1. Mechanisms Underlying Behavior with Prof. Ajay Mathuru

Field: Neuroscience

Location: Singapore

Length: 10 weeks, approx. 9 May 2016 – 15 July 2016

Number of hours per week: 40

Are you curious about the kind of research that happens in a neuroscience lab in a

modern biology research institute? Have you wondered how new drugs get

discovered? Does genome editing and making transgenic animals sound like an

exciting way to spend a summer? If yes, there are 3 possible projects for you to

participate in.

These projects are based on the ongoing research in the lab. The exact work you will

be involved would depend on the stage of progress in these projects. The main

research interest driving these projects is to study how behavior arises from activity

of neural circuits using zebrafish (a small, freshwater aquarium vertebrate species).

The possible projects are:

1. Understanding the neural basis of nicotine addiction.

2. Social communication of fear and its attenuation by emotional contagion

3. Studying alarm behavior evoked by the release of a kairomone (a pheromone

that is recognized by multiple species).

For more information on these projects, visit

https://mechunderlyingbehavior.wordpress.com/research/

Student responsibilities

In most of these projects, the exact thing you do depends on a few different factors,

including your skills in the lab and past experience, but you can expect to be

involved in one or more of the following:

a) Performing and analyzing behavioral studies,

b) Designing new assays to study behavior,

c) Imaging neural activity of transgenic fish,

d) Creating new transgenic fish using molecular cloning techniques, and

e) Creating/using computational tools to analyze behavioral and physiological data.

Working Environment

You will work at the Institute of Molecular and Cell Biology, an A*STAR research

institute in Biopolis, Singapore. There will be other members in the lab working on

similar projects. It is likely that you will learn most of your skills from one of these

lab members.

Your time in the lab (10 weeks) is not adequate for a completely independent

project. However, you will be expected to work on your own and run the

experiments yourself. How early this happens after you start depends on how well

you pick up some of the skills required in your project.

Requirements

Some experience with molecular biology (e.g. Bio lab) or with handling fish for

experiments is desirable. Experience with programming would be useful. If this will

be your first neurobiology or biology lab experience, it is highly desirable that you

be willing to consider committing time during the rest of the academic year, or

breaks and subsequent semesters. Biological work takes many months, and it also

takes a while to become proficient with basic skills in the lab and to make significant

progress in a project.

Irrespective of past experience, you will need to be comfortable working with

animals (fish) and will need to complete an animal ethics certification course before

you can start working in the lab. You will also need to complete a laboratory safety

course in the institute before you can start working.

Additional information

There will be at least 1 week (May 15 to 23) when I will be away. On these and other

days there will be a research officer who will supervise you.

Although 10 weeks is very short for a completely independent project, depending on how much you are able to accomplish in that time, it could become the grounds for further research. Your main aim should be to learn as much as you can in this time.

2. Undergraduate Astronomy Institute with Prof. Bryan Penprase

Field: Astronomy/ Astrophysics

Location: Pasadena, California

Length: 6 weeks, approx. 15 June 2016 – 31 July 2016

Number of hours per week: 40

The California Institute of Technology (Caltech) is launching a new program for time

domain astronomy and astrophysics known as the Zwicky Transient Facility (ZTF).

Prof. Penprase is in charge of undergraduate programs, and so there will be an

undergraduate astronomy institute this summer for interested students from

Pomona, Caltech and hopefully Yale-NUS. After the institute, students conduct

research on supernovae, time-variable sources of all kinds, and asteroids in

collaboration with Caltech and Pomona astronomers.

Student responsibilities

Obtain and analyse images from the Palomar Observatory PTF database Construct light curves of various astronomical sources using Python image

processing commands Determine astronomical coordinates of newly discovered sources, and help

plan for follow-up observations using other telescopes. Read primary astrophysical literature, summarise findings clearly and help

develop new research projects using the PTF and ZTF databases. The student will be supervised by Prof. Penprase and various collaborators from Caltech and Pomona. Working environment The student would probably be mixed in with Caltech or Pomona students on summer undergraduate research programs. There would be a group of about 10-15 other undergraduates working on astronomy topics to teach each other various aspects of astronomy and help each other figure things out. Requirements

Computer skills are a must – knowledge of Python and another language would be best. Good analysis skills, knowledge and familiarity with physics and astrophysics. Some tenacity and ability to pick up unfamiliar and new science is also key.

3. Computational Modelling of Plant Metabolism with Prof. Maurice

Cheung

Field: Biochemistry/ Computer Science

Location: Singapore (or anywhere with a computer)

Length: 10 weeks, approx. 23 May 2016 – 29 July 2016

Number of hours per week: 35-40

This project aims to study the systems-level properties of plant metabolism using a computational modelling approach. The project will involve developing a plant metabolic model or modelling approach, and running model simulations to study metabolic fluxes in plants. The results of this work will provide modelling tools to further our understanding of plant metabolism, which will be important for guiding the engineering and/or breeding of plants for greater productivity. Student responsibilities During the project, you will be expected to: a) Look up primary literature for curation of metabolic model b) Explore the computation tools for metabolic modelling c) Write programming scripts to construct and simulate the model d) Organise tables of results and plot graphs for model simulations Working environment You will only need your computer to work and you can work wherever is best for you. There is a group of students who are working in the same area with the same computational tools, so you can discuss your work and seek help with others, especially troubleshooting with technical problems. The work will mainly be independent - you will be working on your model and running your own simulations.

Requirements Desirable: Basic programming skills in Python, familiarity with metabolic modelling software (e.g. COBRApy).

4. Cartogram Algorithms with Prof. Michael Gastner

Field: Computer Science/ Mathematics

Location: Singapore

Length: 9 weeks, approx. 9 May 2016 – 8 July 2016

Number of hours per week: 40

Density-equalizing maps, also known as cartograms, are map projections where regions (such as countries or provinces) are represented by an area proportional to user-specified numbers. (See https://en.wikipedia.org/wiki/Cartogram for figures showing such maps.) The numbers represented by these maps can be population counts, gross domestic products, the prevalence of a disease or any other demographic quantity of interest. Finding algorithms to rescale the regions and still maintain their contiguity has been of intense interest to cartographers for about one century. In 2004 Prof. Gastner was one of the creators of an algorithm that has since become the standard in the field and was popularized by books such as "The Atlas of the Real World" (Dorling et al., 2010). Although the existing algorithm produces striking images, it should still be possible to better preserve shapes. On several idealized maps, Prof. Gastner has tested a new algorithm that promises to be faster and creates less distortion. The goal of the summer research project is to take the existing C algorithm and implement it as an R package. There is already an R package "Rcartogram" available, but not written by Prof. Gastner. The first step will be to analyze that package, write a document detailing how it works, develop a list of possible improvements and develop a new improved package. Student responsibilities You will have to analyze existing code, learn how to write R packages and familiarize yourself with R graphics. You will have to keep good records of your findings, maintain well-commented code and, by the end of the project, write a document that can be easily followed by others. Working environment

You should be motivated to work independently. Prof. Gastner can meet with you several times a week and explain the C algorithm to the extent necessary for your

project, and direct you to relevant literature. However, during the project you will spend significant time working by yourself on your own computer (laptop). Requirements You should have some background in programming or software development. This does not have to be specifically in R, but you should have at least enjoyed working with R in Quantitative Reasoning.

Additional information You should have your own laptop. If you are a Windows user, it will be convenient to establish a Linux partition on your machine because Linux has many free tools for software development. If you are a Mac user, you should be ready to go. At this point, you do not need to commit to a longer project. Therefore I do not

recommend that a publication is your primary motivation to decide for this project.

5. Quantum Information and Computation with Prof. Ng Hui Khoon

Field: Physics

Location: Singapore

Length: 8 weeks, possible to extend to 10 weeks (approx. 29 May 2016 - 21 July

2016)

Number of hours per week: 40

Prof. Ng’s research interests lie in the field of quantum information and quantum computation, a line of research that focuses on discovering the connections between information and quantum physics, and how to make use of quantum effects to do certain computation or communication tasks more efficiently. Her specific interests cover two areas: 1) Understanding and control of noise in quantum information processing systems, 2) Estimation of quantum properties of physical systems. You will have the opportunity to work independently on one aspect of these topics; the precise project scope will be decided based on your interest and background, as well as the needs of on-going projects within her group. Past projects involving YNC undergraduates include a study of a specific error correction technique – known as continuous-time quantum error correction – in the presence of noise with non-Markovian properties, the derivation of an effective noise model for an atom exposed to a single-mode electromagnetic field, and contributing to the building of a numerical code capable of classical simulation of certain aspects of a quantum computer. Student responsibilities The work will be theoretical in nature, and will likely involve numerical simulation. You will get to experience how a theoretical physicist does research: together with Prof. Ng, you will start with choosing and planning a specific research question that can be completed in the summer period; you will learn the basic background physics needed before the start of the internship; you will work through the calculations, helped along by discussions with Prof. Ng and other graduate students/postdocs within the group. The internship will end with you writing a report and presenting your results to the group.

Working environment The research internship will be at the Centre for Quantum Technologies (CQT) in NUS, where Prof. Ng holds a joint appointment. CQT is a research institute focusing on quantum information science, quantum foundations, as well as quantum computation. The Centre houses more than 100 researchers from all over the world, working on topics in physics, computer science, and mathematics. During your internship, you will be assigned a desk within CQT. There, you will have the opportunity to interact with fellow undergraduate and graduate students working in the Centre, as well as postdocs or research fellows who can be discussion partners and offer additional guidance, both on your specific problem, and on research in general. You will also have the chance to attend talks held regularly at the Centre, to hear about new research results by visitors at the Centre. You should expect to work with another student from YNC; each of you will have your own specific research question, but they will be closely related, as having a partner to discuss matters with is often very helpful.

Requirements The student must have a strong interest in theoretical physics and mathematics. It will be a plus point if the student already knows how to write computer code; the numerical simulation will be done using a scientific programming language, usually either MATLAB or Mathematica.

6. Fundamentals of Cell Organization and Determination with Prof.

Nicholas Tolwinski

Field: Biology

Location: Singapore

Length: 8 weeks, dates are flexible

Number of hours per week: 40

This research lab focuses on fundamental questions of cell organization and determination during development. The student will explore the organizing principles and molecular mechanisms that underlie this cell biological process. The lab is currently exploring how subsets of cells within a larger tissue respond to extracellular signals and undergo transformation, while the cells surrounding them do not. Student responsibilities The student will learn and apply biochemical and genetic methods to study cells and tissues, and how they communicate with each other.

Working environment The student will work in a team to tackle problems, so he/ she must be able to work well with others. Requirements Laboratory experience is desirable but not required.

7. Stalk-eyed Fly Biology with Prof. Philip Johns

Field: Biology

Location: Singapore, with possible excursions to Malaysia, Indonesia, Brunei.

Length: 8 weeks, approx. 16 May 2016 – 8 July 2016

Number of hours per week: 35-40

Our aim is to study the evolution of sexually selected traits in stalk-eyed flies. Stalk-eyed flies (family Diopsidae) have eyes on the ends of eyestalks that function as sexual ornaments, similar to deer antlers, for example. Some species are monomorphic, while other species are sexually dimorphic, with males having longer eyestalks than females. Some species are elaborate, where the males’ eyestalks might be longer than their bodies. Depending on the species, males use their eyestalks in fights over females, and females choose among males, typically mating with the males with the longest eyestalks. Complicating the issue is an X-linked selfish genetic element, "sex-ratio", that causes some males to sire all-female broods, and that is strongly associated with short eyestalks in some species. In this study, we will sample genetic and morphological information from several

populations and species in the area. We will capture flies, measure them, isolate

DNA and RNA, and depending on the kind of fly, we may perform certain

behavioural experiments. The genetic information will contribute to a comparative

transcriptome, which we will continue to analyse through the summer and beyond.

Student responsibilities

Students will help with the collection and identification of flies from a variety of species, populations, and locations. Students will measure a variety of morphological characters, dissect target tissues, isolate genetic materials, and prepare these for eventual genomics. Students will use techniques ranging from basic field skills, to basic microscopy and basic molecular genetic tools. Working environment In many ways, this project will be slightly schizophrenic: we will spend part of our time collecting flies in the field, which typically means remote forested areas. We will spend other times doing wet-lab work on campus.

Requirements Enthusiasm, comfort with insects and other arthropods, curiosity, humour, intelligence, and good taste in music, are all prerequisites. Having "lab hands" is recommended but not required. (Lab hands are made, not born.) We will probably continue to work on the data from this summer’s project for months to come.

8. Theoretical Physics with Prof. Shaffique Adam

Field: Theoretical Physics

Location: Singapore

Length: 10 weeks, dates are flexible

Number of hours per week: 40

I encourage any students interested in summer research in theoretical physics to contact me prior to applying. The exact details of the project will be worked out in consultation with the student, but would likely involve some currently fashionable aspect of theoretical quantum condensed matter physics. In 2014, two Yale-NUS students worked with me on the electronic structure of moire superlattices, where twist angle between two 2D materials can change the system from metallic to insulating (see e.g. http://goo.gl/up0gnA). In 2015, three Yale-NUS students worked with me on making a mapping between a random resistor network model and an effective medium theory model for describing inhomogeneity induced magnetoresistance. Two of them will present their findings in March 2016 at the annual meeting of the American Physical Society in Baltimore, MD.

Student responsibilities Research in theoretical physics requires long hours of focused attention that can sometimes be frustrating. This is why I prefer having students work in pairs, and perhaps also in collaboration with another member of my research group. Although I am flexible regarding the dates, for the experience to be productive for everyone involved, over the course of the summer, students should plan on spending 10 solid weeks of about 40 to 50 hours per week.

Working environment Students will be part of a large research effort at the Center for Advanced 2D Materials. This is a vibrant research environment with almost 100 researchers at all career stages. Prof. Adam’s research group currently has 3 postdocs, 3 graduate students, 3 Research Assistants and 3 undergraduate students.

Requirements Strong math skills and/or programming skills are desirable.

9. Synthetic Organic Chemistry with Prof. Stanislav Presolski

Field: Chemistry

Location: Singapore

Length: 8-10 weeks, between 9 May 2016 – 31 July 2016

Number of hours per week: 40

The goal of this summer project is to establish a synthetic protocol for the preparation of photochromic catalysts. Student responsibilities Organic synthesis of novel photo-active molecules and their analytical characterization. Working environment Graduate-school-like synthetic organic chemistry research environment: state-of-the-art lab equipment, close supervision and mentorship at first, but full independence later on.

Requirements Strong desire to learn advanced synthetic organic chemistry techniques. Prior chemistry courses are recommended, but not required. Since this will only be the beginning of a multi-year project, ability to commit to the research in the future would be preferred.

10. Nanostructural Basis for Iridescent Structural Colors with Prof. Vinod Saranathan

Field: Optics, Material Science and Evolutionary Biology

Location: Singapore

Length: 8 weeks, approx. 16 May 2016 – 8 July 2016

Number of hours per week: 35

The Yale-NUS Biophotonics lab is interested in understanding the precise optical and nanostructural basis for the production of vivid interference or structural colours in nature in order to understand their origin evolution and diversification. It is hoped that studying such structural color producing nanostructures evolved over millions of years of selection may provide biological inspiration for next generation devices and technology in sensing and photonics. Here are two projects that may appeal to you: A) Understanding the origin, and diversification of iridescent structural colours within certain generas of insects to understand what role structural colour differences (these may be cryptic or invisible to Humans) may play in keeping species boundaries intact and whether rapid diversification are associated with changes in colouration patterns. B) Understanding the comparative structural and optical properties of thin-films (think oil slick effect) and multi-layer reflectors in iridescent bird feathers. These nanostructures produce the amazing scintillating iridescent colours of hummingbirds, and even the purple-green iridescence on the neck of the lowly rock dove. Prof. Saranathan is also open to other proposals as long as they are structural colours related.

Student responsibilities

You will learn to do collections-based research working with recently collected and museum based specimens of insects.

You will also be using state-of-the-art micro-spectrophotometric equipment to precisely measure colors from regions a few microns across.

On the structural side, you will be learning to use state-of-the-art Electron Microscopes. These skills will come in very handy whether you decide to stay in biology or move on to a career in the physical sciences and engineering.

Working environment The Yale-NUS Biophotonics Lab is based within the NUS Nanoscience and Nanotechnology Institute (NUSNNI), located at the T-Lab (opposite the NUS Cultural Centre, a short 10-minute walk away from YNC down Clementi Rd). You will be working alone or in close proximity to another undergrad student (albeit working on a different project). However, NUSNNI is always teeming with friendly and knowledgeable graduate students and postdocs. There very well may also be an opportunity to conduct synchrotron X-ray scattering experiments on light scattering biological nanostructures at Argonne National Labs in Chicago, IL and at the Singapore Synchrotron Light Source (SSLS) here at NUS, either in the summer or fall. Requirements

Eagerness, diligence and enthusiasm for learning new skills and concepts, and ability to work independently.

Prior scripting experience (C/C++/R etc.) is desired but not required.

11. Bioinformatics, Biodiversity and Molecular Systematics with

Prof. William Piel

Field: Biology

Location: Singapore

Length: 7-8 weeks between 21 May 2016 – 31 July 2016

Number of hours per week: 30-40

Research with Prof. Piel will involve either bioinformatics (in silicō) or biodiversity

and natural history (in ecō) or molecular systematics (in labō). Below are some

examples of projects that might appeal to prospective students, but students are not

limited to these ideas. Students are free to brainstorm their own projects.

1. Finding a solution to ‘Generic Phylogenetic Querying’ — Structured Query Language (SQL) is used in programmatic querying of relational databases. Phylogenetic trees can be stored in relational tables and queried using special indexing approaches, such as transitive closure. While these approaches can easily find particular topologies, biologists would benefit from the ability to find general topologies that are not necessarily bound to a particular set of leaf identities. The challenge for the student researcher is to find a solution to this problem, and/or take an existing solution and test its robustness.

2. UV Reflective Patterns in Pitcher Plants — Although the interior and exterior of pitcher plants look about the same to our eyes, in a number of species, the interiors are known to reflect UV light (e.g. Joel, Juniper, and Dafni. 1985. New Phytol., 101: 585-593). While these UV patterns are probably designed to attract insect prey, exactly how this is accomplished has not been studied.

3. Independent Origins of the Orb Web — almost all orb-weaving spiders share one common and ancient evolutionary origin. One piece of evidence for this common origin is found in details associated with web construction, such as the sequence of leg movements for localization and deposition of silk. A rare exception to the common origin of the orb web is with spiders in the genus Fecenia, which build webs that look superficially similar to the classic orb web but are, in fact, evolutionarily unrelated. The phylogenetic relationships, as well as details of web building behaviors, are not well worked-out.

Here are three possible research questions:

The exact method by which Fecenia builds webs has never before been

witnessed or documented. You can be the first person to figure out how they

do it using infrared cameras and other such instruments.

The kinds of silk proteins available for use by Fecenia are unclear. Using

genomics tools, data-mine the transcriptomes of spiders to infer the suite of

silk polymers available to Fecenia.

The phylogenetic relationships between Fecenia and its kin are not well

worked out. Do PCR, DNA sequencing, and phylogenetic analysis to uncover

the history of these species.

Student responsibilities Project 1: Daily tasks include brainstorming algorithms, instantiating databases, coding solutions, importing/exporting data, and testing the efficacy of solutions. Project 2: Students can conduct experiments to test how the presence or absence of UV patterns affects prey capture, and compare and contrast UV coloration in New World and unrelated Old World pitcher plants. Project 3: Depending on the project type, students would be using infrared cameras to capture web building, using genomics tools, data mining, PCR, DNA sequencing and phylogenetic analysis.

Working environment Students will be interacting with the professor, a post-doc, a graduate student, and any other undergraduates in the lab. Depending on the specific project, these can be suitable for those who enjoy problem solving, can work independently, have patience, and enjoy the outdoors.

Requirements Project 1: Prior knowledge of SQL (in particular, PostgreSQL) is not required as long as there exists an intrepid willingness to learn quickly. Additionally, knowledge of, or the willingness to learn, a scripting language (e.g. Python or PERL) is needed to interface with the database. If working with critters, it is best not to be arachnophobic or entomophobic.