School of Science Department of Chemistry 9 Molecular Dynamics Simulations of DNA Memory Supervisor: SU Haibin / CHEM Student: WANG Martin Shen / CHEM-IRE Course: UROP 1100, Fall UROP 2100, Spring Accurate and efficient models for tertiary structure predictions of nucleic acids are growing increasingly necessary for understanding the topology and function of non-coding RNA’s and DNA’s in terms of their biological activity, and more importantly, essential for fields involved de novo nucleic acid design like aptamers and nucleic acid nanostructures. This report will introduce potentials and important limitations for using a Transformer Encoder network for an all-computational method to predict distance-based trends in nucleic acids, and how the properties of Transformers in interpreting structural data may be advantageous for this application. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: CHANG Ka Pui / CHEM Course: UROP 3200, Fall The COVID-19-causing virus SARS-CoV-2 is still frequently mutating since December 2019, signified by emerging variants such as BA.2.86 (Pirola) and EG.5 (Iris). The trimeric spike glycoprotein, as the major mutational hotspot, plays an important role in viral infection by binding its receptor-binding domain to humans’ angiotensin-converting enzyme-2 receptor, which affinity is modulated by single amino-acid polymorphism (SAP), deletion, insertion, and N-linked glycosylation in the spike. By modelling the evolutionary trajectory of the virus by a composite metric based on previous appearance of spike mutations, it is hoped to accurately predict leading mutations that would show up in future emerging variants, to monitor the virus’ mutational landscape and facilitate further medical research. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: HONG Runnan / MATH-STAT Course: UROP 1100, Fall The impact of mutation rate and Ka/Ks value on multiple variants, as well as the adaptability and evolutionary dynamics of SARS-CoV-2 are two conference topics that impressed me. The discussion of mutation rate and Ka/Ks value emphasizes the neutral evolution theory, which believes that the evolution of neutral mutations is a kind of random drift, while beneficial mutations can be fixed in the population. In the research on SARSCoV-2, its highly variable characteristics have been emphasized, with special attention being paid to the XBB.1.5 family. This family may have strong immune evasion capabilities. Analysis of infections worldwide shows that the XBB.1.5 family is the main virus causing infections. The study of global trends provides important information to better understand the evolution of the virus, which is critical for global health agencies to more effectively respond to virus transmission and prevention.
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