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PubMed2001

[Numerical study of the effects (correction of efects) of size of inlets and outlets of ventilation system in experimental space station cabin].

OBJECTIVE: To make the status of flow and heat transfer fit the requirement of comfortable condition in the experimental cabin and ventilation and cooling in the apparatus cabin of the space station. METHOD: In present numerical simulation, a model approximate the practice at condition of the ventilation pipeline and influence of inlet and outlet was used, so that there is no need of supposing the distribution of outlets. In microgravity condition, the influence of the size of inlets and outlets on the flow field in the experimental space station cabin was studied. According to different function zones in the experimental space station cabin, the region at evenness parameter was put forward. RESULT: The taper inlet and crescent outlet had the best integrated performance. CONCLUSION: The use of variational section was recommended in designing and building of ventilation project in space station cabin.

Air Conditioning↗
PubMed1992

A reduced set of coordinates for modeling DNA structures: (I). A B-to-A transition pathway driven by pseudorotational angle.

The A-DNA and the B-DNA are two well characterized polymorphous forms of DNA duplex. By using Metropolis Monte Carlo Simulations in a reduced coordinate space, we have shown that the B in equilibrium with A transitions can be induced by forcing pseudorotational angle (W) to change between C3'-endo and C2'-endo puckerings. The energy barrier for the transition pathway is less than 10 Kcal.mol-1. Base-pair parameters x-displacement (Dx) and roll (rho), which have the largest differences between the two forms of structures, cannot drive the transition. Our results support the view that the bistable states of the DNA duplex are due to the bistable structures of the sugar ring.

Computer Simulation↗
PubMed2006

Effect of the increase in the height of lumbar disc space on facet joint articulation area in sagittal plane.

STUDY DESIGN: Computerized tomography (CT) of the lumbar spine cadaveric specimens was used to evaluate the effect of increasing the height of the disc space in the lumbar spine to the facet joint articulation in the sagittal plane. OBJECTIVE: To show how the facet joint articulation is affected by increasing the height of the disc space in the lumbar spine. SUMMARY OF BACKGROUND DATA: The Charité Artificial Disc (DePuy Spine, Inc., Raynham, MA) was successful in relieving low back pain in the majority of patients, yet there was still a significant number of patients who did not obtain pain relief, or their pain even worsened. The etiology of their pain is still not known. To our knowledge, no study has addressed the effect on the facet joints when the disc height is increased. METHODS: CT images passing through the center of the L3-S1 facet joints (sagittal plane) were obtained from 15 cadaveric lumbar spine specimens. The articulation overlap of facet joints in sagittal plane from the L3 to S1 was measured. A 1-mm incremental increase to a total 5 mm in disc space height was performed to simulate the changes seen in disc replacement. The change in the facet joint articulation overlap in sagittal plane at normal and each displacement was then measured. There were 5 lumbar spine specimens dissected to validate the technique and standardize the measurements. Mean, percentages, and standard deviation values were calculated for all measured dimensions. RESULTS: No significant difference was found between the measurements on CT and gross specimens (P > 0.05). In 15 specimens, the mean facet joint articulation overlap on the sagittal plane was: 16.29 +/- 1.20 mm (left) and 16.22 +/- 1.16 (right) at the L3-L4 level; 17.81 +/- 1.18 mm (left) and 17.74 +/- 1.18 mm (right) at the L4-L5 level; and 18.18 +/- 1.18 mm (left) and 18.23 +/- 1.15 mm (right) at the L5-S1 level. There is no significant difference between the measured values on left and right sides (P > 0.05). Each 1-mm incremental increase in disc space at the L3-L4 level translated to a decrease in the facet joint articulation overlap in the sagittal plane by 6%, and the mean facet joint space increased 0.4 mm. At the L4-L5 level, the articulation overlap decreased by 6%, and the facet joint space increased 0.5 mm. At the L5-S1 level, the articulation overlap decreased by 4%, and the facet joint space increased 0.7 mm. CONCLUSIONS: There is a significant decrease of the facet joint articulation overlap in sagittal plane and an increase in the facet joint space following an increase in the lumbar disc space. The inappropriate increase of the height of disc space will result in facet joint subluxation.

Humans↗
PubMed2006

Explanation of the stability of thermophilic proteins based on unique micromorphology.

Two mesophilic/thermophilic variants of the G-domain of the elongation factor Tu were studied via molecular dynamics simulations. By analyzing the simulation data via the Voronoi space tessellation, we have found that the two proteins have the same macromolecular packing, while the water-exposed surface area is larger for the thermophile. A larger coordination with water is probably due to a peculiar corrugation of the exposed surface of this species. From an enthalpic point of view, the thermophile shows a larger number of intramolecular hydrogen bonds, stronger electrostatic interactions, and a flatter free-energy landscape. Overall, the data suggest that the specific hydration state enhances macromolecular fluctuations but, at the same time, increases thermal stability.

Bacterial Proteins↗
PubMed1983

Computer simulation of transport phenomena during dialysis deglycerolization of red blood cells.

A computer simulation model has been developed to aid in the understanding, parameter prediction, and performance optimization of a unique dialysis process where glycerol is removed from cryopreserved red blood cells using a semipermeable membrane pouch fixed in a mildly agitated transport cell. The dynamic system considered here consists of flow channels and the membrane blood pouch which contains the red blood cells, extracellular fluid, and cryopreservatives. Dialysate flows over the membrane surfaces while salt enters the pouch preventing osmotic hemolysis. The glycerol diffuses rapidly from the red cells and plasma across the membrane into the dialysate which carries it out of the transport cell. The system is discretized into completely mixed subdomains. Constituent transport and solvent flux are modeled with the transient convection-diffusion equation and linear equations of nonequilibrium thermodynamics, respectively. The integrated compartment method was used to solve for the principal variables, that is, salt and glycerol concentrations, water flow rates, and pressure in space and time. The computer simulation model, calibrated and verified with in-house data sets, is a reliable, cost-effective and flexible tool for dialysis system investigations, prediction, and optimal design.

Biological Transport↗
PubMed1991

Mass-weighted molecular dynamics simulation of the protein-ligand complex of rhizopuspepsin and inhibitor.

The mass-weighted molecular dynamics simulation method was developed previously for sampling the multidimensional conformational space of linear and cyclic polypeptides and studying their conformational flexibility. Herein results from molecular dynamics simulations of the protein-ligand complex of the aspartyl protease rhizopuspepsin and a polypeptide inhibitor are reported. The dihedral conformational space sampling for the linear peptide inhibitor in situ was found to be increased in the mass-weighted simulation as in other molecular systems previously studied. More significantly, the physical space of the enzyme binding pocket was also sampled efficiently in the simulations and multiple binding sites were identified for the inhibitor. These results suggest that it may be possible now to study, by computer simulations, the putative initial enzyme-inhibitor complex suggested experimentally from the time-dependent kinetics of enzyme inhibition by slow-binding inhibitors (Morrison, J. F., and C. T. Walsh. 1988. Adv. Enzymol. 61:201), and/or conformational substates in protein-ligand complexes suggested in the study of reassociation dynamics of myoglobin and carbon monoxide following photolysis (Austin, R. H., K. W. Beeson, L. Eisenstein, H. Frauenfelder, and I. C. Gunsalus. 1975. Biochemistry. 14:5355). Moreover, the intermediate binding steps and the molecular flexibility of the inhibitor shown in the MWMD simulation may have crucial roles in the ligand binding process.

Amino Acid Sequence↗
PubMed2004

Controlling the false positive rate in fuzzy clustering using randomization: application to fMRI activation detection.

Despite its potential advantages for fMRI analysis, fuzzy C-means (FCM) clustering suffers from limitations such as the need for a priori knowledge of the number of clusters, and unknown statistical significance and instability of the results. We propose a randomization-based method to control the false-positive rate and estimate statistical significance of the FCM results. Using this novel approach, we develop an fMRI activation detection method. The ability of the method in controlling the false-positive rate is shown by analysis of false positives in activation maps of resting-state fMRI data. Controlling the false-positive rate in FCM allows comparison of different fuzzy clustering methods, using different feature spaces, to other fMRI detection methods. In this article, using simulation and real fMRI data, we compare a novel feature space that takes the variability of the hemodynamic response function into account (HRF-based feature space) to the conventional cross-correlation analysis and FCM using the cross-correlation feature space. In both cases, the HRF-based feature space provides a greater sensitivity compared to the cross-correlation feature space and conventional cross-correlation analysis. Application of the proposed method to finger-tapping fMRI data, using HRF-based feature space, detected activation in sub-cortical regions, whereas both of the FCM with cross-correlation feature space and the conventional cross-correlation method failed to detect them.

Algorithms↗
PubMed2004

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

Binding Sites↗
PubMed1993

Diffusion of extracellular K+ can synchronize bursting oscillations in a model islet of Langerhans.

Electrical bursting oscillations of mammalian pancreatic beta-cells are synchronous among cells within an islet. While electrical coupling among cells via gap junctions has been demonstrated, its extent and topology are unclear. The beta-cells also share an extracellular compartment in which oscillations of K+ concentration have been measured (Perez-Armendariz and Atwater, 1985). These oscillations (1-2 mM) are synchronous with the burst pattern, and apparently are caused by the oscillating voltage-dependent membrane currents: Extracellular K+ concentration (Ke) rises during the depolarized active (spiking) phase and falls during the hyperpolarized silent phase. Because raising Ke depolarizes the cell membrane by increasing the potassium reversal potential (VK), any cell in the active phase should recruit nonspiking cells into the active phase. The opposite is predicted for the silent phase. This positive feedback system might couple the cells' electrical activity and synchronize bursting. We have explored this possibility using a theoretical model for bursting of beta-cells (Sherman et al., 1988) and K+ diffusion in the extracellular space of an islet. Computer simulations demonstrate that the bursts synchronize very quickly (within one burst) without gap junctional coupling among the cells. The shape and amplitude of computed Ke oscillations resemble those seen in experiments for certain parameter ranges. The model cells synchronize with exterior cells leading, though incorporating heterogeneous cell properties can allow interior cells to lead. The model islet can also be forced to oscillate at both faster and slower frequencies using periodic pulses of higher K+ in the medium surrounding the islet. Phase plane analysis was used to understand the synchronization mechanism. The results of our model suggest that diffusion of extracellular K+ may contribute to coupling and synchronization of electrical oscillations in beta-cells within an islet.

Animals↗
PubMed2002

Energy metabolism pathways in rat muscle under conditions of simulated microgravity.

Evidence from rats flown in space suggests that there is a decrease in the ability of the soleus muscle to oxidize long chain fatty acids during space flight. The observation suggests that a shift in the pathways involved in muscle fuel utilization in the absence of load on the muscle has occurred. It is also possible that the reduction is part of a general down-sizing of metabolic capacity since energy needs of inactive muscle are necessarily less. The rodent hind limb suspension model has proved to be a useful ground based model for studying the musculo-skeletal systems changes that occur with space flight. Microarray technology permits the screening of a large number of the enzymes of the relevant pathways thereby permitting a distinction to be made between a shift fuel utilization pattern or a general decrease in metabolic activity. The soleus muscle was isolated from 5 control and 5 hindlimb suspended rats (21 days) and the Affymetrix system for assessing gene expression used to determine the impact of hindlimb unloading on fuel pathways within the muscle of each animal. RESULTS: Suspended rats failed to gain weight at the same rate as the controls (337 +/- 5 g vs 318 +/- 6 g, p < 0.05) and muscle mass from the soleus was reduced (135 +/- 3 mg vs 48 +/- 4 mg, p < 0.05). There was a consistent decrease (p < 0.05) in gene expression of proteins involved in fatty acid oxidation in the suspended group whereas glycolytic activity was increased (p < 0.05). Gene expressions of individual key regulatory enzymes reflected these changes. Carnitine palmitoyltransferase I and II were decreased (p < 0.05) whereas expression of hexokinase, phosphofructokinase and pyruvate kinase were increased (p < 0.05). CONCLUSION: Disuse atrophy is associated with a change in mRNA levels of enzymes involved in fuel metabolism indicative of a shift in substrate utilization away from fat towards glucose.

Journal Article↗
PubMed2006

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.

The assembly of simple transmembrane helix homo-oligomers is studied by combining a generalized Born implicit membrane model with replica exchange molecular dynamics simulations to sample the conformational space of various oligomerization states and the native oligomeric conformation. Our approach is applied to predict the structures of transmembrane helices of three proteins--glycophorin A, the M2 proton channel, and phospholamban--using only peptide sequence and the native oligomerization state information. In every case, the methodology reproduces native conformations that are in good agreement with available experimental structural data. Thus, our method should be useful in the prediction of native structures of transmembrane domains of other peptides. When we ignore the experimental constraint on the native oligomerization state and attempt de novo prediction of the structure and oligomerization state based only on sequence and simple energetic considerations, we identify the pentamer as the most stable oligomer for phospholamban. However, for the glycophorin A and the M2 proton channels, we tend to predict higher oligomers as more stable. Our studies demonstrate that reliable predictions of the structure of transmembrane helical oligomers can be achieved when the observed oligomerization state is imposed as a constraint, but that further efforts are needed for the de novo prediction of both structure and oligomeric state.

Cell Membrane↗
PubMed2025

Tumor microenvironment governs the prognostic landscape of immunotherapy for head and neck squamous cell carcinoma: A computational model-guided analysis.

Immune checkpoint inhibition (ICI) has emerged as a critical treatment strategy for squamous cell carcinoma of the head and neck (HNSCC) that halts the immune escape of the tumor cells. Increasing evidence suggests that the onset, progression, and lack of/no response of HNSCC to ICI are emergent properties arising from the interactions within the tumor microenvironment (TME). Deciphering how the diversity of cellular and molecular interactions leads to distinct HNSCC TME subtypes subsequently governing the ICI response remains largely unexplored. We developed a cellular-molecular model of the HNSCC TME that incorporates multiple cell types, cellular states, and transitions, and molecularly mediated paracrine interactions. Simulation across the selected parameter space of the HNSCC TME network shows that distinct mechanistic balances within the TME give rise to the five clinically observed TME subtypes such as immune/non-fibrotic, immune/fibrotic, fibrotic only and immune/fibrotic desert. We predict that the cancer-associated fibroblast, beyond a critical proliferation rate, drastically worsens the ICI response by hampering the accessibility of the CD8&#x2009;+&#x2009;killer T cells to the tumor cells. Our analysis reveals that while an Interleukin-2 (IL-2) + ICI combination therapy may improve response in the immune desert scenario, Osteopontin (OPN) and Leukemia Inhibition Factor (LIF) knockout with ICI yields the best response in a fibro-dominated scenario. Further, we predict Interleukin-8 (IL-8), and lactate can serve as crucial biomarkers for ICI-resistant HNSCC phenotypes. Overall, we provide an integrated quantitative framework that explains a wide range of TME-mediated resistance mechanisms for HNSCC and predicts TME subtype-specific targets that can lead to an improved ICI outcome.

Tumor Microenvironment↗
PubMed2004

Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers.

Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25 degrees along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 A to as high as 34 degrees at a=5.3 A at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.

Alkanes↗
PubMed2002

A countermeasure to ameliorate immune dysfunction in in vitro simulated microgravity environment: role of cellularnucleotide nutrition.

Considerable evidence suggests that space travelers are immunosuppressed, presumably by microgravity environmental stresses, putting them at risk for adverse effects, such as opportunistic infections, poor wound healing, and cancer. The purpose of this study was to examine the role and mechanisms of nucleotide (NT) supplementation as a countermeasure to obviate immunosuppression during space travel. The in vitro rotary cell culture system, a bioreactor (BIO), was used to simulate the effect of microgravity and to isolate the neuroendocrine effects inherent to in vitro models. The splenocytes from normal mice were cultured in BIO and control tissue culture (TC) flasks with and without phytohemagglutinin (PHA) for mitogen assays. The culture medium was then supplemented with various concentrations of a nucleosides-nucleotides mixture (NS + NT), inosine, and uridine. Cytokines interleukin (IL)-1beta, IL-2, IL-3, tumor necrosis factor-alpha, and interferon (IFN)-gamma were measured from the supernatant by enzyme-linked immunosorbent assay. In the PHA-stimulated cultures the cellular proliferation in the BIO was significantly decreased as compared with the TC flask cells. BIO-cultured cells in the presence of NS + NT maintained mitogen responses similar to the control TC flask cells. The maintenance of the mitogen response in BIO was observed by the supplementation of uridine and not of inosine. These results are in agreement with our earlier results from unit gravity experiments that showed that pyrimidines are more effective in pleiogenic immunoprotection to hosts. Cytokines IL-1beta, IL-2, and IFN-gamma in the BIO supernatants of cells cultured in the presence of NS + NT had a significantly higher response than the control vessel. Thus, supplemental NT, especially pyrimidines, can confer immune protection and enhance cytokine responses during space travel.

Animals↗
PubMed2002

k-space filtering in 2D gradient-echo breath-hold hyperpolarized 3He MRI: spatial resolution and signal-to-noise ratio considerations.

In this work some of the factors that can influence the signal-to-noise ratio (SNR) and spatial resolution in MR images of inhaled hyperpolarized gases are systematically addressed. In particular, the effects of RF depletion of longitudinal polarization and image gradient diffusion dephasing were assessed in terms of their contribution to a k-space filter. By means of theoretical simulations and a novel method of experimental validation using a variable transverse magnetization of the 1H signal, systematic quantitative and qualitative investigations of the effects of k-space filtering intrinsic to imaging of hyperpolarized gas were made. A 2D gradient-echo image is considered for a range of flip angles with centric, sequential, and half-Fourier Cartesian phase-encoding strategies, and the results are assessed in terms of SNR and spatial resolution in the reconstructed images. Centric phase encoding was found to give the best SNR at higher flip angles, with a trade-off in spatial resolution compared to sequential phase encoding. A half-Fourier approach potentially offers increased SNR through the use of higher flip angles without compromising the spatial resolution, which is comparable to that achieved with sequential encoding.

Fourier Analysis↗
PubMed2000

Bone changes during simulated weightlessness in rats.

Weightless environment due to prolonged Space mission results in decreased mineralisation of the weight bearing bones. Hind limb unweighting (HU) in rats by tail suspension was used to simulate the effect of weightlessness on tibia. Adult male albino rats were divided into two groups as (i) Control (CON, n = 12) and (ii) HU for 15 days (HU, n = 18). After 15 days of HU tibia from all the animals were removed and subsequently dried and ashed. The calcium content of these bones were then determined. HU resulted in atrophic changes in the weight bearing bone, tibia, due to the reductions of water content (-35.8%), organic matrix (-12.2%) and calcium content (-33.4%). The reduction in the dry wt of tibia (-13.5%) was due to proportionate reductions in the organic matrix and total mineral content of the bone. The reduction in the mineral content was solely due to the reduction in calcium content of the bone.

Animals↗
PubMed2001

Generalized-ensemble algorithms for molecular simulations of biopolymers.

In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.

Algorithms↗
PubMed1999

Biomechanical effects of intraspecimen variations in trabecular architecture: a three-dimensional finite element study.

Trabecular architecture is considered important in osteoporosis and has been quantified by a variety of mean parameters characteristic of a whole specimen. Variations within a specimen, however, have been mostly ignored. In this study, the theoretical effects of these intraspecimen variations in architecture on predicted mechanical properties were investigated through a three-dimensional finite element parameter study that simulated variations in trabecular thickness in a controlled manner. An irregularly spaced lattice of different sized rods was used to simulate trabecular bone in three distinct volume fraction ranges, representing young, middle-aged, and elderly vertebral bone. Beta distributions (a type of non-normal distribution) of trabecular thickness with coefficients of variation of either 25%, 40%, or 55% were applied to the rods in each model, and 225 simulations of uniaxial compression tests were performed to obtain modulus values. Percent modulus reductions of 22% and 43% were predicted when the intraspecimen coefficient of variation in trabecular thickness was increased from 25% to 40% and from 25% to 55%, respectively, for models of equal volume fraction. Furthermore, this trend was predicted to be independent of volume fraction. We conclude, therefore, that consideration of the intraspecimen trabecular thickness variation in conjunction with volume fraction may improve the ability to predict trabecular modulus compared with use of volume fraction alone. Further, the model suggests that if age, disease, or drug treatments increase trabecular thickness variation, this may be detrimental to mechanical properties.

Adult↗