in situ Nanomechanical Investigations of Bone

PhDMineralized collagen fibrils(MCFs)are the fundamental building blocks that contribute to the extraordinary mechanical behaviour of bone. Despite its importance in defining bone mechanics, especially the high resistance to fracture recorded in bone tissue, MCFs have yet to be mechanically tested and and, thus, MCF contributions to the global mechanical properties of bone is unclear. In this thesis, a complete strategy for performing direct mechanical testing on nanosized fibrous samples including MCFs from bone using a novel in situ atomic force microscope (AFM) – scanning electron microscope (SEM) combination was scanning electron microscope (SEM) combination was established. This technique was used to mechanically test MCFs from antler bone tissue for the first time and resultant stress behaviour was recorded to highlight the inhomogeneous response of fibrils, which is associated with fibrillar compositional heterogeneity. Mechanical properties of MCFs and bone tissue were found to be controlled by biomineralization process using additional tensile testing of MCFs and bulk samples from mouse limb bones at different ages. Extrafibrillar mineralization was found to have effects on the Young’s modulus of bone tissue rather than fibrils, indicating the importance of fibrillar interfaces in controlling overall mechanical behaviour of bone tissue. Interfaces between fibrils in bone were examined by carrying out single fibril pullout tests. A weak but reformable interface, dominated by ionic bonds between fibrils, was recorded and the sacrificial bond reforming activity at the interface was found to be be dependent on pullout strain rate. Finally, considerations of bone as a fibrous composite was used to evaluate nanomechanical testing data, with approximately 50 % of the bone fracture energy accounted for in failure of fibril interfaces

Thermal-induced slippage of soft solid films

The dynamics of interfacial slippage of entangled polystyrene (PS) films on an adsorbed layer of polydimethylsiloxane (PDMS) on silicon was studied from the surface capillary dynamics of the films. By using PS with different molecular weights, we observed slippage of the films in the viscoelastic liquid and rubbery solid state respectively. Remarkably, all our data can be explained by the linear equation, J = -M∇P and a single friction coefficient, ξ, where J is the unit-width current, M is mobility and P is Laplace pressure. For viscous films, M is accountable by using conventional formulism. For rubbery films, M takes on different expressions depending on whether the displacements associated with the slip velocity, v (~∇P/ξ), dominate or elastic deformations induced by ∇P dominate. For viscoelastic liquid films, M is the sum of the mobility of the films in the viscous and rubbery states.Accepted manuscrip

Sympathy and Punishment: Evolution of Cooperation in Public Goods Game

An important way to maintain human cooperation is punishing defection. However, since punishment is costly, how can it arise and evolve given that individuals who contribute but do not punish fare better than the punishers? This leads to a violation of causality, since the evolution of punishment is prior to the one of cooperation behaviour in evolutionary dynamics. Our public goods game computer simulations based on generalized Moran Process, show that, if there exists a \'behaviour-based sympathy\' that compensates those who punish at a personal cost, the way for the emergence and establishment of punishing behaviour is paved. In this way, the causality violation dissipates. Among humans sympathy can be expressed in many ways such as care, praise, solace, ethical support, admiration, and sometimes even adoration; in our computer simulations, we use a small amount of transfer payment to express \'behaviour-based sympathy\'. Our conclusions indicate that, there exists co-evolution of sympathy, punishment and cooperation. According to classical philosophy literature, sympathy is a key factor in morality and justice is embodied by punishment; in modern societies, both the moral norms and the judicial system, the representations of sympathy and punishment, play an essential role in stable social cooperation.Public Goods Game, Cooperation, Social Dilemma, Co-Evolution, Sympathy, Punishment

Improved Chou-Fasman method for protein secondary structure prediction

BACKGROUND: Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. However, this method has its limitations due to low accuracy, unreliable parameters, and over prediction. Thanks to the recent development in protein folding type-specific structure propensities and wavelet transformation, the shortcomings in Chou-Fasman method are able to be overcome. RESULTS: We improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform. (b) Substitute the original secondary structure conformational parameters with folding type-specific secondary structure propensities. (c) Modify Chou-Fasman rules. The CB396 data set was tested by using improved Chou-Fasman method and three indices: Q3, Qpre, SOV were used to measure this method. We compared the indices with those obtained from the original Chou-Fasman method and other four popular methods. The results showed that our improved Chou-Fasman method performs better than the original one in all indices, about 10–18% improvement. It is also comparable to other currently popular methods considering all the indices. CONCLUSION: Our method has greatly improved Chou-Fasman method. It is able to predict protein secondary structure as good as current popular methods. By locating nucleation regions with refined wavelet transform technology and by calculating propensity factors with larger size data set, it is likely to get a better result

Protein structural class prediction based on an improved statistical strategy

<p>Abstract</p> <p>Background</p> <p>A protein structural class (PSC) belongs to the most basic but important classification in protein structures. The prediction technique of protein structural class has been developing for decades. Two popular indices are the amino-acid-frequency (AAF) based, and amino-acid-arrangement (AAA) with long-term correlation (LTC) – based indices. They were proposed in many works. Both indices have its pros and cons. For example, the AAF index focuses on a statistical analysis, while the AAA-LTC emphasizes the long-term, biological significance. Unfortunately, the datasets used in previous work were not very reliable for a small number of sequences with a high-sequence similarity.</p> <p>Results</p> <p>By modifying a statistical strategy, we proposed a new index method that combines probability and information theory together with a long-term correlation. We also proposed a numerically and biologically reliable dataset included more than 5700 sequences with a low sequence similarity. The results showed that the proposed approach has its high accuracy. Comparing with amino acid composition (AAC) index using a distance method, the accuracy of our approach has a 16–20% improvement for re-substitution test and about 6–11% improvement for cross-validation test. The values were about 23% and 15% for the component coupled method (CCM).</p> <p>Conclusion</p> <p>A new index method, combining probability and information theory together with a long-term correlation was proposed in this paper. The statistical method was improved significantly based on our new index. The cross validation test was conducted, and the result show the proposed method has a great improvement.</p

The Influence of in-medium NN cross-sections, symmetry potential and impact parameter on the isospin observables

We explore the influence of in-medium nucleon-nucleon cross section, symmetry potential and impact parameter on isospin sensitive observables in intermediate-energy heavy-ion collisions with the ImQMD05 code, a modified version of Quantum Molecular Dynamics model. At incident velocities above the Fermi velocity, we find that the density dependence of symmetry potential plays a more important role on the double neutron to proton ratio $DR(n/p)$ and the isospin transport ratio $R_i$ than the in-medium nucleon-nucleon cross sections, provided that the latter are constrained to a fixed total NN collision rate. We also explore both $DR(n/p)$ and $R_i$ as a function of the impact parameter. Since the copious production of intermediate mass fragments is a distinguishing feature of intermediate-energy heavy-ion collisions, we examine the isospin transport ratios constructed from different groups of fragments. We find that the values of the isospin transport ratios for projectile rapidity fragments with $Z\ge20$ are greater than those constructed from the entire projectile rapidity source. We believe experimental investigations of this phenomenon can be performed. These may provide significant tests of fragmentation time scales predicted by ImQMD calculations.Comment: 24 pages, 9 figures, to be published in Phys. Rev.