Three-point Model Research Articles

Specific Cation Effects on SCN- in Bulk Solution and at the Air-Water Interface.

The large and sparsely hydrated thiocyanate anion, SCN-, plays a prominent role in the study of specific ion effects in biological, colloid, and atmospheric chemistry due to its extreme position in the Hofmeister series. Using atomistic modeling of aqueous SCN- solutions, we provide novel insight at the molecular scale into the experimentally observed differences in ion pairing, clustering, reorientation dynamics, mutual diffusion, and solubility between the sodium, Na+, and the potassium, K+, salt. Compared to KSCN, NaSCN has a less pronounced tendency to ion pairing; nevertheless, at high salt concentrations, we observe a strong attraction between Na+ cations and the nitrogen end of SCN-, resulting in larger and more closely packed ion clusters. To accurately model aqueous SCN- solutions in computer simulations, we develop a thermodynamically consistent force field rooted in quantum-chemical calculations and refined using the Kirkwood-Buff theory. The force field is compatible with the extended simple point charge and three-point optimal point charge classical water models and reproduces experimental activity derivatives and air-water surface tension for a wide range of salt concentrations.

Fracture behavior of highly toughened poly(lactic acid)/ethylene-co-vinyl acetate blends

AbstractPoly(lactic acid) (PLA) is brittle which restricts the range of its applications. The toughness of PLA was effectively improved in this work by incorporation of rubber grade ethylene-co-vinyl acetate (EVM). For example, the elongation at break of PLA increased by about 50 times after the addition of the EVM (10–30 wt%), although the EVM was not miscible with the PLA matrix. Furthermore, the notched impact toughness of PLA/EVM blend (70/30 wt/wt) reached to 85 kJ/m2even at a temperature as low as −10°C. The critical temperatures of brittle-to-ductile transition (BDT) for PLA/EVM blends are observed at −20~0°C depending on the composition, while no BTD transition appeared for neat PLA. The impact fracture surface morphology of PLA and PLA/EVM blends observed by SEM indicates that the toughening modification was achieved through obvious matrix yielding. Moreover, the toughening behavior of the PLA/EVM blends was also interpreted quantitatively by using a single-edge notched three-point bending model (SEN3PB). The SEN3PB experiments reveal that the fracture energy was consumed in an outer plastic zone away from the fracture surface rather than in the inner fracture process zone, which accounts for the high toughness of the PLA/EVM blends.

Does Cytosine Methylation Stabilize the BI Substate of DNA?

The local conformation of DNA plays a critical role in the recognition-and-binding process of transcription factors. In particular, the most common form of the DNA double helix, B-DNA, exists as a conformational equilibrium between BI and BII substates that are associated with changes in major and minor groove dimensions. It has been hypothesized that cytosine methylation, the most common epigenetic modification and one that is often found in so-called CpG islands, modulates transcription factor binding affinity by altering the BI-BII equilibrium in the neighborhood of methylation sites. Indeed, previous molecular dynamics studies have suggested that cytosine methylation leads to a uniform stabilization of the BI substate in CpG islands. In this work we first benchmark the ability of the latest Amber DNA force fields and a variety of three-point water models to reproduce BI-BII equilibrium in the Dickerson dodecamer and reduce terminal base pair fraying. Using the best-performing combinations, we then re-examine the conformational effects of cytosine methylation in a prototypical CpG island, (GC)5. We find that the BI substate is stabilized for GpC steps in such sequences, but that the BII substate is stabilized for the CpG steps. More interestingly, the Amber ff99bsc0 DNA force field used in previous studies yields opposite conclusions. These findings highlight the need for continued fixed-charge force field development for nucleic acids, as well as solution state experimental datasets involving epigenetic modification that can serve as benchmarks for simulation accuracy.

Two-component structural phase-field crystal models for graphene symmetries.

We extend the three-point XPFC model of Seymour & Provatas (Seymour & Provatas 2016 Phys. Rev. B93, 035447 (doi:10.1103/PhysRevB.93.035447)) to two components to capture chemical vapour deposition-grown graphene, and adapt a previous two-point XPFC model of Greenwood et al. (Greenwood et al. 2011 Phys. Rev. B84, 064104 (doi:10.1103/PhysRevB.84.064104)) into a simple model of two-component graphene. The equilibrium properties of these models are examined and the two models are compared and contrasted. The first model is used to study the possible roles of hydrogen in graphene grain boundaries. The second model is used to study the role of hydrogen in the dendritic growth morphologies of graphene. The latter results are compared with new experiments.This article is part of the theme issue 'From atomistic interfaces to dendritic patterns'.

Theoretical and experimental analysis on the small punch creep deformation of Incoloy800H

Abstract The small punch creep deformation behavior estimation of Incoloy800H was performed theoretically and experimentally in this study. The results indicate that three creep stages of the small punch test are similar to that of the conventional creep tests. Considering the deformation characteristics and geometry form, an obvious initial elastic-plastic deformation is presented and the primary creep stage is proven to be nonnegligible in the small punch test. Both the three-point bending model and the modified geometric model were proposed. It indicates that creep strain is proportional to small punch deflection in the primary and steady creep stages. Meanwhile, membrane stretching model was modified and a constant stress phase during deformation was found. The results indicate that small punch character parameters are capable to replace traditional creep data in the creep curve analysis of Incoloy800H. Thus, the creep curves with three deformation phases were analyzed and predicted by both of the modified Norton-Bailey model and modified theat model. Finally, the primary, steady and tertiary creep stages were described, and the creep life prediction of Incoloy800H was realized.

Low-Energy Collisions of Protonated Enantiopure Amino Acids with Chiral Target Gases

Here we report on the gas-phase interactions between protonated enantiopure amino acids (l- and d-enantiomers of Met, Phe, and Trp) and chiral target gases [(R)- and (S)-2-butanol, and (S)-1-phenylethanol] in 0.1–10.0 eV low-energy collisions. Two major processes are seen to occur over this collision energy regime, collision-induced dissociation and ion-molecule complex formation. Both processes were found to be independent of the stereo-chemical composition of the interacting ions and targets. These data shed light on the currently debated mechanisms of gas-phase chiral selectivity by demonstrating the inapplicability of the three-point model to these interactions, at least under single collision conditions.Graphical

Characterization of compression behaviors of Acupoint Catgut-embedding monofilaments for the human body: A test method of monofilaments by the three-point bending model

Acupoint Catgut-embedding therapy (ACET) is considered an advanced method for the treatment of juvenile pseudomyopia. However, the existing test methods of ACE monofilaments cannot meet the desire for accurate measurement and convenient operation. This paper presents a study of the compression behaviors of ACE monofilaments developed for the human body. To investigate a convenient and accurate test method for monofilaments, different materials, including polypropylene (PP), polylactic acid (PLA) and polyglycolide acid (PGA), were designed to a curved rod shape based on the three-point bending model used in this work. Variables, including the number of winding laps, the diameter of the compression platens and the compression rate of specimens, were discussed by the platform compression method. Properties such as radial force, the compression modulus and recovery ratio were also tested and analyzed. The results revealed that the winding lap of 25r was selected as the most suitable number according to the principles of stability and accuracy. The diameter of the compression platen should be larger than the outer diameter of the specimens, due to which the diameter of 5 mm was less than expected in this work. Meanwhile, the average value of the maximum radial force ( F) was PP (98.35 cN) > PLA-1 (84.67 cN) > PGA (63.68 cN) > PLA-2 (39.24 cN) > PLA-3 (20.15 cN). The compression rate of 50% should be selected as the optimum parameter. In conclusion, this test method of monofilaments was successfully developed and has a potential application for the characterization of compression behaviors of ACE monofilaments for the human body.

Analysis of volumetric response of pituitary adenomas receiving adjuvant CyberKnife stereotactic radiosurgery with the application of an exponential fitting model.

Tumor control rates of pituitary adenomas (PAs) receiving adjuvant CyberKnife stereotactic radiosurgery (CK SRS) are high. However, there is currently no uniform way to estimate the time course of the disease. The aim of this study was to analyze the volumetric responses of PAs after CK SRS and investigate the application of an exponential decay model in calculating an accurate time course and estimation of the eventual outcome.A retrospective review of 34 patients with PAs who received adjuvant CK SRS between 2006 and 2013 was performed. Tumor volume was calculated using the planimetric method. The percent change in tumor volume and tumor volume rate of change were compared at median 4-, 10-, 20-, and 36-month intervals. Tumor responses were classified as: progression for >15% volume increase, regression for ≤15% decrease, and stabilization for ±15% of the baseline volume at the time of last follow-up. For each patient, the volumetric change versus time was fitted with an exponential model.The overall tumor control rate was 94.1% in the 36-month (range 18–87 months) follow-up period (mean volume change of −43.3%). Volume regression (mean decrease of −50.5%) was demonstrated in 27 (79%) patients, tumor stabilization (mean change of −3.7%) in 5 (15%) patients, and tumor progression (mean increase of 28.1%) in 2 (6%) patients (P = 0.001). Tumors that eventually regressed or stabilized had a temporary volume increase of 1.07% and 41.5% at 4 months after CK SRS, respectively (P = 0.017). The tumor volume estimated using the exponential fitting equation demonstrated high positive correlation with the actual volume calculated by magnetic resonance imaging (MRI) as tested by Pearson correlation coefficient (0.9).Transient progression of PAs post-CK SRS was seen in 62.5% of the patients receiving CK SRS, and it was not predictive of eventual volume regression or progression. A three-point exponential model is of potential predictive value according to relative distribution. An exponential decay model can be used to calculate the time course of tumors that are ultimately controlled.

Validation of surface coating with nanoparticles to improve the flowability of fine cohesive powders

Fluidization of fine cohesive powders is seriously restricted by the strong interparticle cohesion. The rational combination of nanoparticles with fine cohesive powders is expected to obtain composite particles with improved flowability. In this work, we firstly reviewed the sandwich and three-point contact models regarding the fundamental principles of nano-additives in reducing cohesiveness. Based on these previous models, the effects of the size of nanoparticles, their agglomeration and coverage on the surface of cohesive powders in reducing interparticle forces were theoretically analyzed. To validate the theory effectiveness for the irregularly shaped cohesive powders, an extreme case of cubic powders coated with silica nanoparticles was fabricated, and the flowability of the composite particles was determined experimentally. Ultimately, based on force balance of a single particle, a semi-theoretical criterion for predicting the fluidization behavior of coated powders was developed to guide the practical applications of improving the flowability of cohesive powders through structural design and modulation.

Moment redistribution in cold-formed steel continuous beams

The external envelope of steel framed industrial buildings normally involves the use of purlins and rails spanning between the main hot-rolled frames to support the roofing/cladding. These purlins are typically light-gauge cold-formed steel members of complex shape for which the thin-walled nature of the material means that local instabilities will significantly influence their structural behaviour. Economic design should be based on failure of the system, recognising the opportunity for redistribution of moments. This paper presents the findings from a numerical investigation of the degree of moment redistribution in continuous cold-formed steel beams subjected to a downward (gravity) uniformly distributed load (UDL). Three types of nonlinear finite element analysis were validated against previously reported physical tests: (i) continuous two-span beams subjected to a UDL, (ii) single span beams subjected to a central point load producing a moment gradient and (ii) single span beams subjected to two point loads producing a central region under pure bending. The interior support moments from the continuous beam models were compared against reference moment capacities from the three-point bending models. Based on various different section sizes, covering a range of cross-sectional slenderness, full moment redistribution with no drop-off in moment at the interior support was found to be possible only for stocky sections but not for slender sections. In the case of slender sections, local and distortional buckling caused a reduction in interior support moment prior to failure of the system. Hence a design formula is proposed to estimate the post-peak reduction of interior support moment from its initial peak, and this reduced moment capacity is then used in conjunction with the full span moment to determine the load-carrying capacity of the system. Comparisons show the proposed approach to offer accurate prediction of observed system failure loads.

Mechanical characteristics of individual TiO2 nanowire and TiO2 nanowire bundle on micro-manipulator nanoprobe system

The individual TiO2 nanowire and TiO2 nanowire bundle were prepared through a simple hydrothermal reaction of alkali with the titanium (Ti) metal and with TiO2 powder, respectively. A newly developed test platform which contained the MM3A micro-manipulator nanoprobe system installed in the scanning electron microscope (SEM) chamber was then introduced for the test of the mechanical properties of titanium dioxide nanowires (TiO2 NWs), either an individual or a bundle. The mechanical characteristics of the individual TiO2 NW and the TiO2 NW bundle were determined using a micro-cantilever model and a three-point bending model, respectively. In the tests, a nanoprobe tip was used to apply lateral force and deflect NWs. The load and deflection were measured simultaneously by Spring Table and SEM. And then Young's modulus were calculated based on their respective theoretical formula. The average value of Young's modulus for an individual TiO2 NW and a bundle of TiO2 NWs were found to be 120.39GPa and 92.01GPa, respectively. The TiO2 NW Young's modulus exhibits no obvious size effect while the scale of TiO2 NW was in the range of 100nm−100μm. The bending method in this new test platform could be widely applied to measure the mechanical properties of all 1D nanostructures under different scale conveniently and accurately, which is helpful for the feasibility of replacing current electrical and optical devices with NWs integrated devices.

Molecular simulation of water vapor outgassing from silica nanopores.

The outgassing problem is solved numerically by molecular dynamics. A slit-shaped nanopore consisting of cavity and channel is built with an implicit tabulated wall potential that describes the water–silicon/silica interaction. A flexible three-point water model is used for the simulation. The effects of varying the system temperature, outlet pressure, geometry, and materials of the nanopore on the outgassing rate are investigated. The results show that the temperature plays an important role in the outgassing rate, while the effect of the outlet pressure is negligible as long as it is in the high to medium vacuum range. The geometry of the channel also has an influence on the outgassing rate, but not as much as the surface material. Three different types of silica materials are tested: silicon, silica-cristobalite (hydrophilic material), and silica-quartz (super hydrophilic material). The fastest outgassing rate is found for a silicon nanopore. It is also found that a thin water film is formed on the surface of the silica-quartz nanopore. This material shows hardly any outgassing of water.

Signature Extraction From Rotating Targets Based on a Fraction of HRRPs

Motion or structure signatures, extracted from radar echoes, are of great potential in target identification. Traditional techniques for signature extraction rely primarily on the assumption that the time series of the signal contains at least one oscillation or more during the illumination time. However, as many applications involve short duration signals or long duration signals, they are only partially useful in real-world scenarios. The conventional signature extraction algorithms may suffer from degraded precision. This paper presents a three-point model for signature extraction availing the characteristics of the high resolution range profiles (HRRPs) of rotating targets with stepped-frequency signal (SFS). The frequency and the length of rotating targets can be estimated accurately from a fraction of the HRRPs in slow-time-range plane. The accuracy and efficiency of the estimation are demonstrated by simulated and experimental trials.

Modelling of deformation behavior of polymeric woven fabric prepreg-based composite materials in flexure and short beam interlaminar shear testing

The mechanisms of deformation behavior of woven fabric prepreg-based carbon-fiber composites with different reinforcement lay-up schemes are studied. The FEM stress-strain analysis is carried out for specimens in flexure and short beam interlaminar shear testing environments. Both methods are based on a three-point bend model. Theoretical grounds underlying the mechanisms governing the deformation of laminates in bending tests are studied. Tests were performed on specimens having different thickness and with different ratios of the distance between supports to the specimen thickness. The effects of the monolayer properties specified in the model, such as the modulus of elasticity in the z-direction and the interlaminar shear modulus, on the effective characteristics of the material are investigated. The problems of correct experimental determination of the interlaminar shear modulus related to the large thickness of specimens, the difficulty of manufacturing and the peculiarities of measurement and identification of the obtained values of deformation in shear are considered. Flexural modules versus actual monolayer thickness and unsupported lengths versus specimen thickness and width are plotted. The necessity of registration of shear deformation in three-point bend testing for proper design of experiments and execution of calculations is shown. The accuracy and adequacy of the structural and bending characteristics are verified against the testing modes. The results confirm the relevance and validity of any given factor in modeling the stress-strain state of tested specimens.

Insignificant in vitro falcipain-2 inhibitory activity of novel 2-(4-(substituted benzoyl) piperazine-1-yl)-N-phenylacetamide derivatives

Background: The cysteine protease, falcipain-2 (FP-2) is an important drug target for the management of infection by the human malaria parasite Plasmodium falciparum . The rapid emergence of resistance is the main problem with all antimalarial agents. Hence, the discovery of novel, effective drugs to counter the spread of malaria parasites that are resistant toward existing agents, especially drugs that can act on new targets, is urgently necessary. Materials and Methods: A novel series of 2-(4-(substituted benzoyl) piperazine-1-yl)- N -phenylacetamide derivatives was designed using the ligand-based approach, employing a three-point pharmacophore model. It consists of an aromatic group (monocyclic/bicyclic), which is attached to the hydrophobic moiety; commonly an aromatic residue through hydrogen bond donor (HBD) and hydrogen bond acceptor (HBA) atom(s) acting as the linker. The new chemical entities were synthesized from the key intermediate N -phenyl-2-(piperazine-1-yl) acetamide, by coupling it with various substituted acids in the presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC.HCl) and 1 hydroxybenzotriazole (HOBt). The obtained compounds' structures were confirmed by 1 H NMR and by mass spectral data. Results: All the synthesized compounds were evaluated for their in vitro FP-2 inhibitory activity. Two compounds 5l and 5q showed very weak enzyme inhibition activities (3-5%) and the remaining 15 compounds showed no inhibition at 10 μm concentrations. However, unlike other reported FP-2 inhibitors, none of these molecules showed potent activity. Conclusion: This series of compounds did not have or had very less antimalarial activity.

Determination of Glomerular Filtration Rate in Adult Horses and Donkeys by Single IV Administration of Iohexol

The aim of the present article was to estimate glomerular filtration rate (GFR) using iohexol (IOX) clearance and evaluate the use of limited sampling models to establish an accurate and clinically suitable test in adult horses and donkeys. Iohexol was administered IV as a bolus at the dose of 75.5 mg/kg in eight horses and eight donkeys through the right jugular vein. Samples were collected through the left jugular vein before marker's administration (time 0) and at 15, 30, 60, 90, 120, 180, 240, 360 minutes, and 12 hours after its injection. Iohexol plasmatic concentrations were determined by high-performance liquid chromatography; plasma clearance was determined by use of a one-compartment model corrected by use of the Brochner-Mortensen formula. The nine-point clearance value was considered a reference for the evaluation of simplified methods. Correlation analysis between the glomerular filtration rate values obtained by the nine-point clearance method and the GFR values determined by the application of simplified sample combinations were performed using Pearson test, linear regression analysis, and one-way ANOVA test; P < .05 was considered significant. Plasma clearance of IOX in horses was 2.58 ± 0.21 mL/min/kg and 1.80 ± 0.10 mL/min/kg in donkeys. No significant difference in GFR estimation was noted among the values estimated by simplified models to those by nine-point method. The mean plasma clearance of IOX determined with three-point clearance model was 2.36 ± 0.14 mL/minute/kg in horses and 2.05 ± 0.40 mL/minute/kg in donkeys. This article reported the determination of GFR in horses and donkeys by single IV administration of IOX. Simplified models were evaluated.

Whole-genome QTL analysis for MAGIC.

An efficient whole genome method of QTL analysis is presented for Multi-parent advanced generation integrated crosses. Multi-parent advanced generation inter-cross (MAGIC) populations have been developed for mice and several plant species and are useful for the genetic dissection of complex traits. The analysis of quantitative trait loci (QTL) in these populations presents some additional challenges compared with traditional mapping approaches. In particular, pedigree and marker information need to be integrated and founder genetic data needs to be incorporated into the analysis. Here, we present a method for QTL analysis that utilizes the probability of inheriting founder alleles across the whole genome simultaneously, either for intervals or markers. The probabilities can be found using three-point or Hidden Markov Model (HMM) methods. This whole-genome approach is evaluated in a simulation study and it is shown to be a powerful method of analysis. The HMM probabilities lead to low rates of false positives and low bias of estimated QTL effect sizes. An implementation of the approach is available as an R package. In addition, we illustrate the approach using a bread wheat MAGIC population.

Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models

Long-term molecular dynamics simulations are used to compare the single particle dipole reorientation time, the diffusion constant, the viscosity, and the frequency-dependent dielectric constant of the coarse-grained big multipole water (BMW) model to two common atomistic three-point water models, SPC/E and TIP3P. In particular, the agreement between the calculated viscosity of BMW and the experimental viscosity of water is satisfactory. We also discuss contradictory values for the static dielectric properties reported in the literature. Employing molecular hydrodynamics, we show that the viscosity can be computed from single particle dynamics, circumventing the slow convergence of the standard approaches. Furthermore, our data indicate that the Kivelson relation connecting single particle and collective reorientation time holds true for all systems investigated. Since simulations with coarse-grained force fields often employ extremely large time steps, we also investigate the influence of time step on dynamical properties. We observe a systematic acceleration of system dynamics when increasing the time step. Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties. By contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough.

Development of Method for Three-Point Data Estimation and SVR-QSAR Model to Screen Anti Cancer Leads

Present work deals with generation of virtual samples as mathematical modeling of empirical data on the basis of empirical data. The generated samples were used for development of QSAR model. The method deals with extrapolation of sample vector in such a manner that there is conservation of the empirical data distribution. The data distribution has been judged with statistical parameters. The method was implemented with anticancer activity of Gossypol acetic acid against BCL2 target for colorectal cancer. Considering the virtual samples only for model development, model training showed a regression coefficient for leave one out cross validation as 0.996 with 66 virtual samples, and a regression coefficient with external test set data (51 samples) as 0.993. External test set data which were never used in the virtual sample generation showed predicted regression coefficient value of >0.61. On the basis of QSAR model, nine compounds were suggested as anti-BCL2 active compounds. The suggested compounds were further validated by docking study with Gossypol acetic acid and 'Tetrahydroisoquinoline amide substituted phenyl pyrazole' cocrystallized with chimeric BCL2-XL (PDBID: 2W3L) protein.

Insights into the complexity of chiral recognition by a three-point model

The three-point model and molecular simulation are used to understand the enantioselective adsorption of a homologous series of chiral compounds on a common chiral selector that is incorporated on a solid surface. We demonstrate how the enantioselectivity of homologous chiral compounds may go down, go up, remain the same, or even reverse. Conditions that lead to consistent enantioselectivity for homologous chiral compounds are also proposed.