Eric Sembrat's Test Bonanza

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Abstract

Protein and chitosan are two types of biopolymers abundant in nature. Proteins are the “workhorse” molecules of life and their dynamical behavior governs human physiological functions and underlies many diseases. Chitosan, a polysaccharide produced from shellfish, can be used to make smart hydrogels that find a wide range of applications in medicine, pharmacy, and bioelectronics. In this talk, I will introduce a computer simulation tool called continuous constant pH molecular dynamics (CpHMD) and discuss how it can be used to advance the understanding of the electrostatic mechanisms and dynamical behavior of proteins and chitosan-based materials. In the first two examples, CpHMD was used to reveal nucleophilic hotspots [1] and conformational landscape of protein kinases [2], which are cellular signaling molecules involved in cancer and many other diseases.

These studies led to a new strategy for targeted covalent inhibitor design and suggested a paradigm shift in our understanding of conformational plasticity of kinases, which presents a challenge but also opportunity in kinase drug discovery. In the later examples, CpHMD was used to explore pHresponsive self-assembly [3] and switchable crosslinking mechanisms for programming hydrogel materials [4]. Our work demonstrated a pKa gradient for a dynamical polysaccharide system and how it allows a persistent but erasable gradient in the structural and mechanical properties of the formed hydrogel.

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Abstract

At the beginning of the 20th century, Einstein changed how we think about time. Now, early in the 21st century, the measurement of time is being revolutionized by the ability to cool a gas of atoms to temperatures millions of times lower than any naturally occurring temperature in the universe.   

Atomic clocks, the best timekeepers ever made, are one of the scientific and technological wonders of modern life.  Such super-accurate clocks are essential to industry, commerce, and science; they are the heart of the global positioning system (GPS), which guides cars, airplanes, and hikers to their destinations. 

Today, the best primary atomic clocks use ultracold atoms, achieve accuracies of about one second in 300 million years, and are getting better all the time. At the same time, a new generation of atomic clocks is leading us to re-define what we mean by time.  

Super-cold atoms, with temperatures that can be below a billionth of a degree above absolute zero, use and allow tests of some of Einstein's strangest predictions. 

This public lecture will be a lively, multimedia presentation, including exciting experimental demonstrations and down-to-earth explanations about some of today's hottest (and coolest) science.

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DNA is an iconic molecule that forms a double helical structure, providing the basis for genetic inheritance, and its physical properties have been studied for decades. In this talk, I will present evidence that sequence and methylation dependent physical properties of DNA such as flexibility and self-association may be important for biological functions [1,2]. In addition, I will present a new application of DNA where mechanical modulations of cell behavior can be studied at the single molecule level using rupturable DNA tethers [3]. We found that cells can change their behavior dramatically in response to just two molecules strongly tugging on them [4].

 

References.

[1] R. Vafabakhsh and T. Ha, “Extreme bendability of DNA less than 100 base pairs long revealed by single molecule cyclization”, Science 337, 1097-1101 (2012). 

[2] T. Ngo, Q. Zhang, R. Zhou, J. G. Yodh and T. Ha, “Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility”, Cell 160, 1135-1144 (2015). 

[3] X. Wang and T. Ha, “Defining Single Molecular Forces Required to Activate Integrin and Notch Signaling”, Science 340, 991-994 (2013). 

[4] M. Roein-Peikar, Q. Xu, X. Wang and T. Ha, “Ultrasensitivity of cell adhesion to the presence of mechanically strong ligands,” Physical Review X (2016).

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Abstract

Wrinkling instability of compressed stiff thin films bound to soft substrates has been studies for many years and the formation and evolution of wrinkles is well understood. Similar wrinkling instabilities also play important role in biology during the development of organs, such as brains and guts, and during the formation of bacterial biofilms grown on soft substrates. In recent years, the wrinkling instability has been exploited to create structures with tunable drag, wetting, adhesion, and to create a template for wire formation. While these studies successfully demonstrated the proofs of concepts, the quantitative understanding is still lacking, because very little is known about how wrinkled surfaces deform in response to interactions with environment. To address this issue, we investigated the linear response of wrinkled structures to external forces. By mapping the problem to the Landau theory of phase transitions, we demonstrated that the linear response to external forces diverges near the onset of wrinkling instability with the usual mean field exponent found in critical phenomena. Interactions with environment also dictate the morphology of wrinkled patterns in growing biological systems.

I will discuss the formation of wrinkling patterns in bacterial biofilms grown on agar substrates, which usually have radial stripe patterns near the outer edge and zigzag herringbone-like patterns in the core. The observed wrinkling patterns result from uneven stress distribution in the biofilm as a consequence form the depletion of slowly diffusing nutrients underneath the biofilm, which are required for the bacterial growth.

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Howey Physics Building Lecture Halls Undergo Multiphase Renovation

Friday, August 2, 2019

Originally constructed in 1967, the Howey Physics Building is undergoing a major renovation for the first time in more than 50 years. With an emphasis on respecting the historic character of the structure, while balancing the needs for improved instructional space, renovation efforts (which began on four of its lecture halls in May) will occur over several semesters. 

“Being an older building with heavily used instructional spaces for large lecture courses, it is expected that this renovation will be a welcome change for students and faculty alike,” said Sabrina Miller, assistant registrar for Academic Scheduling in the Office of the Registrar.

In the first phase of construction, which will last through mid-August, much of the older infrastructure will be addressed with the replacement of the water piping and the HVAC system. Additional renovations during this time will include addressing a structural problem with the floor slab, replacing lobby masonry, and updating and expanding the restrooms including creating a gender-inclusive restroom. 

Because the Institute is focused on ensuring that courses scheduled in the building are a good fit for capacity and accessibility, the renovation project will be halted at the end of the summer to allow for Fall 2019 classes to resume in all four halls of the building.

The project will resume during the Spring 2020 semester, with a focus on lecture halls 3 and 4. During that time, hall 2 will serve as a construction noise buffer, and hall 1 will remain open for classes. During the Summer 2020 semester, all four lecture halls will be undergoing renovation. At the end of the summer, work in lecture halls 3 and 4 will be complete, and construction will shift to lecture halls 1 and 2 during the Fall 2020 semester. The entire renovation project should be completed in time for classes starting in January 2021.

Further updates will be available as the renovation progresses. 

Media Contact: 

Nicolas Palfrey
Facilities Design & Construction Project Manager

Summary: 

Originally constructed in 1967, the Howey Physics Building is undergoing a major renovation for the first time in more than 50 years.

Intro: 

Originally constructed in 1967, the Howey Physics Building is undergoing a major renovation for the first time in more than 50 years.

Alumni: 

NASA Administrator Gets Closeup Look at Georgia Tech’s Role in Future Space Missions

Friday, August 2, 2019

With the 50th anniversary of the Apollo 11 moon landing still fresh in everyone’s minds, NASA Administrator Jim Bridenstine this week came to Georgia Tech to get a status report on what the next generation of astronauts may take with them into space five years from now.

“We have to make sure we get this right, because quite frankly, if we’re going to land on the moon in 2024, we have to start now,” Bridenstine said during a July 31 tour of NASA-related research labs in the Daniel Guggenheim School of Aerospace Engineering and the School of Chemistry and Biochemistry.

The NASA delegation included Georgia Congressman Tom Graves; representatives for U.S. Senator David Perdue and Congressman Jody HiceMike Green, director for communications & operations and chief of staff of NASA’s Space Technology Mission Directorate; and Robert Knotts, Georgia Tech’s director of federal relations.

“When you look at what Georgia Tech is doing with NASA, there’s a lot of not just research, but applications that Georgia Tech is developing,” Bridenstine said. He was referring to the studies underway in the REVEALS(Radiation Effects on Volatiles and Exploration of Asteroids and Lunar Surfaces) lab run by chemistry and physics professor Thomas Orlando.

REVEALS focuses on the physics and chemistry involved in how solar winds and micrometeorite impacts could help produce water – from molecular hydrogen and oxygen – for astronaut habitats on the Moon. The research also studies how the lunar regolith – the dirt, rocks, and other materials covering solid rock – could be harvested for building materials. REVEALS is also looking at the development of superdurable graphene-based composites for spacesuits, as well as how radiation detectors could be integrated into the suit materials to provide real-time readouts.

“These efforts will mitigate health risks,” Orlando said. “Bridenstine and Graves were able to see the prototype detectors, the polymers and [their] antistatic properties, as well as the novel table-top accelerator we will use to test these.  These efforts are very important to NASA's ARTEMIS program, which plans to sends humans to the Moon by 2024.”

Back to the Moon with ARTEMIS

The NASA delegation’s visit to Georgia Tech included presentations at the School of Aerospace Engineering, which showed off samples of its nanosatellites known as CubeSats. These are currently used in RANGE(Ranging and Nanosatellite Guidance Experiment) and TARGIT (Tethering and Ranging Mission of the Georgia Institute of Technology.)

A RANGE CubeSat successfully launched in December 2018, making it the first time a Georgia Tech-built satellite was placed in orbit. Georgia Tech aerospace engineering students were also involved in the July 2019 launch of Lightsail-2, a CubeSat containing a solar sail from the Planetary Society championed by noted science advocate Bill Nye.

“Georgia Tech is building some of the propulsion capabilities for some of the CubeSats that are going to be going around the Moon for ARTEMIS 1 [an unmanned flight set to launch in 2020]” Bridenstine said. “We have not been to the Moon with humans since 1972. We’re going back. The first mission will be uncrewed. It’ll be a crew-type vehicle but without crew.”

Bridenstine was impressed with what he saw. “All of those in situ resource utilization capabilities that are being developed here at Georgia Tech on behalf of NASA are amazing,” he said. Bridenstine held samples of the graphene-based materials being tested for future spacesuits and examined them while Phillip First, a professor in the School of Physics who is part of the REVEALS team, explained his research.

“When radiation goes through a material and creates some kind of defect, you detect it in most cases with luminescence in the material.” First said. “We want an electrical readout, so that you can dynamically monitor exactly the amount of radiation exposure.”

The REVEALS team, along with members of the School of Industrial and Systems Engineering, and the Georgia Tech Research Institute, also contribute to HOME, a new NASA-funded space research institute led by former astronaut Steve Robinson, REVEALS co-investigative lead based at the University of California, Davis. Orlando said HOME leverages Georgia Tech’s strengths in data analytics, autonomous control, sensors, and robotics.

“REVEALS is part of the Center for Space Technology and Research, which was started eight years ago with the intention of contributing significantly to future long-term efforts in space science and technology,” Orlando said. “The efforts in REVEALS and HOME have been, and will continue to be, the cornerstone of Georgia Tech’s efforts in human flight and human exploration of destinations such as the Moon and Mars.”

The student-led difference

At the REVEALS portion of the tour, Orlando told Bridenstine that the research had attracted more students to the Institute. “They would not have come to Georgia Tech unless we had this program,” he said. “Georgia Tech already has a very strong program, but this has been a real magnet for bringing in people who are interested in space exploration.”

Some of Orlando’s students participated in the presentations, and that also impressed Bridenstine.

“The best thing about all of this is that Georgia Tech is embedding its students into these projects,” he said. “NASA turns to Georgia Tech is do these projects, but the most valuable thing is that the students are getting hands-on exposure to these capabilities. They’re not just learning chemistry, calculus, physics, and all of the mathematics that are necessary. They’re also applying that in real time to very real projects that are critically important to NASA, so that when they graduate, ultimately they’re ready to go to work.

“We’re thrilled with the partnership – the relationship between NASA and Georgia Tech – and we’re looking forward to it continuing for a long time.”

Content Images: 
Intro: 

Jim Bridenstine surveys College of Sciences research on space suits, habitats.

Alumni: 

Jasmine Howard and Her Favorite Element

Tuesday, August 6, 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.

The August edition features Jasmine A. Howard, an MBA candidate in the Scheller College of Business. 

After graduating from Red Bank High School, in Chattanooga, Tennessee, Howard attended the University of Tennessee, Knoxville. She earned a B.S. in business administration in 2012. 

Howard says she chose to do her MBA in the Scheller College of Business "for its academic specialties in business analytics and technology management, for the world-class outcomes of the Jones MBA Career Center, and for the tight-knit collaborative community of the full-time MBA program."

Howard spent this summer as a product marketing intern at Mailchimp, in Atlanta. When the academic year resumes, she will be a graduate assistant in Scheller's marketing department. 

After she earns the MBA, Howard plans to "work in technology or media in a role that leverages my strengths in strategy, marketing analytics, and communications."

Howards favorite element is gold. Find out why in 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/.

July 2019, Jennifer Leavey, principal academic professional, director of the Georgia Tech Urban Honeybee Project, and much more

June 2019, Benjamin Breer, undergraduate double major in physics and aerospace engineering 

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 August we have Jasmine Howard, an MBA candidate in the Scheller College of Business.

Intro: 

To celebrate the International Year of the Periodic Table, Tech students, faculty, and staff talk about their favorite elements. For August we have Jasmine Howard, an MBA candidate in the Scheller College of Business.

Alumni: 

Hackers Could Use Connected Cars to Gridlock Whole Cities

Monday, July 29, 2019

In the year 2026, at rush hour, your self-driving car abruptly shuts down right where it blocks traffic. You climb out to see gridlock down every street in view, then a news alert on your watch tells you that hackers have paralyzed all Manhattan traffic by randomly stranding internet-connected cars.

Flashback to July 2019, the dawn of autonomous vehicles and other connected cars, and physicists at the Georgia Institute of Technology and Multiscale Systems, Inc. have applied physics in a new study to simulate what it would take for future hackers to wreak exactly this widespread havoc by randomly stranding these cars. The researchers want to expand the current discussion on automotive cybersecurity, which mainly focuses on hacks that could crash one car or run over one pedestrian, to include potential mass mayhem.

They warn that even with increasingly tighter cyber defenses, the amount of data breached has soared in the past four years, but objects becoming hackable can convert the rising cyber threat into a potential physical menace.

“Unlike most of the data breaches we hear about, hacked cars have physical consequences,” said Peter Yunker, who co-led the study and is an assistant professor in Georgia Tech’s School of Physics.

It may not be that hard for state, terroristic, or mischievous actors to commandeer parts of the internet of things, including cars.

“With cars, one of the worrying things is that currently there is effectively one central computing system, and a lot runs through it. You don’t necessarily have separate systems to run your car and run your satellite radio. If you can get into one, you may be able to get into the other,” said Jesse Silverberg of Multiscale Systems, Inc., who co-led the study with Yunker 

Freezing traffic solid

In simulations of hacking internet-connected cars, the researchers froze traffic in Manhattan nearly solid, and it would not even take that to wreak havoc. Here are their results, and the numbers are conservative for reasons mentioned below.

“Randomly stalling 20 percent of cars during rush hour would mean total traffic freeze. At 20 percent, the city has been broken up into small islands, where you may be able to inch around a few blocks, but no one would be able to move across town,” said David Yanni, a graduate research assistant in Yunker’s lab.

Not all cars on the road would have to be connected, just enough for hackers to stall 20 percent of all cars on the road. For example, if 40 percent of all cars on the road were connected, hacking half would suffice.

Hacking 10 percent of all cars at rush hour would debilitate traffic enough to prevent emergency vehicles from expediently cutting through traffic that is inching along citywide. The same thing would happen with a 20 percent hack during intermediate daytime traffic.

The researchers’ results appear in the journal Physical Review E on July 20, 2019. The study is not embargoed.

[Ready for graduate school? Here's how to apply to Georgia Tech.

It could take less

For the city to be safe, hacking damage would have to be below that. In other cities, things could be worse.

“Manhattan has a nice grid, and that makes traffic more efficient. Looking at cities without large grids like Atlanta, Boston, or Los Angeles, and we think hackers could do worse harm because a grid makes you more robust with redundancies to get to the same places down many different routes,” Yunker said.

The researchers left out factors that would likely worsen hacking damage, thus a real-world hack may require stalling even fewer cars to shut down Manhattan.

“I want to emphasize that we only considered static situations – if roads are blocked or not blocked. In many cases, blocked roads spill over traffic into other roads, which we also did not include. If we were to factor in these other things, the number of cars you’d have to stall would likely drop down significantly,” Yunker said.

The researchers also did not factor in ensuing public panic nor car occupants becoming pedestrians that would further block streets or cause accidents. Nor did they consider hacks that would target cars at locations that maximize trouble.

They also stress that they are not cybersecurity experts, nor are they saying anything about the likelihood of someone carrying out such a hack. They simply want to give security experts a calculable idea of the scale of a hack that would shut a city down.

The researchers do have some general ideas of how to reduce the potential damage.

“Split up the digital network influencing the cars to make it impossible to access too many cars through one network,” said lead author Skanka Vivek, a postdoctoral researcher in Yunker’s lab. “If you could also make sure that cars next to each other can’t be hacked at the same time that would decrease the risk of them blocking off traffic together.”

Traffic jams as physics

Yunker researches in soft matter physics, which looks at how constituent parts – in this case, connected cars – act as one whole physical phenomenon. The research team analyzed the movements of cars on streets with varying numbers of lanes, including how they get around stalled vehicles and found they could apply a physics approach to what they observed.

“Whether traffic is halted or not can be explained by classic percolation theory used in many different fields of physics and mathematics,” Yunker said.

Percolation theory is often used in materials science to determine if a desirable quality like a specific rigidity will spread throughout a material to make the final product uniformly stable. In this case, stalled cars spread to make formerly flowing streets rigid and stuck.

The shut streets would be only those in which hacked cars have cut off all lanes or in which they have become hindrances that other cars can’t maneuver around and do not include streets where hacked cars still allow traffic flow.

The researchers chose Manhattan for their simulations because a lot of data was available on that city’s traffic patterns.

Also READ: Georgia Tech's cybersecurity researchers tackle the internet of things 

The study was coauthored by Skanda Vivek and David Yanni of Georgia Tech and Jesse Silverberg of Multiscale Systems, Inc. Any findings, conclusions, and recommendations are those of the authors.

Writer & Media Representative: Ben Brumfield (404-660-1408), email: ben.brumfield@comm.gatech.edu

Georgia Institute of Technology
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Atlanta, Georgia  30332-0181  USA

Summary: 

In a future where self-driving and other internet-connected cars share the roads with the rest of us, hackers could not only wreck the occasional vehicle but possibly compound attacks to gridlock whole cities by stalling out a limited percentage of connected cars. Physicists calculated how many stalled cars would cause how much mayhem.

Intro: 

In a future where self-driving and other internet-connected cars share the roads with the rest of us, hackers could not only wreck the occasional vehicle but possibly compound attacks to gridlock whole cities by stalling out a limited percentage of connected cars. Physicists calculated how many stalled cars would cause how much mayhem.

Alumni: 

External Research Funding for FY2019 Ends on a High Note

Tuesday, July 23, 2019

College of Sciences faculty raised a historic amount of external research funding in fiscal year 2019. At $70.5 million, the FY2019 total continues the College’s steady gains in external grants for the past several years. The ability to attract research funds bodes well for the College’s research productivity, ability to train students, and opportunities for new discoveries in fundamental science for many years to come, says Associate Dean for Research Julia Kubanek.

Scientific research to discover new knowledge and solve problems is hard and costs money, says M.G. Finn, professor and chair in the School of Chemistry and Biochemistry. Results are not guaranteed. “How do we support an endeavor that has many more ‘failures’ than successes?”

External funding is essential. “It helps connect our faculty to the most important fundamental and applied problems among a limitless set of possible projects,” Finn says. “It also provides the resources to give our students the chance to fail repeatedly, and thereby learn how to succeed.  Increasing funding is a good sign that we are selecting good topics to research, failing in productive ways, and ultimately succeeding in uncovering new knowledge and valued applications of that knowledge.”  

The College of Sciences’ success can be attributed to two other factors. Faculty are applying for grant dollars at increasing rates, says Kubanek, who is also a professor in the Schools of Biological Sciences and of Chemistry and Biochemistry. And “we are continuing to submit to federal funding agencies high-quality proposals, despite the increase in reporting, compliance, and other requirements, thanks to staff who support principal investigators in preparing proposals and managing grants.”

 “External funding is essential for our mission of providing students with an outstanding training and fostering a vibrant environment of transformative research,” says Pablo Laguna, professor and chair in the School of Physics. The school saw a dramatic rise in external funding, almost doubling from FY2018. “The rise in external funding in FY2019 reflects the commitment of my colleagues to ensure that we accomplish this mission. New awards in the areas of Astrophysics, Physics of Living Systems, and Atomic and Molecular and Optical Physics were largely responsible for this increase.”

The awards support a wide range of research activities, from exploration of Jupiter’s moon Europa (Britney Schmidt, School of Earth and Atmospheric Sciences), to algebraic geometry and extremal combinatorics (Greg Blekherman, School of Mathematics), to wearable hydration technologies (Mindy Millard-Stafford, School of Biological Sciences).

Support came mostly from public sources. For example, Nepomuk Otte received NASA funding for the project “Development of a Photon Detection Module for the Detection of Cosmogenic Neutrinos.” The project aims to develop instrumentation to detect ultra-relativistic neutrinos of astrophysical origin.

 Neutrinos are elementary particles that help us understand the origin and composition of the highest energy cosmic rays. Cosmic rays are charged particles, which bombard the Earth from all directions. “Where they come from, what their composition is, and how they acquire their relativistic energies is a century-old mystery,” says Otte, who is an associate professor in the School of Physics. “One way to find out is by measuring neutrinos, which are produced by these cosmic rays. With the instrumentation developed in this project it will be possible to build new experiments that have the sensitivity to detect ultra-relativisitic neutrinos for the first time.”  

Meanwhile, Vinayak Agarwal received ongoing National Institutes of Health funding for the project “Understanding Natural Production of Polybrominated Toxins and Pollutants.” Molecules bearing several bromine atoms produced naturally in marine ecosystems can harm human health and the environment. “We do not know how these molecules are made, nor the identities of their producers,” says Agarwal, who is an assistant professor in the Schools of Chemistry and Biochemistry and of Biological Sciences. This research aims to bridge these knowledge gaps and could affect public health policies to mitigate human exposure to natural harmful compounds.

Media Contact: 

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

Summary: 

College of Sciences faculty raised a historic amount of external research funding in fiscal year 2019. At $70.5 million, the FY2019 total continues the College’s steady gains in external grants for the past several years.

Intro: 

College of Sciences faculty raised a historic amount of external research funding in fiscal year 2019. At $70.5 million, the FY2019 total continues the College’s steady gains in external grants for the past several years.

Alumni: 

Abstract

It has been almost 90 years since the neutrino was first proposed. While we have learned a great deal about it in that time, this enigmatic particle continues to puzzle us to this day. Extremely hard to detect, with a tiny mass and rather unusual properties, neutrinos have given us a first glance of what lies beyond the Standard Model of Particle Physics and, more recently, they have opened a new window to explore phenomena in the Universe. In this colloquium, I outline our current neutrino knowledge, the potential for discoveries and the implications they might have to the general physics landscape. I pay particular attention to the role of two fascinating neutrino experiments, IceCube and Canada’s own SNO+, as well as future detection technologies that could change the way we search for these elusive particles.

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