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Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods, it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

The prediction of protein conformation from its amino-acid sequence is one of the most prominent problems in computational biology. But it is NP-hard. Here, we focus on an abstraction widely studied of this problem, the two-dimensional hydrophobic-polar protein folding problem (2D HP PFP). Mathematical optimal model of free energy of protein is established. Native conformations are often sought using stochastic sampling methods, but which are slow. The elastic net (EN) algorithm is one of fast deterministic methods as travelling salesman problem (TSP) strategies. However, it cannot be applied directly to protein folding problem, because of fundamental differences in the two types of problems. In this paper, how the 2D HP protein folding problem can be framed in terms of TSP is shown. Combination of the modified elastic net algorithm and novel local search method is adopted to solve this problem. To our knowledge, this is the first application of EN algorithm to 2D HP model. The results indicate that our approach can find more optimal conformations and is simple to implement, computationally efficient and fast.

Objective To determine if increased relative humidity and temperature simulating intraoral environmental conditions adversely affect flexural properties of dental composites. Methods Specimen fabrication followed ANSI/ADA specification 27 for resin-based filling materials, except that ambient laboratory conditions (47% relative humidity at 22 °C) or simulated intraoral conditions (90% relative humidity at 35 °C) were used when fabricating and polymerizing specimens. Ten specimens were made of each of three commercially available composites at each condition. As per the specification, after aging specimens in 10 ml of deionized water at 37 °C for 24 h, flexural properties were measured using a 3-point bend test. Results A two-factor ANOVA and Fisher's least significant difference (LSD) post hoc (α = 0.05) indicated there were significant differences in flexural modulus and strength as a function of material, with Z250 = TPH > Prodigy. However, neither flexural modulus nor flexural strength of any material was adversely influenced by fabrication conditions. Significance Although the flexural properties did not decrease with respect to fabrication conditions, the flexural modulus of some of the materials (TPH Spectrum and Z250) increased when specimens were fabricated at simulated intraoral temperature and relative humidity. Thus, simulation of these factors may be important in laboratory testing, since the resultant properties may better reflect flexural properties associated with dental composite restorations placed clinically.

The calculation of the scalar compressive and shear anisotropy factors developed for single crystal refractory compounds has been adapted to the anisotropic elastic stiffness coefficients determined by a number of ultrasonic measurements of bone based on transverse isotropic symmetry. Later, this work was extended to include the ultrasonic measurements of bone based on orthotropic symmetry. Recently, the five transverse isotropic elastic constants for both wet and dry human dentin were determined using resonant ultrasound spectroscopy. The five transverse isotropic elastic constants for wet bovine enamel and dentin had been calculated based on modeling of ultrasonic wave propagation measurements and related data in the literature. The scalar compressive and shear anisotropy factors have been calculated from both these sets of data and are compared with a representative set from those published previously for both human and bovine bone and both fluoro- and hydroxyl-apatites.

A finite element (FE) model has been developed based upon the recently measured microscale morphological, chemical and mechanical properties of dentin-adhesive (d-a) interfaces using confocal Raman microspectroscopy and scanning acoustic microscopy (SAM). The results computed from this FE model indicated that the stress distributions and concentrations are affected by the micro-scale elastic properties of various phases composing the d-a interface. However, these computations were performed assuming isotropic material properties for the d-a interface. The d-a interface components, such as the peritubular and intertubular dentin, the partially demineralized dentin and the so-called 'hybrid layer' adhesive-collagen composite, are probably anisotropic. In this paper, the FE model is extended to account for the probable anisotropic properties of these d-a interface phases. A parametric study is performed to study the effect of anisotropy on the micromechanical stress distributions in the hybrid layer and the peritubular dentin phases of the d-a interface. It is found that the anisotropy of the phases affects the region and extent of stress concentration as well as the location of the maximum stress concentrations. Thus, the anisotropy of the phases could effect the probable location of failure initiation, whether in the peritubular region or in the hybrid layer. © 2005 The Royal Society.

We introduce a new method to measure the elastic constants of globular proteins. Gold nanoparticles, tethered to a gold surface by the protein, are driven by an ac electric field while their displacement is synchronously detected by evanescent wave scattering, yielding the mechanical response function of the macromolecular sample in the frequency domain. We apply the method to measure the stiffening of an enzyme upon binding its substrate.

Determining the functional conformation of a protein from its amino acid sequence remains a central problem in computational biology. In this paper, we establish the mathematical optimal model of protein folding problem (PFP) on two-dimensional space based on the minimal energy principle. A novel hybrid of elastic net algorithm and local search method (ENLS) is applied successfully to simulations of protein folding on two-dimensional hydrophobic-polar (HP) lattice model. Eight HP benchmark instances with up to 64 amino acids are tested to verify the effectiveness of proposed approach and model. In several cases, the ENLS method finds new lower energy states. The numerical results show that it is drastically superior to other methods in finding the ground state of a protein.

The interfacial microstructure and spatial distribution of the modulus of elasticity have a profound effect on load transfer at the dentin/adhesive (d/a) interface. The microstructure is influenced by the varying degree of demineralization of intertubular and peritubular dentin during etching as well as the depth of adhesive penetration into the hybrid layer. These factors lead not only to a unique microstructure in the vicinity of the dentinal tubules, but also to a mechanically graded hybrid layer. This article investigates the micromechanical stress distribution at a d/a interface with the use of finite element analysis (FEA). Such analysis is now feasible given the newly measured moduli of elasticity at micro- and nanoscales. The results indicate that the morphological and micromechanical properties of the d/a interface affects the stress field such that the fracture/failure is likely to initiate in the stress-concentration zone of peritubular dentin next to the hybrid/exposed- collagen layer. The results suggest that devising a full-depth high modulus hybrid layer may considerably reduce the stress concentration zone and the magnitude of stress concentration in the peritubular dentin next to the hybrid/exposed-collagen layer. © 2004 Wiley Periodicals, Inc.

For proteins, the mechanical properties of the folded state are directly related to function, which generally entails conformational motion. Through sub-Angstrom resolution measurements of the AC mechanical susceptibility of a globular protein we describe a new fundamental materials property of the folded state. For increasing amplitude of the forcing, there is a reversible transition from elastic to viscoelastic response. At fixed frequency, the amplitude of the deformation is piecewise linear in the force, with different slopes in the elastic and viscoelastic regimes. Effectively, the protein softens beyond a yield point defined by this transition. We propose that ligand induced conformational changes generally operate in this viscoelastic regime, and that this is a universal property of the folded state.