Solvation thermodynamics from cavity shapes of amino acids.

According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.

Fracture behavior of restored teeth and cavity shape optimization: Numerical and experimental investigation.

OBJECTIVES: Since restored teeth are subject to more damages than intact teeth, investigating their fracture behavior is important. However, so far, improvement of the debonding behavior of the restoration and fracture of restored teeth considering the geometry of the restoration and different restorative materials has remained understudied. The aim of this paper is to numerically and experimentally investigate the debonding behavior of the restoration in premolar teeth in order to reduce the stress of restoration thereby reducing the mechanical failure. METHODS: the fracture test for intact and Standard Class-II Mesial-Occlusal-Distal (MOD) restoration premolar teeth restored with several types of composite and conventional adhesive was performed in order to investigate their fracture behavior. The mechanical properties and fracture of composites as well as the adhesives used in experimental tests were obtained through separate standard mechanical tests. In addition, a number of composites and other adhesives were also chosen from other references, and by numerically simulating the fracture process of intact teeth and those restored with the materials of interest, the fracture behavior and yield load limit were investigated and predicted for them. Next, in order to reduce the stresses of bonding region and improve the damage behavior, using the stress-induced material transformation (SMT) optimization algorithm applied as code in finite element (FE) software, the shape of the restoration has been optimized based on different restorative materials. In order to confirm the numerical results, the fracture tests of teeth samples were performed with conventional and optimized restoration forms. Furthermore, using scanning electron microscopy (SEM) method, the fracture surface of the tested samples was examined. RESULTS: since the fracture behavior of teeth restored with different materials is different, the optimized MOD restoration would be also different for each of these restorative materials. By selecting TU-shape for the restoration in each of the samples, the debonding resistance and final fracture of teeth compared to the MOD restoration increased 51% in Pd and 11% in Pf for numerical results and 40% in Pd and 4% in Pf for experimental results. The obtained results suggest that choosing a proper shape for the restoration based on the properties of restorative materials leads to diminished normal and shear stresses and enhanced debonding resistance. Also, the yield load limit of the defective teeth would also improve considerably. SIGNIFICANCE: The clinical importance of this study is to predict strength of restored teeth and cavity shape optimization under variable conditions. Also, this paper introduces effective parameters on strength reduction/enhancement to dentists.

pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules.

pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc.

Efeito da forma geométrica da cavidade e do tipo de adesivo na microinfiltração em restaurações classe V / Effect of the geometric way of the cavity and the sticker type in the microleakage in restorations classe V

Foi avaliada "in vitro" a influência da forma da cavidade e do tipo de adesivo (frasco único e primer autocondicionante) na microinfiltração, em restaurações classe V. Em 40 incisivos bovinos, foram confeccionadas 40 cavidades com margens em esmalte, sendo 20 retangulares e 20 circulares. Em seguida, foram divididas em 4 grupos (n=10), de acordo com o adesivo e a forma geométrica: grupo 1 - circular/adesivo de frasco único; grupo 2 - retangular/adesivo de frasco único; grupo 3 - retangular/adesivo de primer autocondicionante; grupo 4 - circular/adesivo de primer autocondicionante. As cavidades foram restauradas com resina composta Tetric Ceram®, com incremento único. Em seguida, os dentes foram estocados a 37ºC, por 30 dias, e, em seguida, impermeabilizados com esmalte cosmético e imersos em solução de nitrato de prata a 50% por 2 horas, lavados e imersos em solução reveladora por 6 horas. Após isto, foram seccionados, e as amostras, analisadas em lupa estereoscópica de 25X. Os dados foram submetidos à análise estatística não paramétrica de Kruskal?Wallis (p<0,05) em que se constatou diferença estatisticamente significante entre os grupos estudados. Concluiu-se que o adesivo de frasco único associado à cavidade circular comportou-se estatisticamente significante frente às outras combinações; as cavidades circulares comportaram-se significantes em relação às retangulares.

It was evaluated ?in vitro? the shape of the cavity influence and the type of adhesive (single bottle and self-etching primer) on microleakage, in class V restorations. In 40 bovine incisors were prepared 40 cavities with margins in enamel, 20 rectangular and 20 circular. Then, were divided into four groups (n = 10) according to the adhesive and geometrical form: group 1 - circular / single bottle adhesive, Group 2 - rectangular / single bottle adhesive, Group 3 - rectangular / self-etching primer adhesive, group 4 - circular / self-etching primer adhesive. The cavities were restored with composite resin Tetric Ceram? with only one increment. Then the teeth were stored at 37?C, for 30 days, and then sealed with cosmetic nail varnish and immersed in a 50% solution of silver nitrate for 2 hours, washed and immersed in revealing solution for 6 hours. After that, the samples were sectioned and examined under stereoscopic loupe of 25X. Data were subjected to non-parametric Kruskal-Wallis statistical analysis (p <0.05) which showed statistically significant difference among the groups. It was concluded that: The single-bottle adhesive associated with circular cavity behaved statistically significant according to the other combinations, the circular cavities behaved significant in relation to the rectangular.

Predicting prognosis based on the shape of the left ventricular cavity in dilated cardiomyopathy: analysis using rate of improvement in the circle index.

PURPOSE: To elucidate the relation between a quantitative measure of the shape of the left ventricular cavity, cardiac function, and prognosis in patients with dilated cardiomyopathy (DCM). METHODS: The hearts of 20 healthy individuals and 18 patients with DCM were evaluated. Participants were aged 48.5 ± 5.0 years. On the basis of end-systolic four-chamber view echocardiograms, the endocardium of the left ventricle was traced and the resulting curve was segmented using 100 points. A line tangential to the curve was then drawn at each point, and the angle between two adjacent tangential lines was calculated. The deviation of these angles was designated as the circle index. The circle index and hemodynamic findings in patients with DCM were compared, and the rate of improvement in the circle index in these cases of DCM was determined. These patients were then placed into one of two groups: group R (11 patients), those with improvement rates of 10% or higher at time of discharge; and group NR (seven patients), those with rates less than 10%. Diuretic (furosemide) use, New York Heart Association (NYHA) classification, and readmission rate for the two groups were compared 2 years after discharge. RESULTS: The circle index was 2.7 ± 0.9 in the DCM group and 17.5 ± 4.2 in the healthy group (P < 0.01). The circle index in the DCM group was correlated with pulmonary capillary wedge pressure (r(2) = 0.42). Use of furosemide was unchanged in group R 2 years after discharge, but had increased for all patients in group NR. All cases in group R were classified as NYHA I 2 years after discharge. In group NR, in contrast, although all cases were classified as NYHA I at discharge, five of seven cases had deteriorated to NYHA III-IV 2 years later and were readmitted to hospital. CONCLUSION: There appears to be a quantifiable correlation between the circularity of the left ventricular cavity and the circle index. This suggests that rate of improvement after treatment for heart failure could predict prognosis in patients with DCM.

Effect of cavity shape, bond quality and volume on dentin bond strength / 대한치과보존학회지

The aim of this study was to evaluate the effect of cavity shape, bond quality of bonding agent and volume of resin composite on shrinkage stress developed at the cavity floor. This was done by measuring the shear bond strength with respect to iris materials (cavity shape; adhesive-coated dentin as a high C-factor and Teflon-coated metal as a low C-factor), bonding agents (bond quality; Scotchbond(TM) Multi-purpose and Xeno(R)III) and iris hole diameters (volume; 1 mm or 3 mm in diameter x 1.5 mm in thickness). Ninety-six molars were randomly divided into 8 groups (2 x 2 x 2 experimental setup). In order to simulate a Class I cavity, shear bond strength was measured on the flat occlusal dentin surface with irises. The iris hole was filled with Z250 restorative resin composite in a bulk-filling manner. The data was analyzed using three-way ANOVA and the Tukey test. Fracture mode analysis was also done. When the cavity had high C-factor, good bond quality and large volume, the bond strength decreased significantly. The volume of resin composite restricted within the well-bonded cavity walls is also be suggested to be included in the concept of C-factor, as well as the cavity shape and bond quality. Since the bond quality and volume can exaggerate the effect of cavity shape on the shrinkage stress developed at the resin-dentin bond, resin composites must be filled in a method, which minimizes the volume that can increase the C-factor.

Computation of cavity shapes, sizes, and plasticities.

A new molecular mechanics approach has been developed and used to scan the optimum geometry (size and shape) of a host molecule and the energy cost for the deformation of the bonding cavity, based on a general, unspecific guest with given docking sites and a variable size. Lagrange multipliers are used to constrain the sum of internal coordinates (host-guest docking-site distances), and no assumptions with respect to the type and strength of the host-guest bonding have to be made. This new approach has been fully implemented in a molecular mechanics program, and it is used to compute the size, shape, and plasticity of a rigid, asymmetrical, tetradentate (Namine )2 (Npyridine )2 ligand. It is shown that all other methods for the computation of ligand hole sizes that have been reported so far are not able to compute the ligand cavities independently of the metal ion, and they lead to strikingly different shapes, sizes, and plasticities. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 781-785, 1999.