Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “computational modeling”

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

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

At least 1,423 records · Page 79Linked to original sources
PubMed1993

Computer modeling of the tetrasaccharide nystose.

Nystose, O-beta-D-fructofuranosyl-(2-->1)-O-beta-D-fructofuranosyl-(2-->1)- beta-D-fructofuranosyl alpha-D-glucopyranoside, was modeled with the rigid-residue program PFOS and with MM3. The three furanose rings of crystalline nystose trihydrate all are within the 1 kcal.mol-1 contour on an MM3 energy surface that was calculated with a dielectric constant of 4. The calculations showed that in the extended conformation found in the crystal, there was a small influence of the remainder of the residues on the conformation of any given disaccharide segment. Even accounting for intramolecular, interresidue forces, however, the central inulobiose and the sucrose linkages appear to be distorted. These discrepancies are apparently due to crystal packing forces and, for the sucrose linkage, miscalculation of the energy of an overlapping exoanomeric effect, as indicated by studies of a model miniature crystal. The different conformations of the central and terminal inulobiose linkages in the crystal show that conformations in higher oligosaccharides will not always correspond to the global minima on conformational maps for isolated disaccharides.

Carbohydrate Conformation↗
PubMed2006

Computational model of interstitial transport in the spinal cord using diffusion tensor imaging.

Local drug delivery methods, including convection-enhanced delivery (CED), are being used to increase distribution in selected regions of nervous tissue. There is a need for 3D models that predict spatial drug distribution within these tissues. A methodology was developed to process magnetic resonance microscopy (MRM) and diffusion tensor imaging (DTI) scans, segment gray and white matter regions, assign tissue transport properties, and model the interstitial transport of macromolecules. Fiber tract orientation was derived from DTI data and used to assign directional dependence of hydraulic conductivity, K, and tracer diffusivity, Dt, transport tensors. Porous media solutions for interstitial fluid pressure, velocity, and albumin distribution were solved using a finite volume method. To test this DTI-based methodology, a rat spinal cord transport model was developed to simulate CED into the dorsal white matter column. Predicted distribution results correspond well with small volume (approximately 1 microl) trends found experimentally, although albumin loss was greater at larger infusion volumes (>2 microl). Simulations were similar to those using fixed transport properties due to the bulk alignment of white matter fibers along the cord axis. These findings help to validate the DTI-based methodology which can be applied to modeling regions where fiber tract organization is more complex, e.g., the brain.

Animals↗
PubMed2006

Patient-specific computational modeling of cerebral aneurysms with multiple avenues of flow from 3D rotational angiography images.

RATIONALE AND OBJECTIVES: Previous studies of aneurysm flow dynamics based on three-dimensional (3D) rotational angiography (RA) images were limited to aneurysms with a single route of blood inflow. However, aneurysms of the circle of Willis frequently involve locations with more than one source of inflow, such as aneurysms of the anterior communicating artery. The highest resolution images of cerebral vessels are from RA images, but this technique is limited to visualizing only one route of inflow at a time, leaving a significant limitation in the application of 3DRA image sets for clinical studies of patient-specific computational fluid dynamics (CFD) simulations. In this report, subject-specific models of cerebral aneurysms with multiple avenues of flow are constructed from RA images by using a novel combination of image co-registration and surface merging techniques. MATERIALS AND METHODS: RA images are obtained by means of contrast injection in each vessel that provides inflow to the aneurysm. Anatomic models are constructed independently of each of these vascular trees and fused together into a single model. The model is used to construct a finite element grid for CFD simulations of hemodynamics. RESULTS: Three examples of patient-specific models are presented: an anterior communicating artery aneurysm, a basilar tip aneurysm, and a model of an entire circle of Willis with five coincident aneurysms. The method is evaluated with a numeric phantom of an aneurysm in the anterior communicating artery. CONCLUSION: These examples show that this new technique can be used to create merged network numeric models for CFD modeling. Furthermore, intra-aneurysmal flow patterns are influenced strongly by merging of the two inflow streams. This effect decreases as distance from the merging streams increases.

Adult↗
PubMed2001

Computational model of carbachol-induced delta, theta, and gamma oscillations in the hippocampus.

Field potential recordings from the rat hippocampus in vivo contain distinct frequency bands of activity, including delta (0.5-2 Hz), theta (4-12 Hz), and gamma (30-80 Hz), that are correlated with the behavioral state of the animal. The cholinergic agonist carbachol (CCH) induces oscillations in the delta (CCH-delta), theta (CCH-theta), and gamma (CCH-gamma) frequency ranges in the hippocampal slice preparation, eliciting asynchronous CCH-theta, synchronous CCH-delta, and synchronous CCH-theta with increasing CCH concentration (Fellous and Seinowski, Hippocampus 2000;1 0:187-197). In a network model of area CA3, the time scale for CCH-delta corresponded to the decay constant of the gating variable of the calcium-dependent potassium (K-AHP) current, that of CCH-theta to an intrinsic subthreshold membrane potential oscillation of the pyramidal cells, and that of CCH-gamma to the decay constant of GABAergic inhibitory synaptic potentials onto the pyramidal cells. In model simulations, the known physiological effects of carbachol on the muscarinic and K-AHP currents, and on the strengths of excitatory postsynaptic potentials, reproduced transitions from asynchronous CCH-theta to CCH-delta and from CCH-delta to synchronous CCH-theta. The simulations also exhibited the interspersed CCH-gamma/CCH-delta and CCH-gamma/CCH-theta that were observed in experiments. The model, in addition, predicted an oscillatory state with all three frequency bands present, which has not yet been observed experimentally.

Acetylcholine↗
PubMed1990

Computer modeling of subtypes of kappa opioid receptors in adrenal medulla.

The existence of multiple subtypes of kappa opioid receptors in brain and adrenal medulla, has been controversial. We have characterized opioid receptors in frozen membranes from bovine adrenal medulla by use of objective mathematical modeling. [3H]Etorphine, [3H]ethylketocyclazocine (EKC) and [3H][D-Ala2,D-Leu5]enkephalin (DADL) were utilized as labeled ligands. Self- and cross-displacement curves were constructed using the three corresponding unlabeled ligands in the presence or absence of increasing concentrations of DADL. Results indicated: (1) each of the three ligands studied individually showed the presence of heterogeneity of binding sites; (2) sites labeled by etorphine were heterogeneous: 84% of etorphine binding was displaceable by 10(-4) M DADL, while the remaining 16% was DADL non-suppressible; (3) 75% of the binding of EKC was displaceable by DADL while 25% was non-suppressible; (4) mathematical modeling showed the presence of three subtypes of kappa binding sites (a) kappa 1, showing slight selectivity for EKC relative to etorphine; (b) kappa 2, with Kd approximately equal to 1 nM for etorphine, and sufficiently high affinity for DADL (Kd approximately equal to 150 nM) so that it is suppressible by 100 microM DADL; and (c) K3, with no measurable affinity for DADL and a 27-fold selectivity for etorphine relative to EKC. The three subtypes of kappa sites were present at concentrations of 7.4, 75, and 55 fmol/mg protein, respectively. The relative affinities of a series of kappa agonists for the etorphine-binding sites were characterized. The present studies confirm the existence of three subtypes of kappa opioid receptors in bovine adrenal medulla, and indicate the utility of mathematical modeling for characterization of complex receptor systems.

Adrenal Medulla↗
PubMed2004

Impact of the Fåhraeus effect on NO and O2 biotransport: a computer model.

Nitric oxide (NO) and oxygen (O2) transport in the microcirculation are coupled in a complex manner, since enzymatic production of NO depends on O2 availability, NO modulates vascular tone and O2 delivery, and tissue O2 consumption is reversibly inhibited by NO. The authors investigated whether NO bioavailability is influenced by the well-known Fåhraeus effect, which has been observed for over 70 years. This phenomenon occurs in small-diameter blood vessels, where the tube hematocrit is reduced below systemic hematocrit as a plasma boundary layer forms near the vascular wall when flowing red blood cells (rbcs) migrate toward the center of the bloodstream. Since hemoglobin in the bloodstream is thought to be the primary scavenger of NO in vivo, this might have a significant impact on NO transport. To investigate this possibility, the authors developed a multilayered mathematical model for mass transport in arterioles using finite element numerical methods to simulate coupled NO and O2 transport in the blood vessel lumen, plasma layer, endothelium, vascular wall, and surrounding tissue. The Fåhraeus effect was modeled by varying plasma layer thickness while increasing core hematocrit based on conservation of mass. Key findings from this study are that (1) despite an increase in the NO scavenging rate in the core with higher hematocrit, the model predicts enhanced vascular wall and tissue NO bioavailability due to the relatively greater resistance for NO diffusion through the plasma layer; (2) increasing the plasma layer thickness also increases the resistance for O2 diffusion, causing a larger P(O2) gradient near the vascular wall and decreasing tissue O2 availability, although this can be partially offset with inhibition of O2 consumption by higher tissue NO levels; (3) the Fåhraeus effect can become very significant in smaller blood vessels (diameters <30 microm); and (4) models that ignore the Fåhraeus effect may underestimate NO concentrations in blood and tissue.

Biological Transport↗
PubMed1989

Collagen fibril surface structures: freeze-etching data and computer modelling.

In order to investigate the correlation between primary structure and surface profile of collagen, freeze-fractured and deep-etched (dehydrated) collagen fibrils have been compared with a fibril model built directly from the amino acid sequence. The model appeared to be almost identical to the freeze-etched collagen fibril with respect to the most relevant features, such as the gap-overlap ratio and the location of the two main intraperiod ridges (X3 and X2). However, it did not show the minor ridges observed in the gap zone (X1 and Y1), thus suggesting that these structures, although consistently present in collagen fibrils, may in fact be due to post-translational modifications or to non-collagenic material adhering to the fibril.

Amino Acid Sequence↗
PubMed1989

Optimal fitting of computer model simulations to first transit cardiac radionuclide curves--II.

A discrete-time, lumped-parameter mathematical model of the human cardiopulmonary circulation as it appears during a first-transit radionuclide study has been described. An optimal fitting process is used to match curves obtained from the model to curves obtained from first transit studies in order to estimate the parameters of the subject's heart. The development of the optimization technique is described in this paper. The results of testing the effects of overlapping compartments and errors in delay estimates are presented. A parameter determination analysis is performed by applying the optimization algorithm to simulated data. This analysis technique provides a method of estimating many parameters of heart function using a single, simple, rapid procedure. Results of clinical studies will be presented subsequently.

Algorithms↗
PubMed1994

Computer models of DNA four-way junctions.

A modeling scheme that combines a constrained backbone generating algorithm with simple hard-sphere packing calculations is offered to build the four-stranded structures of DNA found in Holliday junctions. Two standard B-DNA duplexes are oriented side by side with helix axes at different relative inclinations and then systematically rotated and translated to identify closely spaced contact-free states. Attempts are subsequently made to introduce a low-energy sugar-phosphate linkage that serves as the site of strand exchange between the two duplexes. The chemical connection is sought using an algorithm which identifies the possible arrangements of the intervening backbone torsions between arbitrarily positioned bases. The goal is to identify the multiple conformational solutions associated with a particular arrangement of neighboring DNA helices in the four-way junction rather than a single optimum structure. The methodology is general, in terms of accommodating four-way junctions with arms of variable conformation and chain length and of dimensions much greater than treated heretofore. The only deformation in the four-way structures relative to B-DNA occurs at the site of backbone exchange, with base stacking and Watson-Crick pairing completely preserved in all models. The arrangements of neighboring bases at these sites resemble the unusual conformational steps found in a number of small molecule nucleic acid crystal structures. An interesting outcome of the calculations is the formation of sterically acceptable four-arm Holliday junctions over a wide range of angles at the cross. The potential mobility of the Holliday junctions is inferred from visualization and energetic analysis of the various models. Long-range electrostatic energies based on different currently available treatments of the dielectric constant are used to estimate the conformational preferences and flexibility of the four-stranded structures. The various dielectric schemes, however, are not in complete agreement on the likely conformational variability of the four-way junctions. The structures suggest a possible mechanism for branch migration and detail a pathway linking the antiparallel uncrossed Holliday structure inferred from solution measurements and the parallel cross-packed helical arrangements observed in single-crystal X-ray studies.

Algorithms↗
PubMed2000

3-Methyladenine-DNA glycosylase I from Escherichia coli-computer modeling and supporting experimental evidence.

TagA (3-methyladenine-DNA glycosylase I) excises 3-methyadenine and 3-methylguanine from alkylated DNA. The structure of this enzyme has not yet been determined experimentally. We propose a three-dimensional model of the TagA protein based on the threading algorithm. The model shows that TagA is a mostly alpha-helical protein, in agreement with circular dichroism measurements. None of the eight cysteines present in the TagA sequence forms a disulfide bridge in the model structure, which has also been experimentally verified with the use of Ellman method.

Algorithms↗
PubMedDate not supplied

Computational model of the jamming avoidance response in the electric fish Gymnotus carapo.

The unperturbed electric organ discharges of Gymnotus carapo fish are highly periodic with interpulse intervals around 40 ms. The 'jamming avoidance response' happens when fish interact and is a transitory interval shortening in the fish with the faster discharge that decreases the likelihood that pulses from it and the other fish will coincide. Our model's basic components match certain experimentally demonstrated facts. First, recurrence equations reproduce the periodic unperturbed discharges. Secondly, when an isolated pulse arrives, the two intervals following that with the pulse are shortened by amounts that decrease up to a minimum and then increase. Simulations demonstrated that this model reproduces satisfactorily the jamming avoidance response. Two additional conditions were demonstrably necessary: (i) one was that every pulse arrive within the hot cophase window (and not elsewhere); (ii) the other condition was that, along successive pulses, the respective cophases decrease by moderate amounts. In short, we conclude that the fish's jamming avoidance response can involve the simple computational rules implied by the proposed equations.

Animals↗
PubMed1995

Structural changes in actin-tropomyosin during muscle regulation: computer modelling of low-angle X-ray diffraction data.

The crystal structure of G-actin monomer has been used together with tropomyosin in a filament model to explain the low-angle X-ray diffraction data from relaxed and activated actin filaments. The four-subdomain actin monomer can be approximated quite well by a four-sphere unit. Orienting this unit and tropomyosin into a filament by searching for the best fit between the computed Fourier transform and the observed vertebrate skeletal muscle low-angle actin layer-lines from muscles at non-overlap sarcomere lengths produced models for the structural changes within the thin filaments (actin plus tropomyosin) between the resting state and the active states, which occur as a result of calcium-activation and independent of myosin interaction with actin. The models are very sensitive to changes in the positions of the centres of mass of the subdomains, but not to the exact shape of the objects used to represent them (e.g. spheres, ellipsoids etc.), as long as the volume is fixed, at the resolution here considered. It is concluded that, even with a four-subdomain structure for the actin molecules, the observed low-angle X-ray diffraction patterns cannot be explained without a substantial azimuthal swing of the tropomyosin strands when resting filaments are calcium-activated. The direction of this swing upon calcium-activation is away from a position close to the proposed major binding site of the myosin head on actin; a result consistent with the original "steric blocking model" of thin filament-based regulation in which the tropomyosin position on actin is crucial for regulation of the myosin crossbridge cycle on actin. Tropomyosin sterically hindering myosin attachment in the "off" state remains a possibility. However, even in the "on" state, the tropomyosin position is close enough to the myosin-binding site to have an effect, where it could regulate the transition of the head from a weak to a strong state. In addition to this tropomyosin movement there are small, but plausible, actin subdomain movements. A tropomyosin shift on its own will not explain the data. Allowance for possible movement of actin subdomain 2 along with the tropomyosin shift still does not explain the data. An additional small movement of subdomain 1; the main myosin-binding subdomain, is postulated.

Actin Cytoskeleton↗
PubMed2003

Computer modeling and nanosecond simulation of the enzyme-substrate complex of the common lymphoblastic leukemia antigen (neprilysin) indicates shared residues at the primary specificity pocket (S1') with matrix metalloproteases.

The common acute lymphoblastic leukemia antigen (neprilysin, CD10, neutral endopeptidase 24.11) is a member of the neprilysin family, and projects functions in signaling pathways in pathophysiological processes such as cancer, Alzheimer's disease and hypertension. Given its pathophysiological importance, an investigation of the natural substrate specificity of this metalloprotease is presented here through the application of enzyme-substrate modeling and molecular dynamics simulations. The results show that the substrate modeled, LATAC downward arrow FG, satisfies a complementary backbone H-bonding with Ala543-Tyr545, thereby suggested to be the putative substrate-binding beta-sheet, analogously to matrix metalloproteases. The modeling further suggests that phenylalanine at the P1' position (substrate) is directed in the same fashion as the synthetic inhibitor of the reference crystal structure and that this enzyme does not bind the P3'/P4' positions of a substrate, as other metalloproteases do. After a specific comparison with one member of the matrix metalloproteases, MMP-3, a common conserved valine residue at the primary S1' subsite was found to be shared between these two otherwise different proteases. These results may prove useful for selective drug design for neprilysin, and lay a foundation for future subsite analysis for other members of the neprilysin family.

Binding Sites↗
PubMed1993

Global characterization of protein secondary structures. Analysis of computer-modeled protein unfolding.

Analyses of structural and molecular shape changes undergone by a protein during an unfolding process are presented. The procedure, based on a spherical shape map method, provides a topological description of a three-dimensional macromolecular structure. Local properties of the backbone are used to derive a global characterization of its fold. A spherical shape map of backbone crossings is associated with a given macromolecular conformation. The map is built by classifying each point on the sphere according to the crossing pattern obtained when the backbone is observed along a direction defined by the center of the sphere and the chosen point. The surface of the sphere can be divided in equivalence classes. All the points within a given class correspond to directions from which the backbone has the same overcrossing pattern. Automatic computation and display of these equivalence classes is discussed, as is the implementation of the technique on a computer graphics workstation. The graphical manipulation simplifies the analysis of these maps when following a change in the conformation of the backbone. The procedure is illustrated with the results of a molecular dynamics computer simulation of the unfolding of the bacteriophage T4 glutaredoxin protein (in the form of its polyglycine model). The method gives a novel description of the differential structural stability for the characteristic secondary structural elements (alpha-helices and beta-sheets) present in the protein. Recognition of the persistence of structural elements over the simulation time is performed in an unbiased manner.

Algorithms↗
PubMed2007

Computer modeling of patient flow in a pediatric emergency department using discrete event simulation.

UNLABELLED: Increasing patient census and department overcrowding are universal concerns in pediatric emergency medicine. Accurate predictions of patient flow and resource utilization in the pediatric emergency department (PED) are important in determining what aspects of PED activity could be modified to improve patient flow, reduce patient waiting times, and increase staff efficiency and morale, and thus direct change more effectively. BACKGROUND: We report (1) the construction of a Patient Flow Model (PFM) using discrete event simulation to test simulated PED staffing scenarios that were designed to alleviate the pressures that result from increased census and overcrowding, and (2) a Physician Scheduling Analysis Tool to assist in physician scheduling. METHODS: Arena discrete event simulation modeling software was used to develop a model of PED patient flow after extensive interviews with PED staff and direct observation of patient flow in July 2005. A total of 517 patients were directly observed, and all modeled aspects of their interaction with PED staff and resources were recorded. Historical demographic patient arrival information was combined with observed patient flow data to provide simulated patient arrival rates for the PFM and was also used to construct the Physician Scheduling Analysis Tool. Validation of the PFM was performed by comparing annual simulated patient flow data with actual patient flow data. Previously determined staffing scenarios were applied to the simulation and the resulting performance indicator outputs examined. RESULTS: The PFM was validated on model-wide and process-specific levels, with excellent validation observed on high acuity-patient length of stay and for highly detailed processes such as triage and registration. Simulation of the addition of a hospital volunteer and a second triage nurse demonstrated reductions in pretriage waiting time and the proportion of patients waiting longer than 30 or 60 minutes for pretriage. Simulation of an extra physician shift to the staff schedule demonstrated reductions in length of stay for patients of all triage categories. CONCLUSIONS: The PFM accurately represents patient flow through the department and can provide simulated patient flow information on a variety of scenarios. It can effectively simulate changes to the model and its effects on patient flow.

Appointments and Schedules↗
PubMed2006

Computational modeling of biologically active molecules using NMR spectra.

The molecular structure and NMR chemical shift information of a compound can be combined to form powerful models of biological activity. NMR spectral data and structure information can be combined on a structural template analogous to 3D-QSAR methodology or orientation independently in spectral space. Surprisingly, quantitative spectrometric data-activity relationship (QSDAR) models built on structure templates are inferior to multi-dimensional QSDAR models built in spectral space. 3D-QSDAR modeling could be useful for estimating chemical toxicity, risk assessment of environmental contaminants and drug lead-compound identifications.

Anti-Bacterial Agents↗