RNA structure analysis : algorithms and applications

In this doctoral thesis, efficient algorithms for aligning RNA secondary structures and mining unknown RNA motifs are presented. As the major contribution, a structure alignment algorithm, which combines both primary and secondary structure information, can find the optimal alignment between two given structures where one of them could be either a pattern structure of a known motif or a real query structure and the other be a subject structure. Motivated by widely used algorithms for RNA folding, the proposed algorithm decomposes an RNA secondary structure into a set of atomic structural components that can be further organized in a tree model to capture the structural particularities. The novel structure alignment algorithm is implemented using dynamic programming techniques coupled by position-independent scoring matrices. The algorithm can find the optimal global and local alignments between two RNA secondary structures at quadratic time complexity. When applied to searching a structure database, the algorithm can find similar RNA substructures and therefore can be used to identify functional RNA motifs. Extension of the algorithm has also been accomplished to deal with position-dependent scoring matrix in the purpose of aligning multiple structures. All algorithms have been implemented in a package under the name RSmatch and applied to searching mRNA UTR structure database and mining RNA motifs. The experimental results showed high efficiency and effectiveness of the proposed techniques

A Tale of Planet Formation: From Dust to Planets

The characterization of exoplanets and their birth protoplanetary disks has enormously advanced in the last decade. Benefitting from that, our global understanding of the planet formation processes has been substantially improved. In this review, we first summarize the cutting-edge states of the exoplanet and disk observations. We further present a comprehensive panoptic view of modern core accretion planet formation scenarios, including dust growth and radial drift, planetesimal formation by the streaming instability, core growth by planetesimal accretion and pebble accretion. We discuss the key concepts and physical processes in each growth stage and elaborate on the connections between theoretical studies and observational revelations. Finally, we point out the critical questions and future directions of planet formation studies.Comment: 48 pages, 8 figures, invited review for Research in Astronomy and Astrophysic

The Librating Companions in HD 37124, HD 12661, HD 82943, 47 Uma and GJ 876: Alignment or Antialignment?

We investigated the apsidal motion for the multi-planet systems. In the simulations, we found that the two planets of HD 37124, HD 12661, 47 Uma and HD 82943 separately undergo apsidal alignment or antialignment. But the companions of GJ 876 and $\upsilon$ And are only in apsidal lock about $0^{\circ}$. Moreover, we obtained the criteria with Laplace-Lagrange secular theory to discern whether a pair of planets for a certain system are in libration or circulation.Comment: 13 Pages, 3 figures, 2 tables, Published by ApJ Letters, 591, July 1, 2003 (Figures now included to match the publication

The Dynamical Simulations of the Planets Orbiting GJ 876

We have performed simulations to investigate the dynamics of the M dwarf star GJ 876 in an attempt to reveal any stabilizing mechanism for sustaining the system.We simulated different coplanar and noncoplanar configurations of two-planet systems and other cases.From the simulations,we found that the 2 :1 mean-motion resonance between two planets can act as an effective mechanism for maintaining the stability of the system.This result is explained by a proposed analytical model.Using this model,we studied the region of motion of the inner planet by varying the parameters of the system,and we detected that the analytical results are well consistent with the numerical simulations.Comment: 17 pages, 8 figures available through authors, to be published in ApJ, June 20,2002 (V572, see figures