Computer simulation of temperature-dependent growth of fractal and compact domains in diluted Ising models.
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Journal Article↗
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Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations.
The immunodominant region on the circumsporozoite surface (CS) protein of the malaria parasite Plasmodium falciparum contains 37 repeated copies of a asparagine-alanine-asparagine-proline (NANP) motif NMR studies of linear synthetic peptides containing one, two or three repeat units provided evidence for nascent type I beta-turns within the NPNA cadence in aqueous solution. The beta-turns could be stabilised upon substituting proline for alpha-methylproline (p(Me)) in the dodecamer (NP(Me)NA)3, without loss of the ability to elicit antibodies cross-reactive with P. falciparum sporozoites. In this work, four 4 ns MD simulations of the dodecapeptide Acetyl-(NP(Me)NA)3, in water, using NOE distance restraints, using 3J-coupling constant restraints, using both these restraints and without restraints, were carried out to determine the conformations of this peptide in aqueous solution. An unrestrained MD simulation of the unmethylated Ac-(NPNA)3 peptide in water was also carried out to investigate the effect of the additional methyl groups on the structure and dynamics of the peptide. The application of NOE distance restraints and 3J-coupling constant restraints leads to contradictory results, probably due to different averaging time scales inherent to the measurement of these data, which exceed the 100 ps averaging applied in the simulations. The additional methyl groups lead to more compact structures, which display enhanced local fluctuations. The central tetrapeptide adopts a type I beta-turn, while the outer motifs display more conformational variability. The three motifs in the methylated dodecamer peptide, however, adopt frequently in the distance restrained MD simulation a compact structure such that the outer motifs appear to form a hydrophobic core by stacking of their two proline rings. This arrangement also suggests how a peptide containing multiple tandemly linked copies of a stable beta-turn NPNA motif might adopt a folded stem-like structure, which conceivably may be of biological relevance in the native CS protein.
Animals↗
Enhancement of dissolution rate of piroxicam using liquisolid compacts.
Piroxicam is a poorly soluble, highly permeable drug and the rate of its oral absorption is often controlled by the dissolution rate in the gastrointestinal. The poor dissolution rate of water-insoluble drugs is still a major problem confronting the pharmaceutical industry. There are several techniques to enhance the dissolution of poorly soluble drugs. Among them, the technique of liquisolid compacts is a promising technique towards such a novel aim. In this study, the dissolution behaviour of piroxicam from liquisolid compacts was investigated in simulated gastric fluid (SGF, pH 1.2) and simulated intestinal fluid (SIF, pH 7.2). To this end, several liquisolid tablets formulations containing various ratios of drug:Tween 80 (ranging from 10% to 50% w/w) were prepared. The ratio of microcrystalline cellulose (carrier) to silica (coating powder material) was kept constant in all formulations. The results showed that liquisolid compacts demonstrated significantly higher drug release rates than those of conventionally made (capsules and directly compressed tablets containing micronized piroxicam). This was due to an increase in wetting properties and surface of drug available for dissolution.
Body Fluids↗
Positron flight in human tissues and its influence on PET image spatial resolution.
The influence of the positron distance of flight in various human tissues on the spatial resolution in positron emission tomography (PET) was assessed for positrons from carbon-11, nitrogen-13, oxygen-15, fluorine-18, gallium-68 and rubidium-82. The investigation was performed using the Monte Carlo code PENELOPE to simulate the transport of positrons within human compact bone, adipose, soft and lung tissue. The simulations yielded 3D distributions of annihilation origins that were projected on the image plane in order to assess their impact on PET spatial resolution. The distributions obtained were cusp-shaped with long tails rather than Gaussian shaped, thus making conventional full width at half maximum (FWHM) measures uncertain. The full width at 20% of the maximum amplitude (FW20M) of the annihilation distributions yielded more appropriate values for root mean square addition of spatial resolution loss components. Large differences in spatial resolution losses due to the positron flight in various human tissues were found for the selected radionuclides. The contribution to image blur was found to be up to three times larger in lung tissue than in soft tissue or fat and five times larger than in bone tissue. For (18)F, the spatial resolution losses were 0.54 mm in soft tissue and 1.52 mm in lung tissue, compared with 4.10 and 10.5 mm, respectively, for (82)Rb. With lung tissue as a possible exception, the image blur due to the positron flight in all human tissues has a minor impact as long as PET cameras with a spatial resolution of 5-7 mm are used in combination with (18)F-labelled radiopharmaceuticals. However, when ultra-high spatial resolution PET cameras, with 3-4 mm spatial resolution, are applied, especially in combination with other radionuclides, the positron flight may enter as a limiting factor for the total PET spatial resolution--particularly in lung tissue.
Adipose Tissue↗
Stochastic roadmap simulation for the study of ligand-protein interactions.
Understanding the dynamics of ligand-protein interactions is indispensable in the design of novel therapeutic agents. In this paper, we establish the use of Stochastic Roadmap Simulation (SRS) for the study of ligand-protein interactions through two studies. In our first study, we measure the effects of mutations on the catalytic site of a protein, a process called computational mutagenesis. In our second study, we focus on distinguishing the catalytic site from other putative binding sites. SRS compactly represents many Monte Carlo (MC) simulation paths in a compact graph structure, or roadmap. Furthermore, SRS allows us to analyze all the paths in this roadmap simultaneously. In our application of SRS to the domain of ligand-protein interactions, we consider a new parameter called escape time, the expected number of MC simulation steps required for the ligand to escape from the 'funnel of attraction' of the binding site, as a metric for analyzing such interactions. Although computing escape times would probably be infeasible with MC simulation, these computations can be performed very efficiently with SRS. Our results for six mutant complexes for the first study and seven ligand-protein complexes for the second study, are very promising: In particular, the first results agree well with the biological interpretation of the mutations, while the second results show that escape time is a good metric to distinguish the catalytic site for five out of seven complexes.
Amino Acid Sequence↗
Laser dentistry: root canal diagnostic technique based on ultraviolet-induced fluorescence spectroscopy.
A diagnostic technique to detect residual tissues at different levels of the root canal during an endodontic treatment is presented. The diagnostic system is based on ultraviolet-induced fluorescence spectroscopy and uses suitable optical fibers for local delivery of excitation light and to collect back fluorescence spectra. Spectra of root canal tissues have been obtained from split teeth by labeling with a fluorescent solution. Residual tissue can be discriminated in respect to healthy dentin because of their different spectral responses: the spectral shape of the first response shows a clear peak at 530 nm because of a selective absorption of the fluorescent dye, whereas for the second response, the spectral curve monotonically increases toward ultraviolet wave-lengths with no particular structure. This technique has been tested on unsplit teeth simulating operative conditions. A compact spectroscopic system has been devised that can be easily integrated in an excimer laser system to perform residual tissue detection during laser cleaning of the canals.
Fiber Optic Technology↗
In vivo assessment of vascular dilatation during percutaneous transluminal coronary angioplasty.
Previous studies of the mechanism of percutaneous transluminal coronary angioplasty used either postmortem specimens or animal models. To characterize the process of vascular dilatation in vivo, a system was devised for recording the instantaneous pressure-volume changes in the angioplasty balloon during inflation within the stenosed artery. The pressure-volume patterns obtained were compared with those observed in vitro with the balloon inflated in materials whose properties simulate stretching (Silastic tubing), compaction (styrofoam) and cracking (dry macaroni). Of 48 narrowings in 46 patients, a pressure-volume pattern of stretching was observed in 56%, compaction in 27% and cracking in only 17%. Of lesions manifesting a stretching pattern, 85% were longer than 5 mm cr had visible calcium deposits, whereas those that compacted were shorter and lacked calcium deposits. Both of these pressure-volume patterns were associated with a successful clinical outcome. Of 8 lesions exhibiting a cracking pattern, 6 showed dissection angiographically; 3 of these resulted in vessel occlusion.
Angioplasty, Balloon↗
Radio frequency (rf) plasma spheroidized HA powders: powder characterization and spark plasma sintering behavior.
The present study describes the synthesis of spheroidized hydroxyapatite (HA) powders using a radio frequency (rf) inductively coupled plasma (ICP) torch. The spheroidized powders were consolidated through a spark plasma sintering (SPS) system. The microstructure and crystallographic phases in the synthesized powders were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffractometry (XRD) and Raman spectrometry. Results showed that the HA feedstock decomposed after rf plasma processing. Crystalline HA, alpha-tri-calcium phosphate (alpha-TCP), tetra-calcium phosphate (TTCP) and calcium oxide (CaO) were detected in the plasma-spheroidized powders. Raman spectra results indicated strong presence of amorphous calcium phosphate (ACP) in the spheroidized powders. The particle size distribution and specific surface area were influenced through the rf plasma working plate power levels. The sintering behavior of the rf plasma synthesized powders was analyzed through the SPS process and the results indicated that the spheroidized powders commence sintering at approximately 900 degrees C and through to 1150 degrees C. After sintering above 1100 degrees C for 3min, the relative densities of the SPS compacts reached 96% of the theoretical value. The SPS compacts were immersed in simulated body fluids (SBF) for different durations and the results confirmed their bioactivities.
Biocompatible Materials↗
Soda-lime-silica glass for radiation dosimetry.
The color developed in a commercially available soda-lime-silica glass when subjected to gamma-irradiation and the stability of such radiation-induced color were studied to test its sensitivity to small doses of gamma-rays (0.0-27 kGy). After irradiation, two absorption bands developed at 400 and 620 nm. The former band exhibited a stronger absorption than the later one. The intensity of both bands showed a gradual increase with increasing irradiation dose and a gradual decrease with increasing fading time after irradiation. The development of these bands is associated with the generation of defects at nonbridging oxygen atoms in the glass lattice and hole centers. The results obtained suggest that this glass simulated the Z of compact bone in terms of gamma rays absorption properties over broad radiation spectra (0.1 to 10 MeV).
Biophysical Phenomena↗
Compact mock loops of the systemic and pulmonary circulation for blood pump testing.
Mock loops are an important tool for in vitro investigations of artificial blood pumps. The simple windkessel, throttle, and atrium principle was used for the mock loop design presented. The components of the systemic and the pulmonary mock loop were designed according to calculated numerical simulation parameters. The loops offer a compact design and simple handling. For simulating biventricular assist or total artificial heart (TAH), both loops can be coupled correspondingly. The numerical simulation and the first results with the loops show very good similarity to physiological data of systemic and pulmonary circulation. The measurements of pump characteristics are significant for quantitative comparison of different pump sizes and types, or driving systems.
Blood Circulation↗
Compact and dissociated dislocations in aluminum: implications for deformation.
Atomistic simulations, confirmed by electron microscopy, show that dislocations in aluminum can have compact or dissociated cores. The calculated minimum stress (sigma(P)) required to move an edge dislocation is approximately 20 times smaller for dissociated than for equivalent compact dislocations. This contradicts the well accepted generalized stacking fault energy paradigm that predicts similar sigma(P) values for both configurations. Additionally, Frank's rule and the Schmid law are also violated because dislocation core energies become important. These results may help settle a 50-year-old puzzle regarding the magnitude of sigma(P) in face-centered-cubic metals, and provide new insights into the deformation of ultra-fine-grained metals.
Journal Article↗
Cohesive finite element modeling of age-related toughness loss in human cortical bone.
Although the age-related loss of bone quality has been implicated in bone fragility, a mechanistic understanding of the relationship is necessary for developing diagnostic and treatment modalities in the elderly population at risk of fracture. In this study, a finite element based cohesive zone model is developed and applied to human cortical bone in order to capture the experimentally shown rising crack growth behavior and age-related loss of bone toughness. The cohesive model developed here is based on a traction-crack opening displacement relationship representing the fracture processes in the vicinity of a propagating crack. The traction-displacement curve, defining the cohesive model, is composed of ascending and descending branches that incorporate material softening and nonlinearity. The results obtained indicate that, in contrast to initiation toughness, the finite element simulations of crack growth in compact tension (CT) specimens successfully capture the rising R-curve (propagation toughness) behavior and the age-related loss of bone toughness. In close correspondence with the experimentally observed decrease of 14-15% per decade, the finite element simulation results show a decrease of 13% in the R-curve slope per decade. The success of the simulations is a result of the ability of cohesive models to capture and predict the parameters related to bone fracture by representing the physical processes occurring in the vicinity of a propagating crack. These results illustrate that fracture mechanisms in the process zone control bone toughness and any modification to these would cause age-related toughness loss.
Aging↗
Estimation of capping incidence by indentation fracture tests.
The purpose of this study was to predict the capping tendencies of pharmaceutical powders by creating indentation fracture on compacts. Three sets of binary mixtures containing different concentrations of each ingredient were used in the study. The binary mixtures were chosen to represent plastic-plastic, plastic-brittle, and brittle-brittle combination of materials. The mixtures were tableted at different pressures and speeds on Prester, a tablet press simulator. These mixtures were also compacted on the Instron Universal Testing Machine 4502. Static indentation tests were done on these compacts at different depths until surface cracking and chipping were observed. The extent of surface cracking and chipping was observed from light microscope and scanning electron microscope images. A rank order correlation was observed between lamination susceptibility and the depth at which indentation failure occurred. It was concluded that indentation fracture tests could provide a useful estimate of lamination properties of pharmaceutical powders.
Acetaminophen↗
Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A).
The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.
Carbohydrate Conformation↗
Refolding simulations of an isolated fragment of barnase into a native-like beta hairpin: evidence for compactness and hydrogen bonding as concurrent stabilizing factors.
Experimental evidence and theoretical models both suggest that protein folding is initiated within specific fragments intermittently adopting conformations close to that found in the protein native structure. These folding initiation sites encompassing short portions of the protein are ideally suited for study in isolation by computational methods aimed at peering into the very early events of folding. We have used Molecular Dynamics (MD) technique to investigate the behavior of an isolated protein fragment formed by residues 85 to 102 of barnase that folds into a beta hairpin in the protein native structure. Three independent MD simulations of 1.3 to 1.8 ns starting from unfolded conformations of the peptide portrayed with an all-atom model in water were carried out at gradually decreasing temperature. A detailed analysis of the conformational preferences adopted by this peptide in the course of the simulations is presented. Two of the unfolded peptides conformations fold into a hairpin characterized by native and a larger bulk of nonnative interactions. Both refolding simulations substantiate the close relationship between interstrand compactness and hydrogen bonding network involving backbone atoms. Persistent compactness witnessed by side-chain interactions always occurs concomitantly with the formation of backbone hydrogen bonds. No highly populated conformations generated in a third simulation starting from the remotest unfolded conformer relative to the native structure are observed. However, nonnative long-range and medium-range contacts with the aromatic moiety of Trp94 are spotted, which are in fair agreement with a former nuclear magnetic resonance study of a denaturing solution of an isolated barnase fragment encompassing the beta hairpin. All this lends reason to believe that the 85-102 barnase fragment is a strong initiation site for folding.
Bacterial Proteins↗
Discriminating compact nonnative structures from the native structure of globular proteins.
Prediction of the native tertiary structure of a globular protein from the primary sequence will require a potential energy model that can discriminate all nonnative structures from the native structure(s). A successful model must distinguish not only alternate structures that are very nonnative but also alternate structures that are compact and near-native. We describe here a method, based on molecular dynamics simulation, that allows generation of hundreds of compact alternate structures that are arbitrarily close to the native structure. In this way, a significant amount of conformational space in the neighborhood of the native structure can be sampled and these alternate structures can be used as a stringent test of protein folding models. We have used two sets of these alternate structures generated for six crystallographically characterized small globular proteins (1200 alternate structures in all) to test eight empirical energy models for their ability to discriminate alternate from native structures. Seven of the models fail to correctly identify at least some of the alternate structures as nonnative. An atomic solvation model is presented that succeeds in discriminating all 1200 alternate structures from native.
Amino Acid Sequence↗
Computer simulations aimed at structure prediction of supersecondary motifs in proteins.
It is well established that protein structures are more conserved than protein sequences. One-third of all known protein structures can be classified into ten protein folds, which themselves are composed mainly of alpha-helical hairpin, beta hairpin, and betaalphabeta supersecondary structural elements. In this study, we explore the ability of a recent Monte Carlo-based procedure to generate the 3D structures of eight polypeptides that correspond to units of supersecondary structure and three-stranded antiparallel beta sheet. Starting from extended or misfolded compact conformations, all Monte Carlo simulations show significant success in predicting the native topology using a simplified chain representation and an energy model optimized on other structures. Preliminary results on model peptides from nucleotide binding proteins suggest that this simple protein folding model can help clarify the relation between sequence and topology.
Amino Acid Motifs↗
Adsorption-desorption model and its application to vibrated granular materials.
We investigate both analytically and by numerical simulation the kinetics of a microscopic model of hard rods adsorbing on a linear substrate, a model that is relevant for compaction of granular materials. The computer simulations use an event-driven algorithm that is particularly efficient at very long times. For a small, but finite desorption rate, the system reaches an equilibrium state very slowly, and the long-time kinetics display three successive regimes: an algebraic one where the density varies as 1/t, a logarithmic one where the density varies as 1/ln(t), followed by a terminal exponential approach. The characteristic relaxation time of the final regime, though incorrectly predicted by mean field arguments, can be obtained with a systematic gap-distribution approach. The density fluctuations at equilibrium are also investigated, and the associated time-dependent correlation function exhibits a power law regime followed by a final exponential decay. Finally, we show that denser particle packings can be obtained by varying the desorption rate during the process.
Adsorption↗