Tag Archive for graduate students

Grad Student Ranasinghe Speaks on Computational Chemistry

#THISISWHY

Duminda Ranasinghe, a Ph.D. candidate in Chemistry, spoke April 16 in Exley in the fourth event of the Graduate Student Speaker Series. (Photos by Hannah Norman ’16.)

Ranasinghe gave a talk titled “Computational Chemistry: Chemistry Without Chemical.”

Ranasinghe gave a talk titled “Computational Chemistry: Chemistry Without Chemical.”

Computational chemistry uses quantum mechanics to predict reactions and molecular properties.

Computational chemistry uses quantum mechanics to predict reactions and molecular properties.

Over the past decade, computational chemistry has become popular with chemists as a tool to explore reactions and molecules. At Wesleyan, researchers are making reliable computational methods, which are accurate and faster than what is currently available.

Over the past decade, computational chemistry has become popular with chemists as a tool to explore reactions and molecules. At Wesleyan, researchers are making reliable computational methods, which are accurate and faster than what is currently available.

Othon, Taylor Students Published in Physical Chemistry Letters

Christina Othon and Erika Taylor, along with physics graduate student Nimesh Shukla, Lee Chen ’15, Inha Cho ’15 and Erin Cohn ’15, are the co-authors of a paper titled “Sucralose Destabilization of Protein Structure” published in The Journal of Physical Chemistry Letters, March 2015. Othon is assistant professor of physics and was PI on the paper. Taylor is assistant professor of chemistry, assistant professor of environmental studies.

Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. This research suggests that people may need to think about the impact of sucralose (a.k.a. Splenda) on their proteins.

Watch Othon explain associated research in this video. She speaks around the 34 minute mark.

Kaus Investigates Protein Structure by Using X-Ray Crystallography

Katie Kaus, a PhD candidate in molecular biology and biochemistry, spoke on "Molecular Detectives: Investigating Protein Structure using X-ray Crystallography" during the Graduate Student Speaker Series March 26 in Exley Science Center.

Katie Kaus, a PhD candidate in molecular biology and biochemistry, spoke on “Molecular Detectives: Investigating Protein Structure using X-ray Crystallography” during the Graduate Student Speaker Series March 26 in Exley Science Center.

The molecular structure of proteins is an important component in studying how proteins interact with each other, providing information about how cellular processes are carried out by specific proteins, Kaus explained. By studying the structure of specific proteins, scientists can understand why germs make us sick.

The molecular structure of proteins is an important component in studying how proteins interact with each other, providing information about how cellular processes are carried out by specific proteins, Kaus explained. By studying the structure of specific proteins, scientists can understand why germs make us sick.

Kaus focused her presentation on members of a family of proteins called bacterial pore forming toxins (PFTs); specifically Vibrio cholerae cytolysin (VCC) and Vibrio vulnificus hemolysin (VVH). These proteins are secreted by pathogenic strains of the aquatic bacteria, V. cholerae and V. vulnificus. V. cholerae is the human pathogen that causes cholera, an endemic disease in several parts of the world. V. vulnificus is found in contaminated seafood, such as raw oysters, as well as contaminated seawater. V. vulnificus most frequently causes gastrointestinal distress but can also cross from the gut into the blood stream resulting in lethal septicemia.

Kaus focused her presentation on members of a family of proteins called bacterial pore forming toxins (PFTs)–specifically Vibrio cholerae cytolysin (VCC) and Vibrio vulnificus hemolysin (VVH). These proteins are secreted by pathogenic strains of the aquatic bacteria, V. cholerae and V. vulnificus. V. cholerae is the human pathogen that causes cholera, an endemic disease in several parts of the world. V. vulnificus is found in contaminated seafood, such as raw oysters, as well as contaminated seawater. V. vulnificus most frequently causes gastrointestinal distress but can also cross from the gut into the blood stream resulting in lethal septicemia.

VCC and VVH are homologous proteins that are secreted by their respective bacteria, bind to macromolecules at the surface of host cells, and undergo structural changes creating lytic pores in the host cell membrane. As part of her research, Kaus is interested in understanding how these bacterial proteins recognize and specifically attack human cells. Guided by biochemical assays, Kaus used a technique called X­-ray crystallography to identify structural relationships between VCC or VVH and the biomolecules each protein binds.

KVCC and VVH are homologous proteins that are secreted by their respective bacteria, bind to macromolecules at the surface of host cells, and undergo structural changes creating lytic pores in the host cell membrane. As part of her research, Kaus is interested in understanding how these bacterial proteins recognize and specifically attack human cells. Guided by biochemical assays, Kaus used a technique called X­-ray crystallography to identify structural relationships between VCC or VVH and the biomolecules each protein binds.

X-­ray crystallography involves obtaining protein molecules in a crystalline form and taking advantage of the manner in which an X­ray beam is diffracted by the atoms that make up these protein crystals, to determine their arrangement within the 3-D space of a protein molecule. Pictured, Kaus looks at crystals under a microscope in Hall Atwater Laboratory.

X-­ray crystallography involves obtaining protein molecules in a crystalline form and taking advantage of the manner in which an X­ray beam is diffracted by the atoms that make up these protein crystals, to determine their arrangement within the 3-D space of a protein molecule. Pictured, Kaus looks at crystals under a microscope in Hall-Atwater Laboratory.

By using this approach, Kaus identified similar, yet distinct molecular mechanisms employed by VCC and VVH to specifically recognize and attack host cell membranes. Understanding how these proteins specifically attack human cells will aid in developing treatments against V. cholerae and V. vulnificus infection.

By using this approach, Kaus identified similar, yet distinct molecular mechanisms employed by VCC and VVH to specifically recognize and attack host cell membranes. Understanding how these proteins specifically attack human cells will aid in developing treatments against V. cholerae and V. vulnificus infection. (Photos by Olivia Drake)

Graduate Student Blasser Hand Crafts Analog Instruments

Graduate student Peter Blasser tunes one of his hand-crafted analog instruments. (Photos by Olivia Drake)

Graduate student Peter Blasser tunes one of his hand-crafted analog instruments. (Photos by Olivia Drake)

#THISISWHY
In this Q&A, we speak with Peter Blasser, a music graduate student. 

Q: What was your first experiences with music? When did you decide that music would be your life work?

A: I was in elementary school in the 1980s when music programs were still part of the public school curriculum. I remember that those music classes were not very noteworthy at the time. In middle school I took a wood shop class and liked working with the tools. After taking classical civilization classes, I started to triangulate all three — I wanted to work with wood to make ancient Greek instruments to see what they sounded like. The first instruments I decided to recreate were ancient stringed instruments.

Blasser changes where the transistors are connected in order to tune the instrument.

Blasser changes where the transistors are connected in order to tune the instrument.

Q: Where did you complete your undergraduate studies?

A: I went to Oberlin College. I initially went as a classics major, but still had a passion for making classical instruments. Oberlin had a conservatory for music, and they offered introductory courses in electronic music. I started to use electronic music to model and tune classical instruments. I also was able to take a course in analog music, learning about transistors and electronics, and how they could be used to make music. This caused me to combine wood and analog electronics, which is all about the flow of the transistors.

Q: What did you do after graduating?

A: I purchased a home in Baltimore about 10 years ago as a space to work on my art. Fixing up the house was an artistic experience in of itself. I also started my own business where I sold analog instruments. I wasn’t making much money, so I spent a lot of time working on poetry, thinking of ideas for my business and exploring my philosophy. I also toured with my instruments, but didn’t like how much I had to promote myself and push my brand.

Q: Why did you choose Wesleyan for your graduate school?

Blasser likes to work with wood, which is frequently used in his instruments.

Blasser likes to work with wood, which is frequently used in his instruments.

A: I decided to attend Wesleyan after developing a friendship with Ron Kuivila, chair of the Music Department. After graduating from Oberlin I never thought I would return to school, but I found that I enjoyed giving lectures and helping other students make their instruments. I also like how Wesleyan’s music program, and art program in general, is experimental — there are no prejudices from students about what music should “be” like. The different departments are porous, there is mixing between different mediums and styles. This enables me to sit with undergraduates and help them make a piece that the student will own, with a shared experience. This made me realize that I enjoy teaching, and in order to become a professor, formal education is required.

Q: What are your plans after Wesleyan?

A: Right now my analog electronics business,

Wesleyan Physics Lab, U.S. Air Force Partner on Groundbreaking Research

Graduate student Eleana Makri and Tsampikos Kottos, the Douglas J. and Midge Bowen Bennet Associate Professor of Physics, work on reflective optical limiter research Feb. 3. (Photo by Hannah Norman '16)

Graduate student Eleana Makri and Tsampikos Kottos, the Douglas J. and Midge Bowen Bennet Associate Professor of Physics, work on reflective optical limiter research Feb. 3. (Photo by Hannah Norman ’16)

#THISISWHY

Graduate student Eleana Makri and Tsampikos Kottos, the Douglas J. and Midge Bowen Bennet Associate Professor of Physics, work on reflective optical limiter research Feb. 3. (Photo by Hannah Norman '16)

Makri and Kottos review their power limiter research.

For many years, pilots in the Air Force, scientists conducting research with high-powered lasers, and others have struggled to protect their eyes and sensitive equipment from being damaged by intense laser pulses. In many cases, this was achieved by intense power filters, which offered protection, but self-destructed. Now they have a solution, which provides protection without damaging the filters themselves, thanks to a research collaboration between the Air Force Research Laboratory (AFRL) and a team of researchers in Wesleyan’s Physics Department.

The research, led by Tsampikos Kottos, the Douglas J. and Midge Bowen Bennet Associate Professor of Physics, is included in the just-released U.S. Air Force Office of Scientific Research 2014 Technical Strategic Plan. The document is published on the Air Force Research Laboratory (AFRL) webpage.

Previous attempts at a solution focused on creating gradually darkening sunglasses to protect the wearer’s eyes when s/he steps into bright sunlight, but return quickly to their normal state when indoors. However, no version could darken quickly enough to protect the wearer from short laser pulses.

As described in the Technical Strategic Plan,

Space Grant Consortium Awards Graduate Students’ Travel Grants

The NASA Connecticut Space Grant Consortium awarded two Student Travel Grants on Nov. 11. Each award is worth $1000.

Lisa Korn, a graduate student in earth and environmental sciences, will attend the Lunar and Planetary Science Conference, held March 16-20 in The Woodlands, Texas. Her advisor is Marty Gilmore, chair and professor of earth and environmental sciences and the George I. Seney Professor of Geology.

Sam Factor, a BA/MA student in astronomy, will use the grant to attend the American Astronomical Society 223rd Meeting, held Jan 4-8 in Seattle, Wash. Factor’s advisor is Meredith Hughes, assistant professor of astronomy. Dilovan Serindag ’15, Jesse Lieman-Sifry ’15 and Trevor Dorn-Wallenstein ’15 also will attend the meeting.

Graduate Students Speak on Taiwanese Music at Ethnomusicology Meeting

Pictured at the Society for Ethnomusicology's Annual Meeting are, from left, Wesleyan's Ender Terwilliger, Po-wei Weng, Joy Lu and Su Zheng.v

Pictured at the Society for Ethnomusicology’s Annual Meeting are, from left, Wesleyan’s Ender Terwilliger, Po-wei Weng, Joy Lu and Su Zheng.

During the 2014 Society for Ethnomusicology’s 59th Annual Meeting, held Nov. 13-16 in Pittsburgh, Pa., Wesleyan graduate students collaborated to present the first panel dedicated to Taiwanese identity and music.

The panel, titled “How Taiwanese Should I Be? Contesting Taiwanese Identities in Local, Regional and Global Contexts,” comprised of Ph.D. candidates Joy Lu and Po-wei Weng, and graduate student Ender Terwilliger.

Su Zheng, associate professor of music, chaired the panel.

Covering Taiwanese opera, Pili Budaixi, and fusion performances, the panel explored the process of identity formation when promoting Taiwanese identity in politically delicate situations domestically and overseas.

In addition, Ph.D. candidates Dustin Wiebe, Min Yang and Fugan Dineen presented papers at the conference.

Makri’s Power Limiter Research Noted in Scientific Reports Article

Makri used a power limiter consisting of a nonlinear lossy layer embedded in two mirror layers. This setup provides a resonant transmission of a low intensity light and nearly total reflectivity of a high-intensity light.

Makri used a power limiter consisting of a nonlinear lossy layer embedded in two mirror layers. This setup provides a resonant transmission of a low intensity light and nearly total reflectivity of a high-intensity light.

A study co-authored by Graduate Research Assistant Eleana Makri and two other Wesleyan researchers is a topic of a Oct. 20 article published in Scientific Reports.

Due to the ultrahigh-speed and ultrawide-band brought by adopting photons as information carriers, photonic integration has been a long-term pursuit for researchers, which can break the performance bottleneck incurred in modern semiconductor-based electronic integrated circuits. The article states that “recently, Makri theoretically proposed the concept of reflective power limiter based on nonlinear localized modes, where a nonlinear layer was sandwiched by two reflective mirrors, thus increased the device complexity.”

The report is based on Makri’s study, titled “Non-Linear Localized Modes Give Rise to a Reflective Optical Limiter” published in March 2014. The paper is co-authored by Tsampikos Kottos, the Douglas J. and Midge Bowen Bennet Associate Professor of Physics; Hamidreza Ramezani Ph.D. ’13 (now a postdoc at U.C. Berkeley) and Ilya Vitebskiy (Sensors Directorate at the Air Force Research Laboratory, Ohio).

The same study was also highlighted in Washington, D.C. at the spring review meeting of the Air Force Office of Scientific Research (AFOSR) as one of the main research achievements in electromagnetics of 2014 that can potentially benefit the U.S. Air Force. Read more about this study in this past News @ Wesleyan article.

Read the full Scientific Report article, titled “Chip-integrated optical power limiter based on an all-passive micro-ring resonator,” online here.

Kottos, Basiri Author Paper Published in Physical Review

Data by Tsampikos Kottos and Ali Basiri.

Tsampikos Kottos and Ali Basiri, a Ph.D. student in physics, are co-authors of a paper titled “Light localization induced by a random imaginary refractive index,” published in Physical Review A 90, on Oct. 13, 2014. Kottos is the Douglas J. and Midge Bowen Bennet Associate Professor of Physics.

In the paper, the authors show the emergence of light localization in arrays of coupled optical waveguides with randomness.

 

 

 

Math Ph.D. Candidate Smith Delivers First Graduate Speaker Series Talk

Brett Smith, a Ph.D. candidate in mathematics, spoke during the first Graduate Speaker Series event Oct. 7 in Exley Science Center. Smith's talk, titled "Mine, Yours and the Truth," focused on American mobster Joe Massino, boss of the Bonanno crime family in New York from 1991 until 2004. "Big Joey" famously said, “there are three sides to every story — mine, yours and the truth.”

Brett Smith, a Ph.D. candidate in mathematics, spoke during the first Graduate Speaker Series event Oct. 7 in Exley Science Center. More than 50 students, faculty and staff attended the event. Smith’s talk, titled “Mine, Yours and the Truth,” focused on American mobster Joe Massino, boss of the Bonanno crime family in New York from 1991 until 2004. “Big Joey” famously said, “there are three sides to every story — mine, yours and the truth.”

By using a graph theory called the Robertson–Seymour theorem, Smith explored the competing questions, "What is the best way to organize a mafia so that you won't be caught?" and "What is the best way to patrol a city to disrupt organized crime?" Smith explained how these questions are one and the same.

By using a graph theory called the Robertson–Seymour theorem, Smith explored the competing questions, “What is the best way to organize a mafia so that you won’t be caught?” and “What is the best way to patrol a city to disrupt organized crime?”
Smith explained how these questions are one and the same.

Three more graduate students will tentatively speak as part of the series this fall and next spring including Duminda Ranasinghe, a chemistry Ph.D. candidate; Katie Kaus, a molecular biology and biochemistry Ph.D. candidate and Peter Blasser, a graduate student in music. For more information, visit the Graduate Studies website.

Naegele, Aaron, Student Researchers Published in Journal of Neuroscience

Jan Naegele, Gloster Aaron and several Wesleyan researchers are the co-authors of an article titled “Long-Term Seizure Suppression and Optogenetic Analyses of Synaptic Connectivity in Epileptic Mice with Hippocampal Grafts of GABAergic Interneurons,” published in the October 2014 edition of The Journal of Neuroscience, Issue 34(40): 13492-13504.

Naegele is professor of biology, professor of neuroscience and behavior, and director of the Center for Faculty Career Development. Aaron is associate professor of biology, associate professor of neuroscience and behavior. The article is co-authored by Diana Lin ’15; graduate students Jyoti Gupta and Meghan Van Zandt; recent alumni Elizabeth Litvina BA/MA ’11, XiaoTing Zheng ’14, Nicholas Woods ’13 and Ethan Grund ’13; and former research assistants/lab managers Sara Royston, Katharine Henderson and Stephanie Tagliatela.

Studies in rodent epilepsy models suggest that GABAergic interneuron progenitor grafts can reduce hyperexcitability and seizures in temporal lobe epilepsy (TLE). Although integration of the transplanted cells has been proposed as the underlying mechanism for these disease-modifying effects, prior studies have not explicitly examined cell types and synaptic mechanisms for long-term seizure suppression. To address this gap, the researchers transplanted medial ganglionic eminence (MGE) cells from embryos into adult mice two weeks after induction of TLE.

The researchers found that TLE mice with bilateral MGE cell grafts had significantly fewer and milder electrographic seizures. These findings suggest that fetal GABAergic interneuron grafts may suppress pharmacoresistant seizures.

 

Grad Student Herman, Sultan Published in Evolution, Faculty 1000

Jacob Herman

Jacob Herman

Biology Ph.D. candidate Jacob Herman and Sonia Sultan, chair and professor of biology, professor of environmental studies, are the co-authors of an article titled “How stable ‘should’ epigenetic modifications be? Insights from adaptive plasticity and bet hedging,” published in Evolution, Issue 68(3), pages 632-43. Herman was the Private Investigator on the paper.

The article also was selected by Faculty 1000, a platform for life scientists that helps scientists to discover, discuss and publish research.

Sonia Sultan

Sonia Sultan

Epigenetics is the study of ways chemical reactions change the way an organism grows and develops, and the factors that influence them. Epigenetic modifications can be stable across the individual’s lifespan and in some species even persist across generations, or they can be reversible, but it is currently unclear how the persistence of epigenetic modifications may evolve. In this paper, Herman and Sultan provide insights from the theoretical advances in adaptive phenotypic plasticity to predict the conditions that would favor the evolution of stable versus reversible epigenetic modification as an adaptive environmental response both within and across generations.

At Wesleyan, Herman is interested in the evolutionary implications of developmental plasticity. In particular, he has been studying transgenerational plasticity, a phenomenon that occurs when environments experienced by parents (or even more remote generations) influence the phenotypes of offspring, without changing the DNA sequence.

“There is a growing body of research in both plants and animals that suggests that transgenerational plasticity can have important ecological and evolutionary impacts, including influences on response to selection and population persistence in stressful environments,” he said.

Polygonum persicaria

Polygonum persicaria

Herman’s doctoral research focused on adaptive seedling responses to grandparental and parental drought stress in the widespread, introduced plant Polygonum persicaria.

“We found that functionally appropriate responses to drought stress persist across at least two generations in this species. These adaptive effects enhanced the growth and survival of ‘grandchild’ seedling offspring grown in drought conditions,” he said.

Herman’s research is one part of the larger effort in the Sultan lab to understand how individual plants respond to key environmental stresses, such as drought, and how those responses influence species’ ecology and evolution.

Learn more about ongoing research in the Sultan Lab here.