SEARCH · PubMed Health

Results for “Computer Simulation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 775 records · Page 43Linked to original sources

PubMed2006

Modelling the biomechanical properties of DNA using computer simulation.

Duplex DNA must remain stable when not in use to protect the genetic material. However, the two strands must be separated whenever genes are copied or expressed to expose the coding strand for synthesis of complementary RNA or DNA bases. Therefore, the double stranded structure must be relatively easy to take apart when required. These conflicting biological requirements have important implications for the mechanical properties of duplex DNA. Considerable insight into the forces required to denature DNA has been provided by nanomanipulation experiments, which measure the mechanical properties of single molecules in the laboratory. This paper describes recent computer simulation methods that have been developed to mimic nanomanipulation experiments and which, quite literally, 'destruction test' duplex DNA in silico. The method is verified by comparison with single molecule stretching experiments that measure the force required to unbind the two DNA strands. The model is then extended to investigate the thermodynamics of DNA bending and twisting. This is of biological importance as the DNA must be very tightly packaged to fit within the nucleus, and is therefore usually found in a highly twisted or supercoiled state (in bacteria) or wrapped tightly around histone proteins into a densely compacted structure (in animals). In particular, these simulations highlight the importance of thermal fluctuations and entropy in determining the biomechanical properties of DNA. This has implications for the action of DNA processing molecular motors, and also for nanotechnology. Biological machines are able to manipulate single molecules reliably on an energy scale comparable to that of thermal noise. The hope is that understanding the statistical mechanisms that a cell uses to achieve this will be invaluable for the future design of 'nanoengines' engineered to perform new technological functions at the nanoscale.

Biomechanical Phenomena↗

PubMed1997

Mechanism and computer simulation of a new robot hand for potential use as an artificial hand.

A prosthetic hand is essential to provide rehabilitation for individuals who lose a hand. A prosthetic hand serves two purposes: cosmetic and functional. In this paper, a prototype of the artificial hand with an emphasis on the functionality purpose is presented. A new mechanism, the NTU-Hand (NTU-Hand, patent number 107115, Taiwan, R.O.C.), which has 5 fingers with 17 degrees of freedom, has been designed and fabricated in our laboratory. Due to the special design of the mechanism, the hand has an uncoupled configuration in which each finger and joint are all individually driven. The size of the hand is almost the same as a human hand. All actuators, mechanical parts, and sensors are on the hand. The compact design makes it feasible to adapt the hand to the injured wrist. A computer simulation with three-dimensional graphics was also built to evaluate the manipulative range of the artificial hand. From the results of this simulation, the relationship between the hand and the grasped object in a specific viewpoint can be obtained.

Artificial Limbs↗

PubMed1996

Computer simulation of PPF distribution under blue and red LED light source for plant growth.

The superimposed pattern of "luminescence spectrum of blue light emitting diode (LED)" and "that of red LED", corresponds well to light absorption spectrum of chlorophyll. If these two kinds of LED are used as a light source, various plant cultivation experiments are possible. The cultivation experiments which use such light sources are becoming increasingly active, and in such experiments, it is very important to know the distribution of the photosynthetic photon flux (PPF) which exerts an important influence on photosynthesis. Therefore, we have developed a computer simulation system which can visualize the PPF distribution under a light source equipped with blue and red LEDs. In this system, an LED is assumed to be a point light source, and only the photons which are emitted directly from LED are considered. This simulation system can display a perspective view of the PPF distribution, a transverse and a longitudinal section of the distribution, and a contour map of the distribution. Moreover, a contour map of the ratio of the value of the PPF emitted by blue LEDs to that by blue and red LEDs can be displayed. As the representation is achieved by colored lines according to the magnitudes of the PPF in our system, a user can understand and evaluate the state of the PPF well.

Agriculture↗

PubMed2001

A computer simulation model for cost-effectiveness analysis of mass screening for Type 2 diabetes mellitus.

The cost-effectiveness analysis of mass screening for Type 2 diabetes mellitus (DM) was performed to elucidate whether, who and how often it should be conducted in Taiwan. A series of Markov process was developed to model the disease natural history of Type 2 DM. A hypothetical cohort with 30,000 residents aged over 30 years in Taiwan was randomly assigned to three arms of screening regimes, biennial, five-yearly and the control group. A Monte Carlo computer simulation was performed to calculate effectiveness of two screening regimes compared with the control group. Direct costs and utilities were incorporated to each corresponding state to calculate the incremental costs per life-years gained and per quality-adjusted life-years (QALYs) for biennial and five-yearly screening regimes. The incremental costs for biennial screening regime were estimated at $26,750 per life-year gained, and $17,833 per QALY. The corresponding figures for five-yearly screening regime were $10,531 per life-year gained and $17,113 per QALY. The incremental costs per life-year gained and per QALY increase with age, ranging from $17,238 for aged 30-39 years to $54,700 for aged over 70 years and from $9193 to 36,467, respectively. In conclusion, mass screening for Type 2 DM, especially in younger subjects, with 5-year inter-screening interval is cost-effective in Taiwan.

Computer Simulation↗

PubMed2000

Molecular determinants of MAO selectivity in a series of indolylmethylamine derivatives: biological activities, 3D-QSAR/CoMFA analysis, and computational simulation of ligand recognition.

A series of indolylmethylamine derivatives were assayed toward MAO-A and MAO-B inhibition. The K(i) values of these compounds are in the range from 0.8 to >10(6) nM for MAO-A or from 0.75 to 476000 nM for MAO-B. The most selective MAO-A or MAO-B inhibitors elicit a ratio of K(i) in the order of 1500 or 1000, respectively. Comparison of MAO-A and MAO-B CoMFA models showed that both the steric and electrostatic properties at the 5 position of the indole ring are determinant for MAO selectivity. Computational simulations of the complex between this part of the ligand and Phe-208 of MAO-A or Ile-199 of MAO-B, experimentally identified as responsible for substrate selectivity, allowed us to further characterize the nature of these enzyme-inhibitor interactions.

Amines↗

PubMed2000

Computer simulation analysis suggests weak balancing selection operative at the MICA locus.

A high degree of polymorphism has been reported at the major histocompatibility class I chain-related gene A (MICA) locus, which is located 46 kb away from HLA-Bin the human major histocompatibility complex (MHC) class I region. Although it is known that the polymorphisms at the conventional MHC class I loci have been maintained by balancing selection, it is unclear whether positive natural selection is also operative in maintaining the polymorphism at the MICA locus. In order to explain the degree of polymorphism at the MICA locus, a computer simulation study was carried out. The high degree of polymorphism at the MICA locus (heterozygosity and number of polymorphic residues) could not be explained solely by balancing selection at the HLA-B locus even if no recombination was assumed between MICA and HLA-B. Although there is no definite evidence indicating that balancing selection is operative at the MICA locus, our results suggest that the MICA gene is subject to weak balancing selection.

Alleles↗

PubMed2000

Computer simulation approach to the quantification of immunogold labelling on plasma membrane of cultured neurons.

Cell culture is a convenient model system to study the expression of plasma membrane-bound proteins in nerve cells. Analysing it with an ultrastructural detail researchers often apply transmission electron microscopy together with immunogold labelling. Plasma membrane profiles are one-dimensional (1D) and provide little information about the topography of membrane-bound proteins. In order to convert 1D estimates of spatial arrangement for preembedding immunogold labelled proteins into two-dimensional (2D) quantities, namely the 2D pattern and density of labelling, this paper presents a simple computer simulation technique. This technique is based on a mathematical model permitting a simulated immunogold labelled membrane to be sampled in a way similar to microtome sectioning. An interlabel distance (ILD) estimate is used to define the position of immunogold particles in membrane profiles. In order to interpret experimental ILD measurements the simulated distribution best fit to the experimental data is selected and the corresponding 2D density and pattern of particle scattering are considered to explain the real situation. Various parameters including a cell section thickness, immunogold particle size etc can be adjusted to suit the demands of a particular experiment. The technique was applied to quantify the NCAM preembedding immunogold labelling in the plasma membrane of cultured rat hippocampal neurons.

Animals↗

PubMed2003

Evidence for dynamic heterogeneities in computer simulations of miscible polymer blends.

The controversial origins of the unusual dynamics of miscible polymer blends are incisively probed through computer simulations. The distribution of mobilities experienced by a probe monomer in a miscible blend of chains with disparate glass transition temperatures is found to be much broader than in the pure polymers, providing clear evidence for local concentration variations in the mixture. These concentration fluctuations yield distinctly different temperature dependences for the dynamics of the two different components, in a manner that closely mimics experiments.

Journal Article↗

PubMed1991

Quantitative study of the susceptibility difference between trabecular bone and bone marrow: computer simulations.

Inherent differences in tissue magnetic susceptibility produce inhomogeneities in the static magnetic field which give rise to an additional dephasing of the transverse magnetization in gradient-echo images. The enhanced dephasing of the signal results in an increase of the apparent relaxation rate 1/T2* and a corresponding decrease in signal intensity. These effects have been used to explain the regional loss of marrow signal intensity in the appendicular skeleton, where in the presence of trabecular bone in the proximal tibia there is an enhanced loss of signal compared to the tibial shaft where there is no trabeculation. It has been postulated that differences in tissue magnetic susceptibility arising due to the marrow--trabeculae interface give rise to magnetic field inhomogeneities and a reduced T2*. In this study computer simulations are used to determine whether susceptibility differences comparable to that between trabecular bone and tissue relate to the reduction of tissue T2* and whether the reduction in T2* is also related to the concentration and magnitude of susceptibility differences. In addition the effects of the spatial distribution of these particulate discontinuities in susceptibility on the measured relaxation time T2* are also estimated. This model demonstrates that 1/T2* increases as the number density and magnitude of such susceptibility differences increase. In a pixel of linear dimension L consisting of material simulating tissue water, the presence of circular point susceptibility differences of dimension 0.001 L with magnetic susceptibility equivalent to trabecular bone, 1/T2*, increases at a rate of 1.60 x 10(-2) s-1/N for N ranging from 25-2500. Differences in magnetic susceptibility that are less than that between soft tissue and trabecular bone are also modeled and the simulations demonstrate that differences in magnetic susceptibility, much lower than that between trabecular bone and tissue equivalent interfaces, also produce a relaxation rate enhancement in gradient-echo images.

Bone Marrow↗

PubMed1991

Different types of rectification at electrical synapses made by a single crayfish neurone investigated experimentally and by computer simulation.

The rectification properties of electrical synapses made by the segmental giant (SG) neurone of crayfish (Pacifastacus leniusculus) were investigated. The SG acts as an interneurone, transmitting information from the giant command fibres (GFs) to the abdominal fast flexor (FF) motoneurones. The GF-SG (input) synapses are inwardly-rectifying electrical synapses, while the SG-FF (output) synapses are outwardly rectifying electrical synapses. This implies that a single neurone can make gap junction hemichannels with different rectification properties. The coupling coefficient of these synapses is dependent upon transjunctional potential. There is a standing gradient in resting potential between the GFs, SG and FFs, with the GFs the most hyperpolarized, and the FFs the most depolarized. The gradient thus biases each synapse into the low-conductance state under resting conditions. There is functional double rectification between the bilateral pairs of SGs within a single segment, such that depolarizing membrane potential changes of either SG pass to the other SG with less attenuation than do hyperpolarizing potential changes. Computer simulation suggests that this may result from coupling through the intermediary FF neurones.

Animals↗

PubMed2006

Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding.

Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2'-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNA-RNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using computer simulations of rRNA secondary structure formation by genetic algorithm. The effects of sRNA binding on rRNA structure are introduced as temporary structural constraints during co-transcriptional folding. Comparisons of the final predictions with simulations without sRNA binding and with phylogenetic structures show that sRNAs with two antisense elements may significantly facilitate the correct formation of long-range interactions in rRNAs, in particular at elevated temperatures. The simulations suggest that the main mechanism of this effect is a transient restriction of folding in rRNA domains where the termini are brought together by binding to double-guide sRNAs.

Archaeoglobus fulgidus↗

PubMed1985

Computer simulation for hormones related to primary thyropathy.

We propose a mathematical model of the human hypothalamus-anterior pituitary-thyroid system regulating basal metabolism, and practice computer simulation concerning primary thyropathy such as Graves' disease, hypothyroidism, T4-toxicosis and T3-toxicosis by use of this model. In order to throw light on properties of the system, indicial responses of the hormones, T4, T3, rT3, and TSH, and the function of the thyroid gland are computed. Medical treatments for Graves' disease and for hypothyroidism are simulated with a view to enhancing clinical significance. Performance of the simulation leads to an interesting result that when the convertion rate of blood T4 to blood T3 increases, explicit T3-toxicosis occurs, although the function of the thyroid gland is normal.

Computers↗

PubMed1996

Loci of movement of selected points on the femoral head during normal gait. Three-dimensional computer simulation.

Wear of ultrahigh-molecular-weight polyethylene and the subsequent lytic response to the particulate wear debris are the dominant problems in total joint arthroplasty surgery. Wear testing apparatus can play a vital role in the in vitro evaluation of the many factors involved in wear, such as head size, surface roughness, materials for the head, and new materials for the socket. Wear of ultrahigh-molecular-weight polyethylene may be influenced by the wear path. For the related polymer, high-density polyethylene, the wear path is critical to wear magnitude. What is the actual path taken by a single point (or by multiple representative points) on the femoral head of a total hip arthroplasty as it passes through the gait cycle? The goal of this computer simulation study was to trace the paths of specific points on the femoral head as they moved against the polyethylene cup during a single cycle of normal gait to illustrate the motions occurring at the intraarticular surface of the hip joint. This study also yielded unusual data on the "distance traversed" by these points during a single gait cycle. It was found that there was not one path, but rather there were many, and the paths varied widely in both shape and length depending on the location on the femoral head. Moreover, the differences in excursion and direction at different sites during the loaded phase were great. In addition, distances traveled by different points on the femoral head of any given size varied by a factor greater than 2. Most of the points traced quasielliptical paths. This automatically means that the paths of neighboring points cross each other, creating multidirectional shear forces on the acetabular cup surface which may be important in the localization and extent of wear. The plots of traces of the points derived from this study can serve as benchmarks for the ability of hip simulators to reproduce the actual distances and paths of travel of individual points on the femoral head.

Computer Simulation↗

PubMed1994

Computer simulation of brain cooling during cardiopulmonary bypass.

A mathematical model of heat transport was used to analyze the effects of convection, metabolism, and conduction on the rate of brain cooling and the final brain temperature during cardiopulmonary bypass. Convection, a function of cerebral blood flow and arterial blood temperature, is by far the most important process to determine the rate of brain cooling. Arterial blood temperature almost entirely determines the final brain temperature. Although conduction (head surface cooling) has little effect on the rate of brain cooling or final brain temperature in adults, it may have moderate effects in infants. Brain metabolic heat production has insignificant direct effects on the rate of brain cooling and final brain temperature in both adults or infants. Computer simulation of convective cooling of the adult brain to 27 degrees C shows that, with routine perfusion techniques, brain temperature equilibration is rapid (16 minutes) and small brain-blood temperature gradients are achieved. Simulation of infant brain cooling to 17 degrees C shows that, to avoid excessive brain-blood temperature gradients, 22 to 26 minutes may be required to achieve brain temperature equilibration.

Adult↗

PubMed2004

Computer simulation and mathematical model of blood glucose behaviour.

This work is considering three significant factors that affect blood glucose level: food intake, hereditary predisposition and stress. Goal of this paper is to observe blood sugar level in human organism as a dynamic MISO (Multi Input, Single Output) system, and to describe it with differential equations and control system blocks. The system has three inputs; food (carbohydrates), hereditary factor and stress, and a single output--blood glucose level. Basically, several logical assumptions have been made, as the result of few medical researches. A model that gives outputs, very similar to real ones (measurements of glucose level in human body) is used for more detailed analysis. This model is very suitable for computer simulations and it can easily be tested for different input arrangements. Using this property of the system, several modes of food consumption have been proposed, in order to retain blood sugar level inside recommended limits.

Blood Glucose↗

PubMed2004

A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences.

BACKGROUND: Determination of genetic relatedness among microorganisms provides information necessary for making inferences regarding phylogeny. However, there is little information available on how well the genetic relationships inferred from different genotyping methods agree with true genetic relationships. In this report, two genotyping methods - restriction fragment analysis (RFA) and partial genome DNA sequencing - were each compared to complete DNA sequencing as the definitive standard for classification. RESULTS: Using the Genbank database, 16 different types or subtypes of papillomavirus were selected as study samples, because numerous complete genome sequences were available. RFA was achieved by computer-simulated digestion. The genetic similarity of samples, based on RFA, was determined from the proportion of fragments that matched in size. DNA sequences of four specific genes (E1, E6, E7, and L1), representing partial genome sequencing, were also selected for comparison to complete genome sequencing. Laboratory error was not taken into account. Evaluation of the correlation between genetic similarity matrices (Mantel's r) and comparisons of the structure of the derived dendrograms (partition metric) indicated that partial genome sequencing (for single genes) had higher agreement with complete genome sequencing, achieving a maximum Mantel's r = 0.97 and a minimum partition metric = 10. RFA had lower agreement, with a maximum Mantel's r = 0.60 and a minimum partition metric = 18. CONCLUSIONS: This simulation indicated that for smaller genomes, such as papillomavirus, partial genome sequencing is superior to restriction fragment analysis in representing genetic relatedness among isolates. The generalizability of these results to larger genomes, as well as the impact of laboratory error, remains to be demonstrated.

Animals↗

PubMed1998

Posterior tilting of the tibial component decreases femoral rollback in posterior-substituting knee replacement: a computer simulation study.

Posterior tilting of the tibial component is thought to increase the range of motion in posterior cruciate-retaining total knee replacement, but its effect on implant motion in posterior cruciate-substituting total knee replacement is unknown. This issue has become of interest recently because manufacturers have introduced instrumentation that produces a posteriorly tilted tibial cut for both implant types. The purpose of this study was to investigate how motion of posterior cruciate-substituting total knee replacement is affected when the tibial component is installed with posterior tilt. Sagittal plane implant motions were predicted from prosthesis geometry with use of a computer simulation in which the femoral condyles were assumed to sit in the bottoms of the tibial condylar wells when the knee was in extension. Rollback of the femoral component was produced by a cam-spine mechanism at higher angles of flexion. The simulations revealed that even small degrees of posterior tilt reduced rollback by limiting the interaction between the cam and spine. Tilting the component posteriorly by 5 degrees caused the cam to contact the spine at a knee flexion angle that was 18 degrees higher than with the untilted component. The results suggest that posterior tilting of the tibial component in posterior cruciate-substituting knee replacement may not produce the same beneficial effects that have been reported for the tilting of tibial components in posterior cruciate-retaining knee replacement.

Arthroplasty, Replacement, Knee↗

PubMed1992

Is the experience with CHART compatible with experimental data? A new model of repair kinetics and computer simulations.

A new incomplete repair model is introduced that differs from previous models of this type by not assuming that repair is complete during long intervals, e.g. "overnight" intervals of 12-24 h. The model was used to assess the risk of myelopathy resulting from continuous hyperfractionated accelerated radiotherapy treatment (CHART) in light of recent experimental data on the rat spinal cord. Model calculations employing biexponential repair kinetics showed that CHART treatments might result in a higher myelopathy risk than an equal dose given in conventional 2-Gy fractions if the parameters obtained from the animal data hold. The probability of observing what has been reported for CHART was determined in computer simulations for different variance scenarios. The chance to observe four myelopathies in the 74 cervical cord patients was estimated to range between 25 and 62%, while the probability to see 0 in 68 thoracic cord patients ranged from 48 to 27%. These numbers were derived from reasonable assumptions about the repair kinetics (e.g. 60% of damage repaired with a half-time of 8 h) so that the over-all probability to observe 4/74 and 0/68 was maximized, and depending on the scenario fell in the range 12-17%. Finally, from these simulations a myelopathy risk of approximately 0.3-1.2% is predicted for the currently employed maximal CHART dose to the spinal cord, i.e. 42 Gy. We conclude that the CHART experience is not compatible with the new experimental data (p < 5%). Incomplete repair is unlikely to be the sole reason for the unexpected toxicity of CHART (p < or = 17%).(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗