Eric Sembrat's Test Bonanza

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Abstract coming soon.

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Abstract

Membrane proteins are the molecular gatekeepers of biology.  They govern the passage of charged and polar species in and out of cells, thus enabling the storage of potential energy that fuels life.  Despite their overwhelming importance, we still do not understand the basic physical reasons why membrane proteins associate and assemble to form stable structures in the lipid bilayer.  For soluble proteins, the burial of hydrophobic groups away from aqueous interfaces is a major driving force, but membrane-embedded proteins cannot experience hydrophobic forces, as the lipid bilayer lacks water. A fundamental conundrum thus arises: how does a greasy protein surface find its greasy protein partner in the greasy lipid bilayer to fold faithfully into its native structure? In our lab, we measure the thermodynamics of membrane protein assembly, directly in lipid bilayers, using model systems of membrane protein dimerization. We approach these three curious questions with a variety of experimental techniques including membrane protein purification and functional reconstitution, electrophysiology, x-ray crystallography, single-molecule TIRF microscopy and computational modeling.  With this, we are able to fully interrogate the physical driving forces that determine how and why greasy membrane proteins form stable structures inside the greasy lipid membrane.

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Abstract

Most pharmaceuticals are small organic molecules that work via noncovalent interactions with biological macromolecules. Although drugs have saved or improved countless lives, drug discovery remains an inexact science that involves much trial and error. My research group has been developing computer modeling tools to quickly characterize noncovalent protein-ligand interactions. Most of our tools are based on implicit ligand theory, a theoretical framework that I derived to predict how tightly molecules bind and how they influence the population of conformations accessed by their targets.

We have established that our methods are able to reproduce results of more computationally expensive approaches. We are working on making them more efficient and feasible to use with large libraries of chemical compounds. We have also advanced the theory of end-point binding free energy methods, in which binding affinity is predicted based on molecular simulations of the bound complex.

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Halloween in June: REGISTRATION IS OPEN

Wednesday, June 19, 2019

General registration is now open for Halloween in June; register here.

The College of Sciences and iGniTe Summer Launch Program present "Halloween in June," a costume party and variety show to celebrate the International Year of the Periodic Table of Chemical Elements on Thursday, June 27.

Come in your best costumes inspired by the periodic table or chemical elements. Winners of various categories will receive fabulous prizes.

Pulsate to the science rock music of Leucine Zipper and the Zinc Fingers (LZZF)

Punk-rock music and science share similar goals—to go boldly (loudly?) where no person has gone before. Leucine Zipper and The Zinc Fingers (LZZF) amalgamate music and science as a synthetic cross-disciplinary project to bring science to the people in a decidedly original medium.

Actual scientists (three of four are Georgia Tech faculty) and life-long punk rockers compose the band, so you can be sure that the lyrics are scientifically valid, and the tunes are rabidly arousing.  See them live and enjoy the spectacle of Earth's first genetically modified rock band!

Wallow in the dirty science of "Carbon and Cubic Feces" with David Hu

David Hu is an IgNobel Prize winner, mechanical engineering professor at Georgia Tech, and author of "How to Walk on Water and Climb Up Walls: Animal Movement and the Robots of the Future."

Human waste has substantial resource value: human urine contains phosphorus, potassium, nitrogen; and human feces contains mostly carbon. David will talk about the physics of excretion. In the law of urination, he will show that animals urinate for a constant duration, independent of body mass. In their study of cubic feces of the wombat, he will show how soft intestines can form corners in feces.

Laugh out loud with Lew Lefton's science humor

Lew Lefton is a faculty member in the Georgia Tech School of Mathematics, the assistant dean of information technology for the Georgia Tech College of Sciences, and associate vice president for research computing at Georgia Tech. With so many roles, he is a very important person.

But Lew is not just your ordinary VIP or computing/mathematics geek.  He's an accomplished and experienced comedian who has done stand up and improv comedy with a geeky twist for over 30 years. His unique talents are best summed up by his business card, which reads: Lew Lefton, Mathematician/Comedian, "He's funny and he can prove it."

Marvel at magic card trick and treats by Matt Baker

Matt Baker is an internationally renowned Georgia Tech mathematics professor by day and an accomplished magician by night. Matt currently serves as associate dean for faculty development in the Georgia Tech College of Sciences.

As a magician Matt has performed three times at the invitation-only Fechter’s Finger Flicking Frolic, the world’s premiere close-up magic convention. In 2018 he recorded a Penguin Live Acts show and lecture in Columbus, Ohio, and spent four days in Spain studying with Juan Tamariz, the world’s greatest living close-up magician. In July 2019, Matt will be lecturing at the International Brotherhood of Magicians Annual Convention in Scottsdale, Arizona.

Matt’s awards for magic include the Atlanta Society of Magicians' Top Dog Award and the Greater Atlanta Magician of the Year award. 

Plus periodic table dart game, photo booth, King of Pops, book signing, and much, much more!

 

Media Contact: 

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Summary: 

Listen to Leucine Zipper and the Zinc Fingers, Lew Lefton, and David Hu. Be amazed with Matt Baker's card magic!

Intro: 

Listen to Leucine Zipper and the Zinc Fingers, Lew Lefton, and David Hu. Be amazed with Matt Baker's card magic!

Alumni: 

Abstract

We will discuss the observations that necessitate a detail study of wind noise effects on the LIGO-India structure and different ways we plan to mitigate such a noise.

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ABSTRACT

I will present the reverberation-mapping study of the lowest-luminosity Seyfert 1 galaxy NGC 4395, based on the monitoring campaign in 2017 and 2018. The time delay of the Hα emission is measured as 83±14 min. Combining with the Hα velocity dispersion 426±1 km/s, black hole mass is determined as ∼10,000 Msun, which is the smallest reverberation mass, and comparable to the low mass end of heavy seed primordial black holes. Interestingly, NGC 4395 is consistent with the M-σ relation, when σ is constrained from the central region, indicating that the relation requires no hierarchical galaxy assembly or AGN feedback.

ABSTRACT

I will highlight some of the main results from a series of studies searching for observational signatures of AGN feedback using low-z AGNs. First, we find no direct evidence of SF quenching since the sSFR of strong outflow AGNs is comparable to that of SF galaxies. In contrast, non-outflow AGNs show much lower sSFR than SF galaxies. Second, our IFU study of z~0.1 AGNs shows that outflow is confined in a relatively small region, suggesting a limited impact of outflows. We typically detect a ring-like star-forming structure at the edge of the outflow, implying both negative and positive feedback for given objects. These results suggest no evidence of instantaneous feedback and the overall impact of AGN feedback seems rather limited in the present-day universe.

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Nature, Governance, and Sustainability in Costa Rica

Friday, June 14, 2019

Editor's Note: This story – narrative, photography, and slide show – is by the Georgia Tech students in the 2019 NGS-CR Study-Abroad Program.

In just five weeks, we interviewed a former vice president of Costa Rica, scrambled up the slopes of a volcano, and came face to face with sloths, vipers, and bullet ants. The Nature, Governance, and Sustainability in Costa Rica (NGS-CR) Study-Abroad Program has been an unbelievable experience. From the remote jungles of Sarapiqui to the stunning peaks of Monteverde, Costa Rica has inspired us to explore and learn at every turn.

Our program started in early May in the capital city of San Jose. We experienced new culture every step of the way, through the museums we visited and atop country’s highest volcano. We made a difference in the community by teaming up with Lead University to reduce plastic pollution by sorting and recycling plastic bottle caps. We also met with Kevin Casas Zamora, a former vice president of Costa Rica, and discussed the nation’s history and current policy concerns.

Next, we went deep into the tropical rainforest to La Selva Biological Station, one of the leading research institutions studying tropical ecology. Hundreds of species of trees towered over us, filled with multicolored bromeliads and orchids and teeming with strange insects and birds. Oh yeah, and sloths! 

Mornings were filled with the warbled calls of birds and the bellows of howler monkeys. Strikingly beautiful yellow and green tree frogs leaped into view when our flashlights found them during our night hikes. Cold rain fell seemingly out of nowhere to dash away the heat of day.

We learned about the history of chocolate, known here as the “drink of the gods.” We heard how locals are educating their communities about climate change and sustainable practices. We left knowing that a single hummingbird can effect change – and with a lot of chocolate.

We then traveled to Monteverde, a mountain town enveloped by clouds, where we welcomed the drop in temperature with open arms. We partnered with the Monteverde Institute, which aims to educate the local community about the importance of sustainability. Visiting small, sustainable farms forced us to confront the unique challenges of sustainable, organic farming.

We trudged through mud and cow manure to visit the farm of a direct descendant of one of the first Quaker families to settle in Monteverde. We were treated to delicious home-cooked meals made from all-natural ingredients, such as fresh, soft tortillas filled with hot gallo pinto, Costa Rica’s national dish, consisting of beans and rice.

Our trip to Monteverde also included delicious tasting of local coffee, and of course, the thrill of zip-lining through the forests.

Our experiences have been part of two interconnected classes, BIOL 4813: Tropical Biology & Sustainability and PHIL 3127: Science, Technology, and Human Values. These classes have integrated biological and social sciences so students can better understand how Costa Rica, the United States, and the world construct political mechanisms to organize societies and sustain natural systems.

Our instructors were Michael Goodisman, an associate professor in the School of Biological Sciences, and Juan Rogers, a professor in the School of Public Policy.

The NGS-CR Study-Abroad Program has been supported by the Office of International Education, the Steve A. Denning Chair for Global Engagement, and the Center for Serve-Learn-Sustain. The program is affiliated with the College of Sciences, and its courses are taught by faculty from the School of Biological Sciences in the College of Sciences and the School of Public Policy in the Ivan Allen College of Liberal Arts.

We are this story’s authors, the participants (and our majors) of the 2019 NGS-CR Study-Abroad Program:

  • Biology: Henry Crossley, Sarah Kuechenmeister, Amelia Smith, and Veronica Thompson
  • Biochemistry: Rajan Jayasankar
  • Environmental engineering: Miriam Campbell, Abigail Crombie, Catherine Mellette, and Isabelle Musmanno
  • Industrial engineering: Laura “CC” Gruber
  • Psychology: Katherine Chadwick
Media Contact: 

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Summary: 

In just five weeks, we interviewed a former vice president of Costa Rica, scrambled up the slopes of a volcano, and came face to face with sloths, vipers, and bullet ants. The Nature, Governance, and Sustainability in Costa Rica (NGS-CR) Study-Abroad Program has been an unbelievable experience. From the remote jungles of Sarapiqui to the stunning peaks of Monteverde, Costa Rica has inspired us to explore and learn at every turn.

Intro: 

In just five weeks, we interviewed a former vice president of Costa Rica, scrambled up the slopes of a volcano, and came face to face with sloths, vipers, and bullet ants. The Nature, Governance, and Sustainability in Costa Rica (NGS-CR) Study-Abroad Program has been an unbelievable experience. From the remote jungles of Sarapiqui to the stunning peaks of Monteverde, Costa Rica has inspired us to explore and learn at every turn.

Alumni: 

Benjamin Breer and His Favorite Element

Monday, June 17, 2019

The monthly series "My Favorite Element" is part of Georgia Tech's celebration of 2019 as the International Year of the Periodic Table of Chemical Elements, #IYPT2019GT. Each month a member of the Georgia Tech community will share his/her favorite element via video.

June’s edition features Benjamin Breer, a  double major in physics and aerospace engineering who just completed his first year at Georgia Tech.

Breer is also an undergraduate researcher in the Magnetospheres in the Outer Solar System research lab, led by Sven Simon, an associate professor in the School of Earth and Atmospheric Sciences.

Breer’s favorite element is hydrogen, the most abundant elements in the universe. “It’s as if you’re walking in a mall," Breer says in the video, "and every single person you see is a hydrogen atom."

Breer also cites research that may point to a sea of hydrogen under the surface of Jupiter – an ocean’s worth of the element that is under so much pressure, it takes a liquid metallic form.

Breer graduated from the Gwinnett School of Mathematics, Science, and Technology, in Lawrenceville, Georgia.

Renay San Miguel, communications officer in the College of Sciences, produced and edited the videos in this series. 

Other videos in this series are available at https://periodictable.gatech.edu/.

May 2019, G. P. "Bud" Peterson, president of Georgia Tech

April 2019: Kimberly Short, Ph.D. candidate

March 2019: Elayne Ashley, scientific glass blower

February 2019: Amit Reddi, assistant professor of chemistry and biochemistry

January 2019: Jeanine Williams, biochemistry major and track star

 

 

Media Contact: 

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Summary: 

To celebrate the International Year of the Periodic Table, Tech students, faculty, and staff talk about their favorite elements. For June, we have Benjamin Breer, a physics major who just completed his first year at Georgia Tech.

Intro: 

To celebrate the International Year of the Periodic Table, Tech students, faculty, and staff talk about their favorite elements. For June, we have Benjamin Breer, a physics major who just completed his first year at Georgia Tech.

Alumni: 

DNA Looping and Unlooping Yields Puzzling Results

Tuesday, June 11, 2019

From end to end, the human genome is about two meters long; yet it can pack to a length that’s about 1/15th the width of a human hair. That six-orders-of-magnitude compaction is accomplished by DNA molecules wrapping tightly around proteins called histones. Furthermore, tight DNA loops play important roles in gene regulation. 

The physics behind these sharp windings is not fully understood. Researchers believe that bendability of nucleic acid sequences is an important mechanical part of the process. Intuitively, researchers think that rigid sequences would not readily bend around the protein, because of the tight curves they would need to form. Conversely, flexible sequences would have more propensity to wind sharply.

For now, researchers don’t really know what sequences can form loops easily or not. But they can make relative comparisons based on the behavior of short sequences with “sticky” ends, which form a loop when they meet.

“While most researchers focus on the looping part, we became interested in the unlooping,” says Harold Kim, an associate professor in the School of Physics and member of the Parker H. Petit Institute of Bioengineering and Bioscience. “We thought unlooping is more closely related to the force exerted by the distorted DNA, just like the restoring force by a spring.”

“By looking into a reaction step that was deemed trivial, we stumbled upon these counterintuitive results.”

UNEXPECTED RESULTS

A recent study of short DNA sequences by Kim and former graduate student Jiyoun Jeong, however, yielded puzzling results. Published last month in Physical Review Letters, the findings could pave the way to properly identifying the sequence dependence of rigidity and flexibility in DNA.

The conventional wisdom is rigid DNA will have trouble looping and, once looped, will rapidly unloop. Conversely, flexible DNA will rapidly loop and slowly unloop. That is, looping and unlooping rates would be inversely correlated.

But when Jeong and Kim measured the looping and unlooping rates of various short DNA sequences, the results surprised them. What they found was a direct correlation: the longer it takes to loop, the longer it also takes to unloop.

EXPLAINING THE PUZZLE

Imagine you have a flexible rod and you try to form a loop. When the ends meet, you’ll have a loop that looks like an inverted teardrop: round at the top and pointed at the bottom, where the ends are joined. If this shape were the final form, looping and unlooping rates would be inversely correlated.

However, DNA is more than just a flexible rod. It is also a stack of base pairs, and stacked base pairs are preferred because the arrangement yields strong attractive interactions. According to Kim, the inverted-teardrop loop can transform into a circle by stacking the base pairs at the sticky ends. Although in this shape the bending stress at the joint increases, the loop doesn’t open easily because it is more stable.

Now imagine putting a flexible segment in the middle of a sequence that alone would have looped slowly. Like a hinge, the flexible segment hastens looping. When looped, the ends can stack to form a teardrop shape, with a sharply pointed top and a rounded bottom at the joint. The stacking, however, is less likely to hold because the teardrop loop requires an even higher bending stress at the joint than the circular loop. With less likelihood of stacking, the loop breaks faster.

In another experiment, they designed a loop geometry where the sticky ends cannot be stacked. Consistent with the stacking model, looping and unlooping rates were inversely correlated.

“By looking into a reaction step that was deemed trivial, we stumbled upon these counterintuitive results,” Kim says. “Now we have the toolkit to measure the stress resistances of different base pair stacks.”

 The work was supported by National Institutes of Health Grant R01GM112882 and National Science Foundation Grant 1517507.

Media Contact: 

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Summary: 

Puzzling results of a recent study of short DNA sequences by Harold Kim and former graduate student Jiyoun Jeong could pave the way to properly identifying the sequence dependence of rigidity and flexibility in DNA.

Intro: 

Puzzling results of a recent study of short DNA sequences by Harold Kim and former graduate student Jiyoun Jeong could pave the way to properly identifying the sequence dependence of rigidity and flexibility in DNA.

Alumni: 

President Peterson and His Favorite Element

Wednesday, May 22, 2019

The monthly series "My Favorite Element" is part of Georgia Tech's celebration of 2019 as the International Year of the Periodic Table of Chemical Elements, #IYPT2019GT. Each month a member of the Georgia Tech community will share his/her favorite element via video.

Dr. G.P. "Bud" Peterson is the 11th president of Georgia Institute of Technology. 

In this capacity he oversees a top-ten public research university with more than 36,900 students and research expenditures of more than $908 million.

Throughout his career, Dr. Peterson has helped establish national education and research agendas, serving on numerous industry, government, and academic task forces and committees. A distinguished scientist, Dr. Peterson was selected in 2008 by President George W. Bush to serve on the National Science Board through 2014. The Board oversees the National Science Foundation (NSF) and advises the President and Congress on national policy related to science and engineering research and education.

Dr. Peterson earned undergraduate degrees in mechanical engineering and mathematics as well as a master's degree in engineering from Kansas State University. He earned his doctoral degree in mechanical engineering at Texas A&M University.

In January 2019, Dr. Peterson announced he will retire as Georgia Tech's president in summer 2019.

His favorite element is .... Watch the video!

Renay San Miguel, communications officer in the College of Sciences, produced and edited the videos in this series. 

Other videos in this series are available at https://periodictable.gatech.edu/.

April 2019: Kimberly Short, Ph.D. candidate

March 2019: Elayne Ashley, scientific glass blower

February 2019: Amit Reddi, assistant professor of chemistry and biochemistry

January 2019: Jeanine Williams, biochemistry major and track star

 

 

Media Contact: 

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Summary: 

To celebrate the International Year of the Periodic Table, Tech students, faculty, and staff talk about their favorite elements. For May, we have President G.P. "Bud" Peterson, the 11th president of Georgia Institute of Technology.

Intro: 

To celebrate the International Year of the Periodic Table, Tech students, faculty, and staff talk about their favorite elements. For May, we have President G.P. "Bud" Peterson, the 11th president of Georgia Institute of Technology.

Alumni: 

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