaccharides.

The purpose of the present study was to determine the confidence with which the small number of 1H NMR nuclear Overhauser effect (NOE) distance constraints measurable across glycosidic linkages in oligosaccharides could be used for solution conformational analysis. This was assessed by use of these constraints in restrained molecular mechanical minimization of the tetrasaccharide Gal beta 1----4(Fuc alpha 1----3)Glc-NAc beta 1----3Gal, a model compound of the Lewis-X antigenic determinant. This presents a particularly severe test case in view of extreme resonance overlap and a dearth of inter-residue distance constraints. It is concluded that these constraints, when used in conventional restrained minimization, result in the generation of 'virtual conformations' and local minima about glycosidic linkages. However, these restraints are nevertheless found to be useful in the initial stages of a conformational analysis strategy involving restrained minimization combined with dynamical simulated annealing to define more accurately the global minimum energy configuration, together with molecular dynamics simulation to explore conformational mobility about this minimum. Theoretical ROE values calculated over the time course of the MD simulation, using a formalism appropriate for the time scale of the internal motion, are compared with those obtained experimentally in the oligosaccharide.

Carbohydrate Conformation↗
PubMed1986

Growth of gram-positive mastogenic bacteria in normal, simulated bulk tank, and mastitic milk held at simulated fluctuating temperatures of farm bulk tank.

Growth of Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus bovis, and Streptococcus uberis was studied in normal milk, simulated bulk tank milk, and aseptic mastitic milk held at simulated fluctuating temperatures of farm bulk tank for 48 h. With the exception of S. bovis, growth rates of the other five bacteria were similar in both normal and simulated bulk tank milk. Mastitic milk inhibited growth of all bacteria studied. A 24-h adjustment period occurred before most of the bacteria started growing. The mastitis level in a dairy herd may be monitored by cultures of bulk tank milk samples and by calculations as discussed in this study.

Animals↗