Machine learning and its applications in reliability analysis systems

In this thesis, we are interested in exploring some aspects of Machine Learning (ML) and its application in the Reliability Analysis systems (RAs). We begin by investigating some ML paradigms and their- techniques, go on to discuss the possible applications of ML in improving RAs performance, and lastly give guidelines of the architecture of learning RAs. Our survey of ML covers both levels of Neural Network learning and Symbolic learning. In symbolic process learning, five types of learning and their applications are discussed: rote learning, learning from instruction, learning from analogy, learning from examples, and learning from observation and discovery. The Reliability Analysis systems (RAs) presented in this thesis are mainly designed for maintaining plant safety supported by two functions: risk analysis function, i.e., failure mode effect analysis (FMEA) ; and diagnosis function, i.e., real-time fault location (RTFL). Three approaches have been discussed in creating the RAs. According to the result of our survey, we suggest currently the best design of RAs is to embed model-based RAs, i.e., MORA (as software) in a neural network based computer system (as hardware). However, there are still some improvement which can be made through the applications of Machine Learning. By implanting the 'learning element', the MORA will become learning MORA (La MORA) system, a learning Reliability Analysis system with the power of automatic knowledge acquisition and inconsistency checking, and more. To conclude our thesis, we propose an architecture of La MORA

FDserver: A web service for protein folding research

*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.
*Availability:* http://sdbi.sdut.edu.cn/FDserve

Competing Orders in a Dipolar Bose-Fermi Mixture on a Square Optical Lattice: Mean-Field Perspective

We consider a mixture of a two-component Fermi gas and a single-component dipolar Bose gas in a square optical lattice and reduce it into an effective Fermi system where the Fermi-Fermi interaction includes the attractive interaction induced by the phonons of a uniform dipolar Bose-Einstein condensate. Focusing on this effective Fermi system in the parameter regime that preserves the symmetry of $D_4$, the point group of a square, we explore, within the Hartree-Fock-Bogoliubov mean-field theory, the phase competition among density wave orderings and superfluid pairings. We construct the matrix representation of the linearized gap equation in the irreducible representations of $D_4$. We show that in the weak coupling regime, each matrix element, which is a four-dimensional (4D) integral in momentum space, can be put in a separable form involving a 1D integral, which is only a function of temperature and the chemical potential, and a pairing-specific "effective" interaction, which is an analytical function of the parameters that characterize the Fermi-Fermi interactions in our system. We analyze the critical temperatures of various competing orders as functions of different system parameters in both the absence and presence of the dipolar interaction. We find that close to half filling, the d_{x^{2}-y^{2}}-wave pairing with a critical temperature in the order of a fraction of Fermi energy (at half filling) may dominate all other phases, and at a higher filling factor, the p-wave pairing with a critical temperature in the order of a hundredth of Fermi energy may emerge as a winner. We find that tuning a dipolar interaction can dramatically enhance the pairings with $d_{xy}$- and g-wave symmetries but not enough for them to dominate other competing phases.Comment: 18 pages, 9 figure

Effects of overexpressing wild-type and variant Rad52 on homologous recombination in human cells

Mitotic homologous recombination (HR) stabilises the genome by repairing harmful double stranded DNA (dsDNA) breaks. Rad52 promotes the annealing of complementary DNA strands and binds to Rad51 suggesting that Rad52 acts in both strand invasion (SI) and single strand annealing (SSA) HR pathways. Overexpression of Rad52 in mammalian cells can greatly stimulate HR, but the degree of stimulation varies widely between studies and inhibitory effects have also been described. The in vivo roles for Rad52 in mammalian cells are thus poorly understood as is the potential of using Rad52 as a tool to promote genome engineering methods [i.e. gene targeting (GT)]. Here I have systematically compared the effects of overexpressing wild-type (wt) and mutant Rad52 proteins on cell viability and various HR assays in human cells. Mutants were designed to test the potential involvement of defined domains/residues in any such effects. Human Rad52 (hRad52) and its derivatives negatively affected cell viability and proliferation which correlated with the presence of C-terminal residues 331-418, rather than, as expected, the Rad51 binding domain which limited inhibitory effects. Negative effects with yeast Rad52 (scRad52) were not observed. Consistent with previous findings, hRad52 inhibited GT, however, this was converted to a stimulatory effect when residues 331-418 were removed. When single stranded oligonucleotide (ssO) templates were used for GT, both hRad52 and its derivatives were stimulatory. These results are consistent with SI and SSA models for dsDNA- and ssO-mediated GT, respectively, and suggest that residues 331-418 cause a dominant-negative effect on SI and their removal promotes the strand annealing activity of the N-terminal domain. ScRad52 stimulated and inhibited GT with ds and ss templates, respectively. Altogether, these results provide the first evidence that truncated forms of hRad52 may serve as useful tools for promoting GT using both ds and ss DNA templates in human cells