Inferring a weighted elastic network from partial unfolding with coarse-grained simulations

A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental C coordinates, and they only take the pairs of C atoms within a given cutoff distance r(c) into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two C atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures. Proteins 2014; 82:119-129. (c) 2013 Wiley Periodicals, Inc.

On the contact stiffness and nonlinear vibration of an elastic body with a rough surface in contact with a rigid flat surface

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The influence of self-weight of elastic 2D structures in topology optimization via numerical technique Smooth Evolutionary Structural Optimization (SESO)

This paper deals with topology optimization in plane elastic-linear problems considering the influence of the self weight in efforts in structural elements. For this purpose it is used a numerical technique called SESO (Smooth ESO), which is based on the procedure for progressive decrease of the inefficient stiffness element contribution at lower stresses until he has no more influence. The SESO is applied with the finite element method and is utilized a triangular finite element and high order. This paper extends the technique SESO for application its self weight where the program, in computing the volume and specific weight, automatically generates a concentrated equivalent force to each node of the element. The evaluation is finalized with the definition of a model of strut-and-tie resulting in regions of stress concentration. Examples are presented with optimum topology structures obtaining optimal settings. (C) 2012 CIMNE (Universitat Politecnica de Catalunya). Published by Elsevier Espana, S.L.U. All rights reserved.

Effect of Ceramic Thickness and Shade on Mechanical Properties of a Resin Luting Agent

Purpose: This study aimed to investigate the influence of ceramic thickness and shade on the Knoop hardness and dynamic elastic modulus of a dual-cured resin cement.Materials and Methods: Six ceramic shades (Bleaching, A1, A2, A3, A3.5, B3) and two ceramic thicknesses (1 mm, 3 mm) were evaluated. Disk specimens (diameter: 7 mm; thickness: 2 mm) of the resin cement were light cured under a ceramic block. Light-cured specimens without the ceramic block at distances of 1 and 3mm were also produced. The Knoop hardness number (KHN), density, and dynamic Young's moduli were determined. Statistical analysis was conducted using ANOVA and a Tukey B rank order test (p = 0.05).Results: The bleaching 1-mm-thick group exhibited significantly higher dynamic Young's modulus. Lower dynamic Young's moduli were observed for the 3-mm-thick ceramic groups compared to bleaching 3-mm-thick group, and no difference was found among the other 3-mm groups. For the KHN, when A3.5 3-mm-thick was used, the KHN was significantly lower than bleaching and A1 1-mm-thick ceramic; however, no difference was exhibited between the thicknesses of the same shade.Conclusions: The dual-cured resin cement studied irradiated through the 1-mm-thick ceramic with the lightest shade (bleaching ceramic) exhibited a better elastic modulus, and there was no effect in KHN of the resin cement when light cured under different ceramic shades and thicknesses (1 and 3 mm), except when the A3.5 3-mm-thick ceramic was used.Clinical Significance: Variolink II irradiated through ceramic with the lowest chroma exhibited the highest elastic modulus; therefore, the light activation method might not be the same for all clinical situations.

The effects of elastic tubing-based resistance training compared with conventional resistance training in patients with moderate chronic obstructive pulmonary disease: a randomized clinical trial

Objective: To investigate the effects of elastic tubing training compared with conventional resistance training on the improvement of functional exercise capacity, muscle strength, fat-free mass, and systemic inflammation in patients with chronic obstructive pulmonary disease.Design: A prospective, randomized, eight-week clinical trial.Setting: The study was conducted in a university-based, outpatient, physical therapy clinic.Subjects: A total of 49 patients with moderate chronic obstructive pulmonary disease.Interventions: Participants were randomly assigned to perform elastic tubing training or conventional resistance training three times per week for eight weeks.Main measures: The primary outcome measure was functional exercise capacity. The secondary outcome measures were peripheral muscle strength, health-related quality of life assessed by the Chronic Respiratory Disease Questionnaire (CRDQ), fat-free mass, and cytokine profile.Results: After eight weeks, the mean distance covered during six minutes increased by 73 meters (69) in the elastic tubing group and by 42 meters (+/- 59) in the conventional group (p < 0.05). The muscle strength and quality of life improved in both groups (P < 0.05), with no significant differences between the groups. There was a trend toward an improved fat-free mass in both groups (P = 0.05). After the first and last sessions, there was an increase in interleukin 1 (IL-1) and interleukin 10 (IL-10) in both groups, while tumour necrosis factor alpha (TNF-) was stimulated only in the conventional training group.Conclusion: Elastic tubing training had a greater effect on functional exercise capacity than conventional resistance training. Both interventions were equally effective in improving muscle strength and quality of life.

In vitro comparison of the force degradation of orthodontic intramural elastic from different compositions

Introduction and Objective: The synthetic intermaxillary elastic emerged as an alternative for clinical use in patients with latex sensitivity. However, there are disagreements about this elastic protocol use according to the force degradation. The aim of this study was to evaluate, in vitro, the forces generated by latex and synthetic elastics over time. Material and methods: Sample size of 840 elastics were used (420 latex and 420 synthetic), delivering medium strength (Dental Morelli®) with internal diameter of 1/8”, 3/16”, 1/4” and 5/16”. The elastics were randomly divided into 7 groups according to the time of the force measuring and immersed into distilled water at 37°C. To measure the force in each group, the elastics were stretched in six progressive increases of 100% of its internal diameter with the aid of a testing machine Emic and measured up to 72 hours. Data were analyzed with SPSS 16.0, using one-way analysis of variance (ANOVA). Results: Immediate force level of synthetic elastics was statistically higher than latex elastics in all strains, for the same size. However, the latex elastics mean force slightly decreased over time, while the synthetic elastics presented an abrupt decrease. Conclusion: The synthetic elastic presented severe force degradation, jeopardizing the cost-benefit ratio, which indicates a higher replacement frequency. The latex elastic showed better mechanical performance in comparison to synthetic ones.

Differential cross sections for elastic and inelastic positronium-hydrogen-atom scattering

A time reversal symmetric regularized electron exchange model was used to elastic scattering, target elastic Ps excitations and target inelastic excitation of hydrogen in a five state coupled model. A singlet Ps-H-S-wave resonance at 4.01 eV of width 0.15 eV and a P-wave resonance at 5.08 eV of width 0.004 eV were obtained using this model. The effect on the convergence of the coupled-channel scheme due to the inclusion of the excited Ps and H states was also analyzed.

Elastic band causing exfoliation of the upper permanent central incisors

Objective. This study reports a case in which elastic band use culminated in the loss of the incisors. Case Report. An 11-year-old white girl was seen complaining of pain, with purulent discharge and severe tooth mobility. The bone destruction detected radiographically in the region, despite its single location and absence in posterior quadrants of the maxilla and/or mandible, was similar to that observed in Langerhans cell disease. To our surprise, an elastic band involving the midportion of the roots of the two upper central incisors was found during biopsy. The debris was removed and a metal wire was placed in permanent maxillary right and left incisors. The patient was followed up, but no improvement in tooth mobility was observed. Bone loss increased, and internal resorption and root exposure occurred, which culminated in the extraction of permanent maxillary right and left incisors. Conclusion. The present case highlights the fact that professionals sometimes are confronted by anamnestic reports never seen before.

Study of elastic properies of Ti3Al intermetallic compound using the ab initio calculation

The elastic properties of a Ti3Al intermetallic compound were studied using full potential (FP LAPW ) with the APW+lo method. The FP-LAPW is among the most accurate band structure calculations currently available and is based on the density functional theory with general gradient approximation for the exchange and correlation potential. This method provides the structural properties of the ground state as bulk modulus, equilibrium lattice parameter, and equilibrium minimum energy, and the elastic properties as shear modulus, young modulus, Zener coefficient (anisotropy), and Poisson coefficient. The calculated elastic properties are coherent with the elastic properties of the material.

First-principles simulation of elastic constants and electronic properties of GaN

The electronic and structural properties and elastic constants of the wurtzite phase of GaN, was investigated by computer simulation at Density Functional Theory level, with B3LYP and B3PW hybrid functional. The electronic properties were investigated through the analysis of the band structures and density of states, and the mechanical properties were studied through the calculus of the elastic constants: C11, C33, C44, C12, and C13. The results show that the maximum of the valence band and the minimum of the conduction band are both located at the Γ point, indicating that GaN is a direct band gap semiconductor. The following constants were obtained for B3LYP and B3PW (in brackets): C11 = 366.9 [372.4], C33 = 390.9 [393.4], C44 = 99.1 [96.9], C12 = 143.6 [155.2], and C13 = 107.6 [121.4].

Influence of nonlinear stiffness on the dynamics of a slender elastic beam under torsional oscillations

This study focuses on analysing the effects of nonlinear torsional stiffness on the dynam-ics of a slender elastic beam under torsional oscillations, which can be subject to helical buckling.The helical buckling of an elastic beam confined in a cylinder is relevant to many applications. Someexamples include oil drilling, medical cateters and even the conformation and functioning of DNAmolecules. A recent study showed that the formation of the helical configuration is a result of onlythe torsional load, confirming that there is a different path to helical buckling which is not related tothe sinusoidal buckling, stressing the importance of the geometrical behaviour of the beam. A lowdimensional model of an elastic beam under torsional oscillations is used to analyse its dynamical be-haviour with different stiffness characteristics, which are present before and after the helical buckling.Hardening and softening characteristics are present, as the effects of torsion and bending are coupled.With the use of numerical algorithms applied to nonlinear dynamics, such as bifurcation diagramsand basins of attraction, it is shown that the nonlinear stiffness can shift the bifurcations and inducechanges in the stability of the desirable and undesirable solutions. Therefore, the proper modellingof these stiffness nonlinearities seems to be important for a better understanding of the dynamicalbehaviour of such beams.

The reduced modulus in the analysis of sharp instrumented indentation tests

In the analysis of instrumented indentation data, it is common practice to incorporate the combined moduli of the indenter (E-i) and the specimen (E) in the so-called reduced modulus (E-r) to account for indenter deformation. Although indenter systems with rigid or elastic tips are considered as equivalent if E-r is the same, the validity of this practice has been questioned over the years. The present work uses systematic finite element simulations to examine the role of the elastic deformation of the indenter tip in instrumented indentation measurements and the validity of the concept of the reduced modulus in conical and pyramidal (Berkovich) indentations. It is found that the apical angle increases as a result of the indenter deformation, which influences in the analysis of the results. Based upon the inaccuracies introduced by the reduced modulus approximation in the analysis of the unloading segment of instrumented indentation applied load (P)-penetration depth (delta) curves, a detailed examination is then conducted on the role of indenter deformation upon the dimensionless functions describing the loading stages of such curves. Consequences of the present results in the extraction of the uniaxial stress-strain characteristics of the indented material through such dimensional analyses are finally illustrated. It is found that large overestimations in the assessment of the strain hardening behavior result by neglecting tip compliance. Guidelines are given in the paper to reduce such overestimations.

Relationship between elastic and mechanical properties of dental ceramics and their index of brittleness

The purpose of the study was to verify the effects of a number of materials' parameters (crystalline content; Young's modulus, E; biaxial flexure strength, sigma(i); Vickers hardness, VH; fracture toughness, K-Ic; fracture surface energy, gamma(f); and index of brittleness, B) on the brittleness of dental ceramics. Five commercial dental ceramics with different contents of glass phase and crystalline particles were studied: a vitreous porcelain (VM7/V), a porcelain with 16 vol% leucite particles (d.Sign/D), a glass-ceramic with 29 vol% leucite particles (Empress/E1), a glass-ceramic with 58 vol% lithium-disilicate needle-like particles (Empress 2/E2), and a glass-infiltrated alumina composite with 65 vol% crystals (In-Ceram Alumina/IC). Discs were constructed according to manufacturers' instructions, ground and polished to final dimensions (12 mm x 1.1 mm). Elastic constants were determined by ultrasonic pulse-echo method. sigma(i) was determined by piston-on-3-balls method in inert condition. VH was determined using 19.6 N load and K-Ic was determined by indentation strength method. gamma(f) was calculated from the Griffith-Irwin relation and B by the ratio of HV to K-Ic. IC and E2 showed higher values of sigma(i), E, K-Ic and gamma(f), and lower values of B compared to leucite-based glass-ceramic and porcelains. Positive correlations were observed for sigma(i) versus K-Ic, and K-Ic versus E-1/2, however, E did not show relationship with HV and B. The increase of crystalline phase content is beneficial to decrease the brittleness of dental ceramics by means of both an increase in fracture surface energy and a lowering in index of brittleness. (C) 2012 Elsevier Ltd and Techna Group Sri. All rights reserved.

Effect of hydrogen bond formation on the elastic molecular scattering: a case study with methanol

Rayleigh optical activities of small hydrogen-bonded methanol clusters containing two to five molecules are reported. For the methanol trimer, tetramer, and pentamer both cyclic and linear structures are considered. After the geometry optimizations, the dipole moments and the dipole polarizabilities (mean, interaction, and anisotropic components) are calculated using HF, MP2 and DFT (B3LYP, B3P86 and BH&HLYP) with aug-cc-pVDZ extended basis set. The polarizabilities are used to analyse the depolarization ratios and the Rayleigh scattering activities. The variations in the activity and in the depolarization for Rayleigh scattered radiation with the increase in the cluster size for both cyclic and linear structures are analysed.