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At least 343 records · Page 19Linked to original sources
PubMed2006

Analytical solutions of the first three frequency shifts of AFM non-uniform probe subjected to the Lennard-Jones force.

The role of higher cantilever modes is important to obtain some material contrast. The analysis of AFM subjected to a short-range force can improve greatly the studies of surface topography and interaction energies and interaction forces, especially for chemical and biological materials. When the tip-sample distance is in the order of inter-atomic spacing, the short-range tip-sample force is usually simulated by the Lennard-Jones model. In this study, the analytical method to determine the frequency shift of AFM subjected to the Lennard-Jones force is proposed. The closed-form solution of the partial differential equation with a nonlinear boundary condition is derived and then the corresponding frequency shifts of higher modes can be determined easily. Moreover, the conventional perturbation method is usually used to determine the frequency shift, but only for the first mode. This is because the original continuous beam system is transformed into a discrete lumped-masses model. Although the above disadvantages exist, the lumped-masses model is simple and intuitive. Using the principle of dynamic strain energy, the conventional perturbation method is revised successfully to determine the frequency shifts of higher modes. The assessment of the generalized perturbation method and the proposed method is made. Finally, the effects of several parameters on the first three frequency shifts are investigated.

Journal Article↗
PubMed1990

Theory for protein mutability and biogenesis.

Using an elementary physical model for protein folding, of self-avoiding short copolymer chains on two-dimensional square lattices, we address two questions regarding the evolution and origins of globular proteins. (i) How will protein native structures and stabilities be affected by single-and double-site mutations? (ii) What is the probability that a randomly chosen sequence of amino acids will be compact and globular under folding conditions? For a large number of different sequences, we search the conformational space exhaustively to find unequivocally the "native" conformation(s), of global minimum free energy, for each sequence. We find that replacing nonpolar residues in the core by polar residues is generally destabilizing, that surface sites are less sensitive than core sites, that some mutations increase the degeneracy of native states, and that overall it is most probable that a mutation will be neutral, having no effect on the native structure. These results support a "Continuity Principle," that small changes in sequence seldom have large effects on structure or stability of the native state. The simulations also show that (i) the number of "convergent" sequences (different sequences coding for the same native structure) is extremely large and (ii) most sequences become quite dense under folding conditions. This implies that the probability of formation of a globular protein from a random sequence of amino acids by prebiotic or mutational methods is significantly greater than zero.

Amino Acid Sequence↗
PubMed2000

First-order phase transition in a nonequilibrium growth process

We introduce a simple continuous model for nonequilibrium surface growth. The dynamics of the system is defined by the Kardar-Parisi-Zhang equation with a Morse-like potential representing a short range interaction between the surface and the substrate. The mean field solution displays a nontrivial phase diagram with a first-order transition between a growing and a bound surface, associated with a region of coexisting phases, and a tricritical point where the transition becomes second order. Numerical simulations in three dimensions show quantitative agreement with mean field results, and the features of the phase space are preserved even in two dimensions.

Journal Article↗
PubMed2006

Fracture spacing in layered materials and pattern transition from parallel to polygonal fractures.

We perform three-dimensional simulations of fracture growth in a three-layered plate model with an embedded heterogeneous layer under horizontal biaxial stretch (representing stretch from directional to isotropic) by the finite element approach. The fractures develop under a quasistatical, slowly increasing biaxial strain. The material inhomogeneities are accounted for by assigning each element a failure threshold that is defined by a given statistical distribution. A universal scale law of fracture spacing to biaxial strain in terms of principal stress ratio is well demonstrated in a three-dimensional fashion. The numerically obtained fracture patterns show a continuous pattern transition from parallel fractures, laddering fracture to polygonal fractures, which depends strongly on the far-field loading conditions in terms of principal stress ratio lambda = sigma(2)/sigma(1), from uniaxial (lambda = 0), anisotropic (0 < lambda < 1) to isotropic stretch (lambda = 1). We find that, except for further opening of existing fractures after they are well-developed (saturation), new fractures may also initiate and propagate along the interface between layers, which may serve as another mechanism to accommodate additional strain for fracture saturated layers.

Journal Article↗
PubMed2002

Image transfer through cirrus clouds. II. Wave-front segmentation and imaging.

A hybrid technique to simulate the imaging of space-based objects through cirrus clouds is presented. The method makes use of standard Huygens-Fresnel propagation beyond the cloud boundary and a novel vector trace approach within the cloud. At the top of the cloud, the wave front is divided into an array of input gradient vectors, which are in turn transmitted through the cloud model by use of the Coherent Illumination Ray Trace and Imaging Software for Cirrus. At the bottom of the cloud, the output vector distribution is used to reconstruct a wave front that continues propagating to the ground receiver. Images of the object as seen through cirrus clouds with different optical depths are compared with a diffraction-limited image. Turbulence effects from the atmospheric propagation are not included.

Journal Article↗
PubMed2000

The acetabular labrum seal: a poroelastic finite element model.

OBJECTIVE: The aim of the study is to investigate the labrum's ability to seal a pressurised layer of synovial fluid within the joint, and to study the influence of this sealing mechanism on cartilage deformation, interstitial fluid pressure and collagen solid matrix stresses. BACKGROUND: Cartilage degeneration has been observed in conjunction with labrum pathology. However, little is known about the function of the labrum. Experimental observations have been reported which are consistent with a sealing function of the labrum. METHODS: The model was an axisymmetric geometric approximation of the acetabular and femoral cartilage layers and the surrounding labrum. A poroelastic formulation was used to account for the solid and fluid components of these hydrated tissues. A sensitivity analysis of the labrum material properties was carried out. RESULTS: With a compressive load of 1200 N applied across the joint model, the labrum could seal a layer of pressurised fluid between the femur and acetabulum, thus preventing contact of the articulating surfaces. With this sealing effect, loads were transferred across the joint predominantly by uniform pressurisation of the interstitial fluid of the cartilage layers. In the absence of this sealing, strains within the solid matrix of the cartilage layers were higher (e.g. 20% vs. 3%). CONCLUSIONS: The labrum can seal against fluid expression from the joint space. This sealing function protects the cartilage layers of the hip. RELEVANCE: Current treatments for labrum damage and early arthrosis may compromise the sealing function of the labrum. With continued study of the function and importance of the labrum, new surgical repair strategies can be developed to maintain the overall function of the hip joint.

Acetabulum↗
PubMed2004

Pattern formation and fluctuation-induced transitions in protein crystallization.

A kinetic model of protein crystallization accounting for the nucleation stage, the growth and competition of solid particles and the formation of macroscopic patterns is developed. Different versions are considered corresponding successively, to a continuous one-dimensional crystallization reactor, a coarse grained two-box model and a model describing the evolution of the space averaged values of fluid and solid material. The analysis brings out the high multiplicity of the patterns. It provides information on their stability as well as on the kinetics of transitions between different states under the influence of the fluctuations.

Binding Sites↗
PubMed2002

Effects of the hindlimb-unloading model of spaceflight conditions on resistance of mice to infection with Klebsiella pneumoniae.

BACKGROUND: It has been well documented in several studies that many immunologic parameters are altered in experimental animals and human subjects who have flown in space. However, it is not fully known whether these immunologic changes could result in increased susceptibility to infection. Hindlimb (antiorthostatic) unloading of rodents has been used successfully to simulate some of the effects of spaceflight on physiologic systems. OBJECTIVE: The objective of this study was to determine the effect of hindlimb unloading on the outcome of Klebsiella pneumoniae infection in mice. METHODS: Hindlimb-unloaded, hindlimb-restrained, and control mice were intraperitoneally infected with one 50% lethal dose of K pneumoniae 2 days after suspension. Mortality and bacterial load in several organs were compared among the groups. RESULTS: Unloaded mice showed significantly increased mortality and reduced mean time to death compared with that seen in the control groups. Kinetics of bacterial growth with smaller infective doses revealed that control mice were able to clear bacteria from the organs after 30 hours. In contrast, unloaded mice had continued bacterial growth at the same time point. CONCLUSION: The results of this study suggest that hindlimb unloading might enhance the dissemination of K pneumoniae, leading to increased mortality. The complex physiologic changes observed during hindlimb unloading, including stress, have a key role in the pathophysiology of this infection.

Animals↗
PubMed2005

Self-organizing continuous attractor network models of hippocampal spatial view cells.

Single neuron recording studies have demonstrated the existence of hippocampal spatial view neurons which encode information about the spatial location at which a primate is looking in the environment. These neurons are able to maintain their firing even in the absence of visual input. The standard neuronal network approach to model networks with memory that represent continuous spaces is that of continuous attractor networks. It has recently been shown how idiothetic (self-motion) inputs could update the activity packet of neuronal firing for a one-dimensional case (head direction cells), and for a two-dimensional case (place cells which represent the place where a rat is located). In this paper, we describe three models of primate hippocampal spatial view cells, which not only maintain their spatial firing in the absence of visual input, but can also be updated in the dark by idiothetic input. The three models presented in this paper represent different ways in which a continuous attractor network could integrate a number of different kinds of velocity signal (e.g., head rotation and eye movement) simultaneously. The first two models use velocity information from head angular velocity and from eye velocity cells, and make use of a continuous attractor network to integrate this information. A fundamental feature of the first two models is their use of a 'memory trace' learning rule which incorporates a form of temporal average of recent cell activity. Rules of this type are able to build associations between different patterns of neural activities that tend to occur in temporal proximity, and are incorporated in the model to enable the recent change in the continuous attractor to be associated with the contemporaneous idiothetic input. The third model uses positional information from head direction cells and eye position cells to update the representation of where the agent is looking in the dark. In this case the integration of idiothetic velocity signals is performed in the earlier layer of head direction cells.

Action Potentials↗
PubMed2004

A tree based lack-of-fit test for multiple logistic regression.

Several omnibus tests have been developed to assess the fit of a regression model. But many of these lack-of-fit tests focus on the simple regression setting. Here, we focus on multiple logistic regression. Pearson's well-known chi-square test statistic and the deviance statistic are no longer valid in the case that the model contains one or more continuous covariates. To overcome this difficulty, Hosmer and Lemeshow proposed a Pearson type statistic based on groups defined by the so-called deciles of risk. We propose a test statistic that is similar in approach to the Hosmer and Lemeshow statistic in that the observations are classified into distinct groups. In the procedure proposed here however, the grouping is not according to probabilities fitted under the null model. We use a recursive partitioning algorithm to divide the sample space into different groups. This generally allows for a more powerful assessment of the model fit. Simulations are carried out to compare the results of the proposed test to that of Hosmer and Lemeshow. Three data examples illustrate the performance of the tree based lack-of-fit test, in comparison to several other tests.

Adult↗
PubMed1983

Monitoring variations of biological impedances using microwave Doppler radar.

A microwave Doppler radar for continuously monitoring time-varying biological impedances is described. The radar compares the phase of the signal scattered from a region of biological tissue with that of the transmitted signal. The phase changes of the scattered signal are an indication of the net impedance changes within the test region due to various physiological processes, for example, the displacements of blood vessels during the cardiac cycle. A Doppler radar, equipped with a matched antenna, was tested with a simulation model and its detection characteristic was found to be a sinusoidal function of the antenna-object spacing. Tests with healthy human subjects were also performed at 3 GHz and 10.5 GHz. It was found that the 3 GHz Doppler radar has significantly greater penetration in tissues but is less sensitive to changes of the biological impedance than the 10.5 GHz system.

Doppler Effect↗
PubMed1993

An ACSL simulation of the respiratory system.

A simulation program for the respiratory system using ACSL (Advanced Continuous Simulation Language) is presented. The underlying model is based on the representation of ventilation as a phasic air movement in lungs during the respiratory cycle. The translation of the model with ACSL instructions is described in particular for continuous processes, such as respiratory gas exchanges, and discrete events, such as changes of respiratory phase. The advantages of using ACSL are discussed, and the utility of such a simulation program in both research and education is demonstrated.

Algorithms↗
PubMed2002

Analysis of kinetics using a hybrid maximum-entropy/nonlinear-least-squares method: application to protein folding.

A hybrid analysis that combines the maximum entropy method (MEM) with nonlinear least squares (NLS) fitting has been developed to interpret a general time-dependent signal. Data that include processes of opposite sign and a slow baseline drift can be inverted to obtain both a continuous distribution of lifetimes and a sum of discrete exponentials. Fits by discrete exponentials are performed with initial parameters determined from the distribution of lifetimes obtained with the MEM. The regularization of the parameter space achieved by the MEM stabilizes the introduction of each successive exponential in the NLS fits. This hybrid approach is particularly useful when fitting by a large number of exponentials. Revision of the MEM "prior" based on features in the data can improve the lifetime distribution obtained. Standard errors in the mean are estimated automatically for raw data. The results presented for simulated data and for fluorescence measurements of protein folding illustrate the utility and accuracy of the hybrid algorithm. Analysis of the folding of dihydrofolate reductase reveals six kinetic processes, one more than previously reported.

Algorithms↗
PubMed2003

Phase retrieval in digital speckle pattern interferometry by use of a smoothed space-frequency distribution.

We evaluate the use of a smoothed space-frequency distribution (SSFD) to retrieve optical phase maps in digital speckle pattern interferometry (DSPI). The performance of this method is tested by use of computer-simulated DSPI fringes. Phase gradients are found along a pixel path from a single DSPI image, and the phase map is finally determined by integration. This technique does not need the application of a phase unwrapping algorithm or the introduction of carrier fringes in the interferometer. It is shown that a Wigner-Ville distribution with a smoothing Gaussian kernel gives more-accurate results than methods based on the continuous wavelet transform. We also discuss the influence of filtering on smoothing of the DSPI fringes and some additional limitations that emerge when this technique is applied. The performance of the SSFD method for processing experimental data is then illustrated.

Journal Article↗
PubMed2000

Thermal physiological consideration of precooling procedures in manned space craft.

OBJECTIVE: To explore a space craft precooling temperature at which excessive thermal stress on the crew member could be prevented or reduced in an overheated launch or reentry module. METHOD: Five young male volunteers wearing a space suit participated in 25 tests at sea level. The space suit was either ventilated in a volume air flow rate of 100 L/min (STPD) with ambient air at temperatures (Ta) of 15 degrees C, 10 degrees C, and 5 degrees C, respectively, or not ventilated. Rectal (Tr), mean skin (Tsk) and mean body (Tb) temperatures were measured. RESULT: At Ta 15 degrees C, Tr decreased without significance (from 37.0 +/- 0.2C to 36.7 +/- 0.3 degrees C) in 120-min tests, whereas mean Tsk and mean Tb decreased significantly, and subjects had local cold strain whether the space suit was ventilated or not; while at Ta 10 degrees C, Tr decreased from 37.0 +/- 0.3 degrees C to 36.3 +/- 0.3 degrees C (P < 0.05), subjects had a whole body cold strain, and both mean Tsk and Tb dropped continuously and significantly. CONCLUSION: Ambient temperature 15 degrees C, at which the thermal comfort states of crew was not significantly degraded, was acceptable after precooling in a space craft.

Adolescent↗
PubMed1976

The wick catheter technique for measurement of intramuscular pressure. A new research and clinical tool.

The wick catheter technique was developed in 1968 for measurement of subcutaneous pressure and has been modified for easy intramuscular insertion and continuous recording of interstitial fluid pressure in animals and humans. Studies in dogs of the anterolateral compartment of the leg in simulation of the compartment syndrome showed the technique to be accurate and reproducible. The wick catheter technique is capable of important clinical applications in the diagnosis and treatment of acute and chronic compartment syndromes.

Animals↗
PubMed1993

Rotating-wall vessel coculture of small intestine as a prelude to tissue modeling: aspects of simulated microgravity.

A new low shear stress, low turbulence microcarrier culture system has been developed at NASA's Johnson Space Center that permits large-scale three-dimensional tissue culture. Tissue culture bioreactors called rotating-wall vessels were used in conjunction with multicellular cocultivation to develop a unique in vitro tissue-modeling system. Normal small intestine epithelium and mesenchymal cells were cocultivated on Cytodex-3 microcarriers and were initiated in two phases. Normal small intestine mesenchymal cells were inoculated into the rotating-wall vessel at 2 x 10(5) cells/ml and allowed to attach and proliferate for 2 to 3 days. Normal small intestine epithelium was then added at an innoculum of 2 x 10(5) cells/ml and cultivation continued for 30 to 40 days. These cocultures attained cell numbers of 4-6 x 10(6) cells/ml and differentiated to form tissue-like masses of 0.4-0.5 cm with minimal necrosis. The masses displayed apical brush borders, differentiated epithelial cells, cellular polarity, extracellular matrix, and basal lamina. Verification of mesenchymal and epithelial cell expression was determined by immunocytochemistry and scanning electron microscopy. These data suggest that the rotating-wall vessel affords a new tissue culture model for investigation of growth, regulatory, and differentiation processes within normal tissues.

Biomarkers↗
PubMed2006

Segmentation and three-dimension reconstruction of Chinese digitized human cerebrum.

OBJECTIVE: A 3D digitized visible model of human cerebrum was built to provide anatomical structure for making plans of cerebral surgical operation and realizing accurate simulation of cerebrum on computer. METHODS: Transverse sectional anatomy data of the cerebrum were chosen from the first Chinese visible human (one male and one female). Semi-automated segmentation and Photoshop software were selected to segment cerebral cortex, white matter, basal nuclei, lateral ventricle, hippocampus, etc. On personal computer, the segmented structures were reconstructed in 3D with volume rendering reconstruction and surface rendering reconstruction. RESULTS: Two accurately segmented images of the main structures of cerebrum were completed. The reconstructed structures can be displayed singly, in small groups or as a whole and can be continuously rotated in 3D space at different velocities. CONCLUSION: Combining volume-rendering reconstruction with surface rendering reconstruction overcomes the defects of surface rendering reconstruction that lack of internal anatomical information, which provides a new method for 3D reconstruction. The reconstructed cerebrum and the main internal structures are realistic, which demonstrates the natural shape and exact position of the structures. It provides an accurate model for the automated segmentation algorithmic study and provides a digitized anatomical mode of cerebrum.

China↗