Undergraduate Research Opportunities Program (UROP) Proceedings 2012-13

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C M Y CM MY CY CMY K

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C M Y CM MY CY CMY K

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Message from the President

ii

Overview of UROP (2012-13)

iii

Abstracts of UROP Projects – 2012-13*

School of Science

2-40

School of Engineering

42-105

School of Business & Management

107-129

School of Humanities & Social Science

131-139

Interdisciplinary Programs Office

141-142

* Abstracts from each School are listed first by alphabetical order of Department name, and then by alphabetical order of Advisor’s surname.

Summary of UROP Courses

UROP 1000

Undergraduate Research Opportunities Program

(0 credit, offered in summer session only)

UROP 1100

Undergraduate Research Opportunities Program Series 1

(1 credit, offered throughout the year)

UROP 1200

Undergraduate Research Opportunities Program Series 2

(1 credit, offered throughout the year; prerequisite is pass in UROP1100, with approval by project advisor)

UROP 1300

Undergraduate Research Opportunities Program Series 3

(1 credit, offered throughout the year; prerequisite is pass in UROP1200, with approval by project advisor)

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The Undergraduate Research Opportunities Program (UROP) has been very

successful since its launch in 2005, with a significant increase in the number of

participating faculty members and students every year. Over 350 students joined

the UROP in the 2012-13 academic year, with up to 140 faculty members

offering almost 300 projects by shouldering additional responsibilities.

Out of the many students who have joined UROP since its launch,

around 28% have pursued postgraduate studies either in Hong

Kong or in leading overseas universities after graduating.

These proceedings present overviews of the various research

projects conducted by our undergraduate students under the

guidance of their faculty supervisors. As a research-based university,

HKUST spares no effort in equipping its students with both fundamental and

applied knowledge. Through UROP, they gain hands-on experience of academic

research using cutting-edge facilities that are typically available to postgraduates

only. Given the encouraging achievements of our UROP participants, I am certain

that this program will continue to thrive as a signature experience at HKUST.

Tony F Chan

President

HKUST

Message from the

President

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In the 2012-13 academic year, the Undergraduate Research

Opportunities Program (UROP) continued to gain popularity

among students. We were also glad to see a growing

number of faculty members offering UROP projects

and numerous students participating in the program

to engage in academic research.

140 supervisors from different disciplines offered 294 projects

this year, and their support and contributions resulted in a steady

increase in student participation. During 2012-13, 353 students

from 18 departments enrolled in the program, an almost 20%

increase compared to the previous academic year. These

students not only perpetuated the growth of the program, but also

helped to broaden the research environment within the university

community.

2013 Mr. Armin and Mrs. Lillian Kitchell

Undergraduate Research Awards

23 students were nominated for the 2013 Mr. Armin

and Mrs. Lillian Kitchell Undergraduate Research

Awards by their UROP project advisors for their

outstanding research performance. Among them, nine were

shortlisted and participated in the final presentation to the UROP

Advisory Board. After careful selection, 1 Winner, 2 First Runner-Ups and 3

Second Runner-Ups were chosen and the award presentation ceremony was held

on April 23, 2013. All of the finalists were invited to present in a poster exhibition

during the UROP Weeks from April 15-26, 2013 at HKUST.

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2 Department of Chemistry

Modeling Protein-ligand Interactions Using Docking and Other Computational

Tools

Advisor: HUANG Xuhui / CHEM

Student: UNARTA Ilona Christy / CHEM

(UROP Course: UROP1100, Spring 2013)

Tropomyosin-related kinases type B (TrkB) is a protein that is important in increasing the long-term survival, differentiation and function of newborn neurons in the adult hippocampus. In this project, the importance of TrkB activation motivates a search for novel small molecules capable of activating TrkB. Hence, the docking and similarity searching of known agonists were performed. The docking of known small molecule agonists produced unsatisfactory results due to a lack of suitable structures in the TrkB extracellular domain. The similarity searching of five known TrkB agonists generated 10 molecules with high similarity and low lipophilicity and toxicity. However, further investigations may be necessary to optimize these molecules by considering other properties such as the number of Hydrogen bond acceptors and donors.

Advisor: HUANG Xuhui / CHEM Student: WANG Ying / CHEM

(UROP Courses: UROP1100, Fall 2012; UROP1200, Summer 2013)

Experimental studies have revealed the importance of a conserved, mobile domain of RMA Polymerase, the Trigger Loop (TL), in substrate recognition and rapid catalysis. Yet the small size and flexibility of TL restricts further experimental studies to obtain the detailed dynamics of its conformational changes. In this project, we conduct theoretical studies employing computational tools to elucidate the dynamics of TL motion and address the question from a different perspective. Based on the results obtained from molecular dynamics simulations, we obtain an initial pathway connecting two states using the Climber morphing algorithm. Selected conformations from the initial path are then used as seeds to perform path dependent Metadynamics simulations. We then test several collective variables in an effort to describe the conformational changes.

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3 Total Synthesis of Penicipyrone and Tenuipyrone Analogues for Biological

Activity Evaluation

Chemical Characterization of Organic Compounds in Atmospheric Particles

Advisor: TONG Rongbiao / CHEM Student: LIU Yuan / CHEM

Four different δ-hydroxyl-α,β-unsaturated ketones have been synthesized for cascade bicyclization reactions with four different 1,3-cyclodiketones, respectively, yielding analogues of the natural products tenuipyrone and penicipyrone. This cascade bicyclization reaction features intermolecular Michael addition and cyclo-ketalization. Generally, the cascade reaction produces high yields for five- and six-membered ring analogues ranging from 50% up to 90% yield, whereas the seven-membered ring analogues require a longer reaction time under harsher conditions to provide the cyclization products with relatively low yields.

Keywords – Cascade bicyclization; Intermolecular Michael addition; Cyclo-ketalization; Tenuipyrone; Penicipyrone

Advisor: YU Jianzhen / CHEM Student: HO Chi Lung / CHEM

(UROP Course: UROP1100, Fall 2012)

Air quality measurement is very important to society in the regulation of industrial pollution. PM2.5 is especially harmful to humans due to its small size, which can easily enter the human body. On March 8, 2012, the Environment Protection department began to announce PM2.5 data on its website, showing that people are growing increasingly concerned about the air quality. In this project, the literature related to the measurements of OC and EC, along with material from the Internet and the Environment Protection department, are summarized here as an introduction to this area of study.

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Advisor: YU Jianzhen / CHEM Student: YIN Shuhui / CHEM

HUmic-Like substances (HULISs) constitute a significant fraction of atmospheric aerosols, which are important in climate change and human health but complicated to study. The development of a suitable method for isolating HULISs has been widely discussed. Solvent efficiency and inert properties are difficult to guarantee simultaneously. In this project, comparison of different elution agents in terms of the above two topics was carried out. Solvent efficiency is determined by varying the amount used for elution and the reaction possibility was reflected in the fluorescence spectra. Methanol shows a relatively high efficiency that provides a recovery of 80% to 90%, and a larger amount produces a higher recovery. Acetonitrile retains a recovery of about 50%, regardless of the amount used. The presence of ammonia in the eluting solvents results in a slightly different spectrum compared with pure acetonitrile or methanol, which show similar spectra. This suggests that changes be made in the spectroscopic properties of the original sample.

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5 Division of Life Science

Characterization of Suppressor Mutations that Antagonize Body Size Control

Genetic Identification of Bone Morphogenetic Protein Signaling Pathway’s

Negative Regulator

Advisor: CHOW King Lau / LIFS Student: XIAO Wendi / BIOL

After conducting genetic screening last summer (“Genetic Identification of Negative Regulator of TGF-beta Signaling Pathway”), we identified several mutated C. elegans strains that display a suppressive effect on the sma-6 loss-of-function mutation.

Successive experiments were conducted – including outcrossing, length measurement and complementation tests – to try to locate the involved genes on specific chromosomes. Outcrossing and mapping were done throughout the characterization process, accompanied by the screening of progenies in each generation. However, most of the experiments are still in progress and some did not yield informative results. Therefore, we cannot yet map the precise location of the genes to define a clear molecular identity of the genes involved.

Advisor: CHOW King Lau / LIFS Student: LI Dongshunyi / BICH

(UROP Courses: UROP1100, Fall 2012; UROP1200, Spring 2013)

The bone morphogenetic protein (BMP) signaling pathway plays an essential role in regulating morphogenesis and orchestrating our body’s tissue architecture. Thanks to its conservation across distant species, it can be studied using C. elegans as a model. To characterize the two enhancer mutations of sma-6 LOF mutation, in this project a series of experiments are conducted for the screening of the related mutations affecting BMP signaling. Last semester progress was made in documenting the characteristics of a few mutations, but subsequent experiments are needed to further characterize the mutations and follow up with the mapping exercise to define the molecular identities of the affected genes.

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6 Screening for Genes Acting in the Hypodermis in a Time-specific Manner

Study of DNA Replication in Human Cells

Advisor: CHOW King Lau / LIFS Student: GU Bida / BIOL

(UROP Course: UROP1000, Summer 2013)

In this project, Q system (Potter et al., 2010) – a transcription-based binary gene expression system recently introduced into C. elegans (Wei et al., 2012) – is reconstituted and will be applied to C. elegans using lon-2 (Gumienny et al., 2007) gene promoter. The purpose is to investigate the role of this gene at different developmental stages using a time-specific gene activation approach. During the cloning process, various molecular manipulations are involved, and while we have made the desired plasmid construct, interesting phenomena and problems are encountered and discussed.

Advisor: LIANG Chun / LIFS Student: DAI Anna / BICH

Normal cell application in the lab is usually supported by DMEM with FBS. In this project, DMEM without FBS is used to starve HCT 116 cells (human colon carcinoma) and Hela cells (human cervix epitheloid carcinoma). After cell starvation, observing the FACs and western blot results individually and comparing the results between these two sets of samples revealed different effects.

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Advisor: LIANG Chun / LIFS Student: LI Yuqiong / BIOL

(UROP Courses: UROP1100, Fall 2012; UROP1200, Summer 2013)

The conserved Cdc14 (cell division cycle 14) protein has been found to inactivate cyclin-dependent kinase (CDK), which is considered to play a vital role in regulating the progression of the mammalian cell cycle. Cdc14 was first identified and further studied in budding yeast, yet the role of this protein remains largely unclear in mammalian cells. Unlike a single Cdc14 protein in yeast cells there are two homologues, Cdc14A and Cdc14B, in mammalian cells. Cdc14B phosphatase is the protein of interest in this project. The cell cycle and protein expression were studied in both 293T and MCF. Using fluorescence-activated cell sorting (FACS) and western blotting to investigate the cell cycle and protein expression, respectively, our result supports that Cdc14B was capable of dephosphorylating MCM2 protein and keeping the proliferating cells in G1/S phase.

Keywords – Cdc14B phosphatase, Cell cycle analysis, Western Blotting, 293T, MCF

Advisor: LIANG Chun / LIFS Student: ZHU Ronghui / BICH

The yeast cell division cycle protein 14 (Cdc14p) has been shown to play an important role in cell cycle and DNA replication. hCdc14B is a human homologue of Cdc14p whose functions in the human cell cycle remain largely unknown. In this project, we show that several budding yeast pre-RC proteins can interact with hCdc14B. Among them, some are also substrates of Cdc14p, which indicates some function similarities between hCdc14B and Cdc14p. At the cell cycle level, the expression level of hCdc14B in HCT116 cells fluctuates in a certain pattern throughout the cell cycle. We propose a possible explanation to interpret this result and investigate the link between hCdc14B and cancer by studying the deviation of the hCdc14B expression level between tumor cells and normal cells.

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8 Study of DNA replication-initiation proteins in budding yeast

Advisor: LIANG Chun / LIFS Student: ANDI PUTRA / BICH

Many criteria must be fulfilled before DNA replication, such as the presence and the right amount of proteins to begin the process. These proteins include the ORC complex, Cdc proteins and the MCM complex. The newly identified protein, Noc3p, shows its significance in the initiation of DNA replication in yeast cells (Zhang et al., 2002). This project shows how it serves as a link between ORC and other initiation proteins before DNA replication can take place. Its homolog in human cells, FAD24 protein or human Noc3 (hNoc3), has been studied extensively in our lab and it is believed that this protein homolog has a similar function in terms of the initiation of DNA replication.

Advisor: LIANG Chun / LIFS Student: KAN Chun Him / BICH

We examine the effects of common coenzymes NAD+ and NADP+, and those of common bivalent cations MgCl2, CaCl2 and ZnCl2 on the ADH and ACDH activity of budding yeast

(Strain W303-1A). ADH and ACDH work in a consecutive manner to oxidize ethanol to acetaldehyde and eventually to acetate. Either NADH or NADPH was produced in both steps. We determined the ACDH activity by adding acetaldehyde to the enzyme reaction medium and the combined activity of ADH and ACDH was discovered through ethanol addition. ADH activity was assumed to be far greater than that of ACDH, and to reach equilibrium in 10 minutes. Hence, the average activity of ADH can be approximated by computing the difference in the average activity between ethanol addition and acetaldehyde addition. After the experiment, we found that NAD+, MgCl2 and CaCl2 stimulated ADH while NADP+, MgCl2 and CaCl2 stimulated ACDH. However, ZnCl2 inhibited both ADH and ACDH.

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Advisor: LIANG Chun / LIFS Student: LI Dongshunyi / BICH

In the DNA replication of eukaryotic cells, the origin recognition complex (ORC) plays a significant role in initiation. The change in its activity has a profound effect on the initiation process. Nevertheless, the detailed process remains unknown. The experiment data in our lab indicate that ORC forms dimers during the G1 to M transition in the G1 phase. We further hypothesize that its dimerization depends on Noc3p. We design a chromatin binding assay and a coimmunoprecipitations assay (co-IP) to test our hypothesis. Before conducting the experiments, two preliminary tests are conducted: the depletion efficiency checking of

Noc3ts::Ura and the expression checking of transformed mutant cells. The results suggest

that the cell cycle of Noc3ts::Ura is likely to be disrupted at 37°C. The expression of plasmids, however, cannot be detected.

Advisor: LIANG Chun / LIFS Student: LIU Siyu / BIOL

(UROP Courses: UROP1100, Spring 2013)

Molecular cloning is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and direct their replication within host organisms (Watson, 2007). During my work and study experiences in the biochemistry lab this semester, I gradually gained a rough understanding of the steps involved in and principles behind molecular cloning.

In this project, we focus on the study and identification of paired interactions between Rice black-streaked virus 2 segments in E. coli, which requires some molecular biology techniques to discover protein–protein interactions and protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The protein used in this experiment is one strain of plant virus protein. By combining the target gene into the plasmid and then using the molecular cloning method to clone this gene, we can screen the clones with desired DNA inserts and biological properties to study their paired interactions. This semester, we are largely concerned with molecular cloning preparation.

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10 Water Quality Survey for Hong Kong's Marine Fish Farming Zones

Advisor: LIANG Chun / LIFS Student: MA Yujia / BIOL

A number of genes were previously found to be related to stomach cancer and DNA replication initiation functions. In this project, reverse transcription and real-time PCR were applied to evaluate the extent of interest genes’ expression. For analysis, Relative Quantity (2^(-delta Ct)) was the main index. The higher the RQ value, the higher level of gene expression.

Keywords – Gene expression, DNA replication initiation, Reverse transcription, Real-time PCR

Advisor: LIU Hongbin / LIFS Co-advisor: LAU Wing Keung / LIFS Student: LAO Hiu Yin / BICH

(UROP Course: UROP1000, Summer 2013) NG Cheuk Hei / BICH

(UROP Course: UROP1000, Summer 2013) YEUNG So Shan / BICH

In this project, we conducted a survey (June 2013) to monitor the water quality of the marine fish farming zones in Hong Kong. Water samples at different depths were collected from each of the marine fish farming zones once or twice a month, as designated by the Agriculture, Fisheries and Conservation Department (AFCD) in Hong Kong. Different hydrographic, water chemistry and biological parameters were measured during or after the sample collection. The level of suspended solids and chlorophyll a were covered as part of the indicator determining water quality.

Advisor: LIU Hongbin / LIFS Co-advisor: LAU Wing Keung / LIFS Student: XIE Siwei / BICH

Water quality is essential for the maintenance of aquaculture in Hong Kong. A water quality survey is conducted regularly to monitor the marine condition in 26 marine fish zones and 5 offshore stations designated by the Agriculture, Fisheries and Conservation Department (AFCD). In this project, the amount of chlorophyll a, a widely used parameter that indicates the level of algal biomass, was measured and discussed. During the sample collection time, it was observed that there were phytoplankton blooms in Ap Chau, Sha Tau Kok (northeastern Hong Kong), Tiu Cham Wan and Tai Tau Chau (eastern Hong Kong). The reasons for these phytoplankton blooms were discussed.

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11 An Exploration of Nuclear Dynamics in Cells and the Syncytia of Developing

Zebrafish Embryos

Visualization of Macromolecule Dynamics within the Contractile Band during

the Cytokinesis of Embryonic Cells

Advisor: MILLER Andrew L / LIFS Co-advisor: HO Sarah E / LIFS Student: XU Kaichun / BICH

The intercellular calcium signal related to the distinguishable Ca2+ signaling period between ~17.5-19.5 hours post fertilization (hpf), which involves both nucleusand cytoplasmic Ca2+ waves, plays an important role in the first spontaneous contraction in the trunk muscle, which occurs at ~17 hpf during muscle development. Inositol-trisphosphate receptors (IP3R) have

been demonstrated to play a critical role in this Ca2+ signaling period. In this project,we illustrate the localization of three analogs of IP3R in the slow muscle cells, including the

nuclear location, their localization and their localization relationship with slow muscle cell myosin heavy chains.

Advisor: MILLER Andrew L / LIFS Co-advisor: HO Sarah E / LIFS Student: CHEN Yiyun / BICH

(UROP Courses: UROP1100, Spring 2013; UROP1200, Summer 2013)

The process of cytokinesis in a zebrafish embryo is regulated by a series of calcium transients regulated by a variety of calcium channels. The STIM1 protein and Ca2+ channel proteins Orai and TRPC are essential in the store-operated calcium entry (SOCE) pathway, which is responsible for replenishing the calcium store in endoplasmic reticulum (ER). 2-Aminoethoxydiphenyl borate (2-APB) is added to inhibit the Orai1 and TRPC channels and abolish SOCE function, resulting in incomplete cytokinesis. In this project, we show that SOCE may be important in regulating the Ca2+ signals during cytokinesis. The aequorin-Ca2+ imaging result indicates that the inhibition of SOCE lowers the amount of Ca2+ released and restrains the furrow-deepening signal from reaching the bottom of the blastodisc, causing incomplete cytokinesis.

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12 Characterization of Novel Cell Cycle Regulators in Cancer Cells

In-depth Characterization of Novel Cell Cycle Regulators in Cancer Cells

Advisor: MILLER Andrew L / LIFS Co-advisor: HO Sarah E / LIFS Student: YU Chung Yan / MBMS

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a novel calcium-releasing second messenger, with its own novel receptor – the two-pore channels (TPCs). NAADP differs from its counterparts inositol 1,4,5-triphosphate (IP3) and cyclic ADP-ribose (cADPR) by using

acidic calcium stores rather than calcium from the endoplasmic reticulum. Calcium transients are known to traverse zebrafish (Danio rerio) eggs during activation, and such transients rely on internal calcium stores, presenting a possible link between NAADP and these calcium transients. However, NAADP is unable to trigger the elevation of the egg chorion, a key-step in egg activation, at its typical efficacious nano-molar concentrations.

Advisor: POON Randy Y C / LIFS Student: CAI Xi / BICH

Cell cycle control must be temporally and spatially precise to ensure the accurate production of two daughter cells, hence its importance. In this project, I identify the candidates of mitotic regulators by applying a down-regulation strategy to investigate the effect of genes on mitosis. The effects are then captured by the difference of mitotic length between the control and the experimental group. To better quantify the change in mitotic length, several anti-microtubule drugs are added to cells to extend the mitosis period.

Advisor: POON Randy Y C / LIFS Student: CAI Xi / BICH

Cell cycle control must be temporally and spatially precise to ensure the accurate production of two daughter cells, hence its importance. In this project, I identify the candidates of mitotic regulators by applying a down-regulation strategy to investigate the effect of genes on mitosis. The effects are then captured by the difference in mitotic length between the control and the experimental group. To better quantify the change in mitotic length, several anti-microtubule drugs are added to the cells to extend the mitosis period. Among the ten genes investigated, four were identified as candidates, which were then verified by different methods and with different anti-mitotic drugs.

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13 Investigating Microtubule Regulation during Cell Proliferation, Migration and

Morphogenesis

Bioactive Compounds from Marine Bacteria Associated with Tunicates from

the Red Sea

Advisor: QI Robert Zhong / LIFS Student: HAU Kwan Tang / BICH

Microtubules play an important role in organizing the cytoplasm of eukaryotic cells. Recently, scientists have suggested that the nucleation of new microtubules requires γ-tubulin, an essential protein that assembles into multi-subunit complexes such as human γ-tubulin ring complexes (γTuRCs). This project employs SDS-page and Western Blot testing to detect the microtubule-associated proteins (Nedd1) (C-Term 344-667WT,C-Term 344-667H615A,C-Term 344-667 H615F) expressed through molecular cloning as a way of investigating the association between tubulin and Nedd1 after changing one amino acid in the amino acid sequence. The mutations of 615 in the C-term 344-667 have no significant effect on the formation of Nedd1 because the intensity of the Western Blot bands of the two mutants are both similar to the wild type.

Advisor: QIAN Peiyuan / LIFS Co-advisor: XU Ying / LIFS Student: HUANG Yuan / SSCI

Bacteria derived from organisms in the Red Sea have been proven to have significant value in biomedical and ecological applications. For example, natural products from marine bacteria show greater advantage over other antifouling agents based on tributyltin (TBT) and copper in terms of toxicity. In this project, various microbiological and chemical methods are applied to culture and purify a bacterium named Slalinisphaera and extract compounds from the fermentation product. By conducting antifouling and antibacterial bioassays in addition to determining their structures, we examine whether these compounds have novel bioactivity and probe the structure-activity relationship.

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14 Hair Testing in Drug Abusers

Advisor: TSIM Karl W K / LIFS Student: CHAN Chi Hin / SSCI

One way to reveal a history of synthetic cannabis consumption is to test hair using HPLC-MS/MS. In this project, this synthetic cannabinoid, JWH-018, is detected after 18 hours incubation with 4 hours sonication to extract from a sample immersed in 100% methanol. Drug separation, identification and quantification are achieved by HPLC-MS/MS. The linear regression analysis is calibrated by internal standard THC-OH-D3 with R2 equaling 0.998. The limit of detection (LOD) and limit of quantification (LOQ) for JWH-018 are both 0.05 pg/μL. The calibration curve ranges from LOQ to 500 pg/μL. The validation parameter, including linearity, sensitivity, precision and accuracy, are evaluated.

Keywords – JWH-018, HPLC-MS/MS, synthetic cannabis, validation

Advisor: TSIM Karl W K / LIFS Student: LAU Chun Yin Oliver / BICH

Methaqualone, a depressant that can affect the central nervous system, is sometimes abused with the abuser subsequently developing addiction, anxiety and depression. In this project, a quantification method was developed using liquid chromatography/tandem mass spectrometry (HPLC/MS-MS) for the determination of methaqualone in human hair. Hair samples were decontaminated, dried and cut. The hair was extracted together with Diazepam-D5 (internal standard) and the analytes were chromatographed and detected by (HPLC/MS-MS) using electrospray ionization. The linearity, repeatability, extraction efficiency, process efficiency and matrix effect were determined to be in accordance with regulations for the validation of the method.

Advisor: TSIM Karl W K / LIFS

Student: LEUNG Wing Yan Yonna / BIOL (UROP Course: UROP1100, Fall 2012)

In this project, the first stage for developing a method of detecting 1-benzylpiperzaine (BZP) and 3-trifluoroethylphenylpiperazine (TFMPP) in hair was launched. The precursor ions for BZP, TFMPP and their respective internal standards, BZP-D7 and TFMPP-D4, were determined, respectively. The MS condition was optimized for the detection of BZP and TFMPP. BZP and TFMPP were extracted with 25% methanol, 25% acetonitrile and 50% ammonium formate. The linear regression analysis was calibrated by deuterated internal standards with an R2 of 0.9986 for BZP and 0.9966 for TFMPP. The limit of detection (LOD) and the limit of quantification (LOQ) for BZP and TFMPP were both 10 pg/uL. Both standard curves were linear from the value of LOQ up to 1000 pg/uL. The matrix effect and extraction efficiency were also determined.

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Advisor: TSIM Karl W K / LIFS Student: LO Wing Hei / SSCI

In this project, a prevalent hair testing method for general psychoactive drugs using high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) underwent the optimization of its extraction method and the condition of its machines to develop a detection system with suitable operating conditions for detecting a synthetic cannabinoid, HU-210, in human hair. The drugs deposited were extracted by incubation, followed by sonication. With the drug identification and quantification by tandem mass spectrometer, the chromatographic separation was achieved in 12 minutes. An internal standard was used in the calibration of linear regression analysis with a correlation coefficient (R2) of 0.994. The limit of detection (LOD) and the limit of quantification (LOQ) for HU-210 were both 5 pg/μL of the hair extract. The linear range was from the value of LOQ to 500 pg/μL of the hair extract. Validation parameters such as linearity, LOD and LOQ, precision and accuracy were determined. In conclusion, an effective detection method was investigated with the use of HPLC-MS/MS to achieve a more precise result.

Keywords – HU-210 Drug abuse hair analysis LCMS⋅ Method development synthetic cannabinoids THC

Advisor: TSIM Karl W K / LIFS Student: ZHANG Minglu / BIOL

In this project, a quantitative HPLC-Chip-MS/MS method was developed for simultaneously measuring the presence of nine commonly abused drugs in the Benzodiazepine family. Method validation was applied to determine the method’s linearity and sensitivity. Linearity is the relationship between the concentration of the analyte in the sample and the corresponding response. Sensitivity is validated by finding the limit of detection (LOD) and limit of quantification (LOQ) of the analyte. As a result, the linear regression analysis was calibrated by deuterated internal standards with an R2 of 0.99. The limit of detection (LOD) and the limit of quantification (LOQ) were 12.5 pg/mg and 125 pg/mg, respectively.

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16 G Proteins and their Regulators in Cancer Biology

Advisor: WONG Yung Hou / LIFS Student: CHEN Yiyun / BICH

The fragile histidine triad (FHIT) gene is a tumor suppressor gene located at region 3p14.2 on the short arm of human chromosome 3, encompassing the most active common fragile site FRA3B locus. The Fhit protein can be phosphorylated by tyrosine-protein kinase Src, which is involved in the G protein signaling pathway. Among different Gα subunits in the G protein family, activated Gαq shows a high affinity for Fhit binding and increases its expression, and

thus may enhance its tumor suppressing activity. In this project, Fhit degradation was not involved in the active Gαq-induced FHIT expression. In HEK293 cells stably expressing Fhit,

Gαq activation inhibited cell growth. We also found that, in the presence of Fhit, activating Gαq

increased cell aggregation in lung cancer cell line H1299 and kidney epithelial cell HEK293.

Advisor: WONG Yung Hou / LIFS Student: CHENG Ka Fai / BICH

RGS proteins are regarded as regulators of G protein signaling that function as GTPase-activating proteins, which catalyst the hydrolysis of the GTP of the activated Gα subunit to deactivate the G protein-coupled receptors’ (GPCRs’) mediated signal cascade. However, studies have shown that RGS proteins have other functions besides their role in G protein signaling, even playing multiple roles in the psychological pathways of cells. RGS20 is a member of the RGS RZ/A subfamily shown to enhance the cell aggregation in NIH3T3 and the cell survival ability in MDA-MB-231 when RGS 20 are overexpressed in the cell. This enhanced cell aggregation ability implies that RGS19 may play a role in cancer metastasis. This project attempts to discover the regulatory rolls of these RGS proteins in various stages of tumor development.

Advisor: WONG Yung Hou / LIFS Student: LEUNG Yuen Mei / BICH

The roles of the regulators of G protein signaling (RGS proteins) in human cancer cells are of emerging interest, as they have been implicated in cell proliferation and metastasis in several mammalian cell lines. Thus, in this project, the effects of transiently and stably transfect RGS19 and RGS20 in human breast adenocarcinoma cells (MDA-MB-231 cells) are characterized. In MTT assays, the RGS19/MDA stable cell line has demonstrated a higher proliferation rate than the RGS20/MDA cell line and the parental MDA cells. In MDA cells stably expressing RGS19 and RGS20, there is an upregulation in NM23-H1 that is one of the isoforms of tumor metastasis suppressor NM23. Elevated levels of NM23-H1 represent the possibility of metastasis in cancer cells due to the presence of RGS19 and RGS20 in the stable cell lines. In addition, there is a downregulation in the expression of ERK after serum starvation in transiently expressed RGS19 and RGS20. Akt signaling is also suppressed after serum starvation.

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Advisor: WONG Yung Hou / LIFS Student: LIU Jijun / BICH

RGS19 is a regulator protein of G-protein signaling and its overexpression enhances cell proliferation in several types of mammalian cells. This project shows that the overexpression of RGS19 can promote the cell growth of MDA human breast cancer cells. The enhanced cell growth may be mediated through the regulation of the AKT pathway and is independent from the activation of the ERK signaling pathway. Moreover, the stable expression of RGS19 upregulates the expression of metastasis suppressor Nm23 in MDA cells. The upregulation of Nm23, however, was not observed in the transiently transfected MDA/RGS19 cells. Thus, these results indicate that the stable expression of RGS19 may be correlated with cancer cell metastasis.

Advisor: WONG Yung Hou / LIFS Student: TANG Lok Kan / BICH

(UROP Course: UROP1100, Summer 2013) TSANG Oi Ling / BICH

(UROP Course: UROP1100, Summer 2013) YU Ho Yan / BIOL

G protein-coupled receptors are essential transmembrance receptors for converting extracellular stimuli into intracellular signals. They are also critical in stimulating second messenger generating systems to further regulate some biological functions. In this project, we examined the signaling integration of G protein-coupled receptors by stimulating receptors with different coupling specificities using HeLa human cervix epithelial cells. We found that the simultaneous stimulation of Gi- and Gq-coupled receptors led to synergistic

ERK activation and iL-8 production, but signaling from Gs seemed to inhibit the synergism

from Gi- and Gq-coupled receptors’ signaling. The simultaneous stimulation of Gi- and Gq

-coupled receptors was also found to have a synergistic relation in terms of intracellular Ca2+ elevation, whereas signaling from Gs-coupled receptors intensified its corresponding activity.

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18 Molecular Study of Genes in Brain Functions and Diseases

Advisor: WONG Yung Hou / LIFS

Student: YU Xiaoying / BICH

(UROP Courses: UROP1100, Fall 2012;

UROP1200, Spring 2013)

Previous studies have shown that a diadenosine triphosphate (Ap3A) hydrolase FHIT may act

as a tumor suppressor. Heterotrimeric guanine nucleotide binding proteins (G proteins) play an important role in signaling pathways. A process called Epithelial–mesenchymal transition (EMT), in which epithelial cells lose their cell polarity and cell-cell adhesion, gain migratory and invasive properties and at last become mesenchymal cells, may influence invasion, the metastasis of carcinoma cells and the generation of life-threatening manifestations of cancer progression. In this project, the effects of FHIT and Gα16 on the

localization of the adhesion proteins in H1299 stable cells and HEK293 stable cells, and the effects of FHIT and Gαq on the localization of the adhesion proteins in 293 stable cells were

studied.

Advisor: XIA Jun / LIFS Student: LIANG Siqi / BICH

AMPA receptor synaptic trafficking is critical to the molecular mechanism of synaptic plasticity, and two proteins – PICK1 (a protein that interacts with C kinase 1) and ICA69 (islet cell autoantigen 69 kDa) – have been found to be involved. The BAR domain complex between PICK1 and ICA69 regulates intracellular AMPAR trafficking. To prepare for a GST pull-down assay to determine the interacting domains, GST constructs were obtained and induced to express in E.coli BL21 by IPTG. An optimum concentration of IPTG was tested and applied to purify the corresponding GST-tagged proteins. A vector, pEGFP-C3, was also modified and linked with a neuroselective promoter to further study the proteins in neurons.

Advisor: XIA Jun / LIFS

Student: WANG Yicheng / BICH

(UROP Courses: UROP1100, Spring 2013; UROP1200, Summer 2013)

The purification of protein, which can then be used as a specific antigen in immunoprecipitation (IP) to purify antibodies, is an important procedure for studying the interested protein. In this project, we use affinity chromatography to purify WW and C-Terminal domains (protein domains of conserved composition that exist in many different kinds of proteins). These purified protein domains are then used to generate antibodies in lab rabbits and eventually purify these antibodies by IP.

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19 Human Complex Disease Genomics and Bioinformatics

Advisor: XUE Hong / LIFS Co-advisor: LIANG Chun / LIFS Student: PANG Chau Yung / BIOL

Tryptophan is an essential amino acid for bacteria growth. Under restrictions to grow in different tryptophan analog mediums, the mutants of Bacillus subtilis can acquire and survive under altered forms of tryptophan, such as 4-fluorotryptophan (4FT), 5-fluorotryptophan (5FT) and 6-fluorotryptophan (6FT). There are 271 essential genes out of 4100 genes indispensable for growth, in which 190 of the genes involved in these tryptophan analogs use mutations and most of them are caused by single nucleotide mutations. In this project, they are examined by purifying the genomic DNA of mutant strains of bacteria, amplifying the target regions of DNA using PCR and comparing the mutant nucleotide between the mutant strains and the wild type strain using DNA sequencing.

Advisor: XUE Hong / LIFS Co-advisor: LIANG Chun / LIFS Student: SUN Xing / BICH

Studies of disease-linked single nucleotide polymorphisms (SNPs) have been yielding valuable knowledge on various diseases. In this project, 18 SNPs in the GABRB2 gene were genotyped on samples from schizophrenia patients by direct sequencing. The admission of novel amino acid analogues into the genetically encoded amino acid ensemble was also studied. B. subtilis Trp-auxotroph QB928 was previously mutated to enable the encoding of 4-fluoroTryptophan (4FT), 5-4-fluoroTryptophan (5FT) and 6-4-fluoroTryptophan (6FT) for indefinite growth. To further investigate the mutations at the gene level, these mutants are cultivated from the stock and their genomes are extracted for sequencing. The genomic DNA of QB928 strain LC33 is then sent in for sequencing.

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20 Receptor-based Drug Development from Chinese Herbal Medicine

Advisor: XUE Hong / LIFS Student: QI Yi / BICH

In previous studies, Calmlin, a drug formula developed from Chinese herbal medicine, and dl-THP, an extractant from one of the four components in Calmlin, were shown to have anti-anxiety properties without sedation and other side effects. In this project, the two drugs’ other potential functions were tested. Dl-THP was tested via a tail suspension test of mice to investigate its anti-depressant properties. Calmlin was tested for its effect on the D-galactose-induced aging model. An MDA test was done on the brain homogenates of mice that had taken D-galactose and Calmlin to examine dl-THP’s relief on MDA level decrease induced by D-galactose. The results showed that dl-THP had an anti-depressant effect on mice and the relieving effect of Calmlin on spatial memory loss and brain MDA level decrease induced by D-galactose was proven by Y-maze spontaneous alternation and MDA tests. The test on L-THP showed no observable toxic effect on mice in one week, despite reports that dl-L-THP caused mice to swell.

Advisor: XUE Hong / LIFS Student: SHING Wai Ho / BICH

Chinese herbal medicine has been used by Chinese for more than 5000 years to cure diseases. There may be some useful substances present in the herbs that affect our bodies’ functions. In this project, we focused on Scutellaria baicalensis (huang qin), which contains wogonin, a flavonoid-like compound with a strong anxiolytic effect. Recent studies have also found that wogonin may have anti-tumor and anti-inflammatory characteristics. An economical method for extracting this substance with high yield and purity will be beneficial. Various methods were adopted to isolate wogonin for the Scutellaria baicalensis extract. The yield and purity of wogonin were monitored by performing HPLC.

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21 Department of Mathematics

Lunar Study Based on Data Obtained by the Chang'E Spacecraft

Advisor: CHAN Kwing Lam / MATH Co-advisor: CHENG Siu Wing / CSE

Student: CHUNG Chak Pong / MATH-GM (UROP Course: UROP1100, Fall 2012) QIU Shao / MAEC

The dataset we use in this project is based on previous work, specifically the lunar craters Einstein and Tsiokovsky with binary classification. It describes what we have tried, the useful tools we have developed and directions for future work. Our work this semester can be divided into three phases. Phase one we study the mechanisms of the support vector machine and related mathematical background. Phase two we study the typical use and skill of the SVM library (a programming library called LIBSVM). With our understanding of SVM in this lunar study, our focus shifts to thinking about how to define the characteristics of lunar craters with mathematical expression so that they can be transformed into useful data input to be tested by SVM. Preliminary algorithms are proposed at the end, directing future work.

Advisor: CHAN Kwing Lam / MATH Co-advisor: CHENG Siu Wing / CSE

Student: CHUNG Chak Pong / MATH-GM

Craters are typical geographical surface features of the Moon. Extensive studies of the Moon’s surface keep drawing attention with increasingly accurate information from lunar space missions. Many papers have been published that detect lunar craters with images, e.g. the Segmentation-based approach by Blue and Stepinski (2007) discusses the pros and cons of the Hough Transform and Edge-based methods. Morpholoogical construction using an ellipse can be found in the work of Kim el al (2005). and feature extraction combined with the support vector machine (SVM) approach is discussed by Vinogradova et al (2002). However, the crater detection problem is not completely sloved, as every approach has its limitations. For example, image-based techniques are limited to certain sunlight conditions and angles from which the images are taken because they produce different gray-scale images in the same place. The SVM approach is not easy because the feature extraction from which SVM can learn the pattern of the crater is subjective and hard to conduct. In view of these difficulties, a method that is less restrictive on noise in the image and assumptions of the craters’ geographical features is needed for wider application.

In this project, our target is to find the locations of craters and related information about their landforms using the digital elevation model (DEM) data and gray scale images provided by the Chinese Chang’E-1 and Chang’E-2 spacecraft. We have tested three different methods to search for craters with DEM data and the gray scale crater images.

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22 Space Orbit Design

Advisor: CHAN Kwing Lam / MATH Co-advisor: WONG Michael K Y / PHYS Student: CHEUNG Yat Fei / PHYS

(UROP Course: UROP1000, Summer 2013) NG Tsz Yu / PHYS

(UROP Course: UROP1000, Summer 2013) NGAI Cheuk Yu / APHYS-ST

Based on the mission to Uranus proposed by the Department of Mathematics and the Centre for Space Science Research, the further evaluation and estimation of that mission is the focus of this project. To ensure that the spacecraft completes the different missions – such as measurements of atmospheric composition, retrograde winds and the off-centered magnetic axis of Uranus – we concentrate on communication and the spacecraft’s power and propulsion system. Instead of the building systems, the scientific instruments and spacecraft components under the constraints of mass, power and volume are another focus of this project.

Advisor: CHAN Kwing Lam / MATH Co-advisor: WONG Michael K Y / PHYS Student: CHU Kin Chiu / PHYS-PM

HEIMONEN Hermanni Juuso Elias / PHYS-PM (UROP Course: UROP1100, Fall 2012)

LEUNG Kai Yin / PHYS-PM

This project began with an analysis of the different aspects of the mission, such as the performance index and the mass penalty at the Jupiter fly-bys. The first task was to devise a method for determining which face of the “football” the spacecraft is visiting at each fly-by to determine the performance index for potential trajectories. This is complicated by the fact that some of the faces are hexagonal while other are pentagonal. Three solutions to this problem have been found based on different methodologies. Although the algorithm to solve the face location problem can be easily applied to the whole truncated icosahedron thanks to its high symmetry, the bugs that result from partial misallocation may occur if the cache data are not correct. The debugging process can be difficult and time consuming if the problem is complicated and the cache data are huge. Therefore, instead of directly checking every part of the code and cache data, the bugs are located with testing data, which are randomly generated, and a 3D graph with proper markings. The random generator for the test data eliminates the chance of neglecting bugs due to systematic selection by humans. Proper marking of the data not only allows problems to be located, but also indicates the reason for them.

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23 Wind Bands on the Giant Planets

Advisor: CHAN Kwing Lam / MATH Co-advisor: WONG Michael K Y / PHYS

Student: HEIMONEN Hermanni Juuso Elias / PHYS-PM (UROP Course: UROP1200, Spring 2013)

We study the behavior of the solutions to low-thrust two-point boundary value problems with different boundary conditions. The limits of the possible launch and arrival velocities are first studied in a simplified two-dimensional transfer analogous to the Lambert problem from Earth to Mars, using large grid searches over possible velocities with a local optimizer. The solutions are then generalized to a three-dimensional problem and the low-thrust solutions are compared with ballistic solutions to the Lambert problem. In the low-thrust boundary value problem we find that the launch velocities form an elliptic region around the ballistic solution, in which the size of the region depends linearly on the thrust of the spacecraft. This also implies that variation in the launch velocity is not uniform in all directions. Finally, the same method is applied to a hyperbolic fly-by at Callisto that could be used to design capture trajectories at Jupiter. This indicates that the method is applicable to a range of mission analysis situations. The results help us understand the nature of the boundary value problems, so that we can potentially improve the techniques in designing low-thrust trajectories.

Advisor: CHAN Kwing Lam / MATH Student: LI Cheung Shun / PHYS

(UROP Course: UROP1000, Summer 2013) YANG Hannan / PHYS

(UROP Course: UROP1000, Summer 2013) YUEN Wai Yin / PHYS-PP

The four planets in the solar system beyond Mars are classified as ‘giant’ planets: Jupiter, Saturn, Neptune and Uranus. They have many similarities and a few differences. First, they are all massive and emit more energy than they get from the Sun. They all have thick gaseous atmospheres. Most importantly, they all have very strong east-west winds and each has a large, long-lived spot that, together, are the focus of this project. With these similarities, one would expect these four planets to possess similar properties. However, the inner two (Jupiter and Saturn) have equatorial winds that blow in the same direction as planetary rotation while the outer two (Neptune and Uranus) have winds that blow in the opposite direction of planetary rotation. In this project, we aim to find out the cause of these differences and similarities using computer programming to analyze numerical data.

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24 Statistical Analysis in Portfolio Construction

Scientific Computing and Flow Visualization

Advisor: CHEN Kani / MATH Student: HU Kun / ECOF

(UROP Courses: UROP1100, Fall 2012; UROP1200, Spring 2013) WANG Qinyu / MATH-PMA

We empirically analyze the use of the penalized least squares method in vast portfolio construction. In particular, the performance of ordinary least squares, ridge (L-2 norm penalty) and LAR-LASSO (L-1 norm penalty) with different gross exposure constraints, the vanilla Markowitz method, the 1/N naïve strategy and no-short sell portfolios are compared. The results indicate that the LASSO method does not significantly dominate the no-short sell portfolios, but produces sparse solutions and offers a theoretical basis for the constraint on gross exposure level.

Keywords— portfolio theory; least square; LASSO; gross exposure constraint; short-sale constraint

Advisor: FUNG Jimmy C H / MATH Student: LAI Yiu Ting / MATH-AM

(UROP Course: UROP1000, Summer 2013) WONG Tsz Fung / MATH-AM

In this project, we visualize planetary boundary flows by means of numerically tracking continuously released inert and weightless particles that advect across the lowest few kilometers of the atmosphere. This is a derivative development based on a system of Fortran 77 codes with the demonstrable skills to track tens of thousands of particles traversing a numerical wind field generated by the mesoscale meteorological model MM5. The current phase of the project entails:

code refactoring, which includes porting to the MATLAB development environment; adaptation to the WRF mesoscale meteorological model results;

memory management improvements intended to enable tracking of millions of particles; and development of novel visualization techniques that may draw upon massively parallel computing and rendering hardware such as GPU engines.

This interim report encapsulates the challenges and accomplishments pertaining to code refactoring and adaptation to the WRF mesoscale meteorological model results.

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25 Asymptotic Methods for High Frequency Wave Phenomena

𝜓 𝑦; 𝑡 + 𝜀 = 𝜓 𝑥; 𝑡 2𝜋𝑖ħ𝜀𝑒

𝑖 𝑥−𝑦 2

2ħ𝜀 _𝑒𝑖𝜀𝑉 𝑥 ħ _𝑑𝑥.

Advisor: LEUNG Shing Yu / MATH Student: AU Ching Yung / MATH-AM

We consider the Schrödinger equation for a particle with unit mass iħ_∂t∂ − H ψ ≡ iħψt− V x ψ +ħ

2

2 ∆ψ = 0, x ∈ R

d_{, t > 0,}

for some initial condition. The goal of the project is to develop a numerical method to efficiently evaluate the integral

Because the above integral equation does not have an analytical solution, we can only solve it numerically. The first part of the project is to use the simplest method to evaluate the integral, i.e. trapezoidal rule. However, this method is not practically useful due to low efficiency. Therefore, we need to seek a faster method. Due to the special property of the integrand, we propose a numerical algorithm in MATLAB based on the Fast Fourier Transform (FFT).

Advisor: LEUNG Shing Yu / MATH Student: LAI Tsun Tak / MATH-PM

(UROP Course: UROP1100, Summer 2013) WONG Lung Fai / MATH

The objectives of this project are to show the methods developed and the corresponding codes, and discuss how to promote the ideas to a higher dimension. We examine methods of finding the normal vectors of finite points of a curve to approximate the wavefront. The waves tested are given to be smooth in two-dimensional space. The details of generalizing the method to three-dimensional space are also discussed.

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26 Efficient Numerical Methods for Dynamic Interface

Advisor: LEUNG Shing Yu / MATH Student: LAI Yiu Ting / MATH

(UROP Course: UROP1100, Fall 2012) YAM Yau Chuen / MATH-MP

We investigate a new method for simulating the propagation of high frequency waves by computer. Relying on calculating the r-offset of the propagated wave, existing plotting methods have two main limitations. After the wave propagates for some time, the curve disperses. There are also some sharp points on the curve where the direction of propagation cannot be determined. We try to solve these problems using a new method – transforming the curve on the plane to a three-dimensional curve and letting it propagate in space while projecting the propagated “tube” on the plane. Then, the required propagated wave is the boundaries of the shadow. The advantages and limitations of this method are discussed.

Advisor: LEUNG Shing Yu / MATH Student: WANG Tianyu / MATH-AM

(UROP Course: UROP1100, Spring 2013) WU Yueshen / CHEM

We develop numerical approaches to resolve the propagation of a Gaussian wave packet and to model diffraction patterns in inhomogeneous media. By using the newly developed lower-order Taylor-expansion based convolution methods in the position space, we model in sequence several different scenarios in one- and two-dimensional cases to obtain the optimal conditions for simulation. We then simulate the diffraction pattern with square-like potentials in a two-dimensional case.

Advisor: LEUNG Shing Yu / MATH Student: XIE Zhaoming / CPEG

The goal of this project is to find out how the level set method can be used to compute the line integral of a circle (namely the arc length) inside a square bounded by [0,1] x [0,1] numerically, and how good the approximation can be.

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27 Visualization of Dynamical Systems using Lyapunov Exponent

Financial Engineering Problems in Trading and Investment

Advisor: LEUNG Shing Yu / MATH Student: HE Xingyu / SSCI

(UROP Course: UROP1100, Summer 2013) YANG Kaiqi / SSCI

We study the pendulum motion with driving force and damping coherent. We assume the initial angle is small enough to make the approximation valid. After the approximation, this differential equation becomes a linear system with an analytic solution. If we do not use the approximation, the system is no longer linear and has no analytic solution. We obtain the trajectories and the FTLE by using a fixed step-length, fourth-order, Runge-Kutta integration scheme via MATLAB.

Advisor: PENG Xianhua / MATH Student: DAI Chaoxing / MAEC

(UROP Course: UROP1100, Fall 2012) WANG Mengxue / MAEC

(UROP Course: UROP1100, Fall 2012) WANG Shuanglong / PHYS-PM (UROP Course: UROP1100, Fall 2012)

We review the CST model on stochastic and its assumptions, parameter estimations and mathematical structures are discussed. Two programs aimed at parameter estimation and hypothesis testing are constructed and their detailed inter and intra structures are presented. We also display the sample output of the two programs and the results are discussed, respectively, along with our ideas about future extensions.

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28 Department of Physics

Quantum Optics and Super-Resolution Microscopy

Characterizing Single-molecule Electronic Properties using Low-temperature

Scanning Tunneling Microscopy

Advisor: DU Shengwang / PHYS Student: SHU Chi / SSCI

Single photons play an important role in modern physics, with their quantum properties allowing them to behave quite differently from classical electromagnetic waves. A single photon can be easily obtained by detecting one photon in an entangled photon pair. Previous work has shown that entangled photons can be generated in a cold atomic assembly, but it is hard to achieve a high-quality entangled photon pair from a hot atomic vapor cell. Our work mainly involves obtaining a good quality entangled photon pair from a four-wave mixing process in an Rb87 cell.

Advisor: LIN Nian / PHYS

Student: CHEN Shen / APHYS-ST

The purpose of this project is to simulate the behavior of Br atoms on a Cu surface using the Metropolis Monte Carlo algorithm developed by Nicholas Metropolis et al. in 1953. In the experiment, when Br atoms were slowly cooled down on a Cu surface to a low temperature (~5K), they formed some steady islands whose characteristics were also affected by the different coverage of the atoms on the Cu surface. The “Br atoms” in the simulation conducted in this project also formed similar islands. The relationship between the forces (bonding and repulsion) in this process were finally decided by considering the differences in the size distribution, shape distribution and the pair correlation function of the simulation and experimental results.

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29 Monte Carlo Simulation of Two-dimensional Supramolecular Assembly

Advisor: LIN Nian / PHYS Student: DU Zhiqian / PHYS-PM

Amorphous graphene is considered to be a two-dimensional Anderson insulator. The analogue of artificial amorphous graphene has been realized by depositing organic molecules on a metal surface placed under grid mode scanning tunneling spectroscopy (STS). In this project, the data are processed to remove noises and the finite-size-scaling behavior is investigated for evidence that the amorphous system is an Anderson insulator. The results do not provide concrete evidence of localization, as the method used is very sensitive to noises. Yet, some features suggest that the localization may exist while overweighed by the bulk states inside the metal substrate.

Advisor: LIN Nian / PHYS Student: FANG Yawen / SSCI

To better understand the mechanisms of two-dimensional single and multi-component metallo-supramolecular polymerization on an Au (111) surface, which has been studied using scanning tunneling microscopy (STM), a computer simulation program using the Monte Carlo method is introduced to simulate this self-assembling procedure. By varying different parameters such as temperature and the density and bonding energy of molecules, the effect on polymerization can be studied separately. In addition, the effects of temperature and molecule density on the heat capacity of the system are also discussed and the results of one- and two-component cases are compared. The comparison of the computer simulation and experimental results suggests that the simulation program needs improvement.

Advisor: LIN Nian / PHYS Student: LI Yuxiao / MAEC

The two-dimensional supramolecular assembly used to generate metal-organic coordination networks on an Au (111) surface is studied using scanning tunneling microscopy. The Monte Carlo method is introduced for use in the computer simulation to help analyze the mechanism and find the law governing the assembly’s behavior. Based on previous studies on this topic, the influence that temperature, concentration, bonding energy and hopping time have on the system have been taken into consideration and certain conclusions have been drawn through the analysis of the simulation results. Moreover, a comparison is made between the similarities and differences of the one- and two-component systems.

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30 Quantum State Calculation of Two-dimensional Supramolecular

Nanostructures

Advisor: LIN Nian / PHYS Student: WU Qi / PHYS

Using a new program designed and programed to realize the original Monte Carlo method through direct sampling, this project discusses the influences and basic mechanisms of some primary factors such as environmental temperature, bonding energy and molecular pressure in the two-dimensional (2D) supramolecular self-assembly process. Generally, some famous phenomena such as kinetic traps are successfully observed in the simulation and the simulation result might theoretically prove that the two-dimensional supramolecular self-assembly in a zero-dimensional case could be practical and efficient. By applying the canonical partition function into the Monte Carlo system, a basically accurate equation is obtained, which makes the further description and prediction of the two-dimensional supramolecular self-assembly process possible.

Keywords—self-assembly; 0-demensional; MC; simulation; partition-function.

Advisor: LIN Nian / PHYS Student: ZHONG Junke / SSCI

To help in understanding the nature and the characteristics of supramolecular assembly, Monte Carlo simulation is performed. Figures and graphs show the supramolecular assembly under the influence of various factors, and the final results such as the number of bonds formed between the molecules and the heat capacity are explained.

Advisor: LIN Nian / PHYS Student: SAHA Shreya / PHY-PP

This project examines the behavior of surface electrons subjected to periodic potential applied to a surface. A suitable MATLAB program can simulate this physical system by numerically solving the two-dimensional Schrödinger equation. Hence, a MATLAB program is designed for the two dimensional potential pillars. The band structure and density of state (DOS) graph are modified with different input parameters and analyzed accordingly. Furthermore, the program can be modified to adapt to practical cases in the future.