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A Mathematical Model Reveals Long-Distance Cell Communication Mechanism
How can tens of thousands of people in a large football stadium all clap together with the same beat even though they can only hear the people near them clapping?
A combination of a partial differential equation and a synthetic circuit in microbes answers this question. An interdisciplinary collaborative team of Professor Jae Kyoung Kim at KAIST, Professor Krešimir Josić at the University of Houston, and Professor Matt Bennett at Rice University has identified how a large community can communicate with each other almost simultaneously even with very short distance signaling. The research was reported at Nature Chemical Biology.
Cells often communicate using signaling molecules, which can travel only a short distance. Nevertheless, the cells can also communicate over large distances to spur collective action. The team revealed a cell communication mechanism that quickly forms a network of local interactions to spur collective action, even in large communities.
The research team used an engineered transcriptional circuit of combined positive and negative feedback loops in E. coli, which can periodically release two types of signaling molecules: activator and repressor. As the signaling molecules travel over a short distance, cells can only talk to their nearest neighbors. However, cell communities synchronize oscillatory gene expression in spatially extended systems as long as the transcriptional circuit contains a positive feedback loop for the activator.
Professor Kim said that analyzing and understanding such high-dimensional dynamics was extremely difficult. He explained, “That’s why we used high-dimensional partial differential equation to describe the system based on the interactions among various types of molecules.” Surprisingly, the mathematical model accurately simulates the synthesis of the signaling molecules in the cell and their spatial diffusion throughout the chamber and their effect on neighboring cells.
The team simplified the high-dimensional system into a one-dimensional orbit, noting that the system repeats periodically. This allowed them to discover that cells can make one voice when they lowered their own voice and listened to the others. “It turns out the positive feedback loop reduces the distance between moving points and finally makes them move all together. That’s why you clap louder when you hear applause from nearby neighbors and everyone eventually claps together at almost the same time,” said Professor Kim.
Professor Kim added, “Math is a powerful as it simplifies complex thing so that we can find an essential underlying property. This finding would not have been possible without the simplification of complex systems using mathematics."
The National Institutes of Health, the National Science Foundation, the Robert A. Welch Foundation, the Hamill Foundation, the National Research Foundation of Korea, and the T.J. Park Science Fellowship of POSCO supported the research.
(Figure: Complex molecular interactions among microbial consortia is simplified as interactions among points on a limit cycle (right).)
2019.10.15 View 27089 -
Two Professors Recognized for the National R&D Excellence 100
< Professor Haeng-Ki Lee (left) and Professor Jeong-Ho Lee (right) >
Two KAIST professors were listed among the 2019 National R&D Excellence 100 announced by the Ministry of Science and ICT and the Korea Institute of S&T Evaluation and Planning.
Professor Haeng-Ki Lee from the Department of Civil and Environmental Engineering was recognized in the field of mechanics and materials for his research on developing new construction materials through the convergence of nano- and biotechnologies.
In the field of life and marine science, Professor Jeong-Ho Lee from the Graduate School of Medical Science and Engineering was lauded for his research of diagnostic tools and therapies for glioblastoma and pediatric brain tumors.
A certificate from the Minister of Ministry of Science and ICT will be conferred to these two professors, and their names will be inscribed on a special 2019 National R&D Excellence 100 plaque to celebrate their achievements. The professors will also be given privileges during the process of new R&D project selection.
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2019.10.15 View 11980 -
Professor Byong-Guk Park Named Scientist of October
< Professor Byong-Guk Park >
Professor Byong-Guk Park from the Department of Materials Science and Engineering was selected as the ‘Scientist of the Month’ for October 2019 by the Ministry of Science and ICT and the National Research Foundation of Korea. Professor Park was recognized for his contributions to the advancement of spin-orbit torque (SOT)-based magnetic random access memory (MRAM) technology. He received 10 million KRW in prize money.
A next-generation, non-volatile memory device MRAM consists of thin magnetic films. It can be applied in “logic-in-memory” devices, in which logic and memory functionalities coexist, thus drastically improving the performance of complementary metal-oxide semiconductor (CMOS) processors. Conventional MRAM technology is limited in its ability to increase the operation speed of a memory device while maintaining a high density.
Professor Park tackled this challenge by introducing a new material, antiferromagnet (IrMn), that generates a sizable amount of SOT as well as an exchange-bias field, which makes successful data writing possible without an external magnetic field. This research outcome paved the way for the development of MRAM, which has a simple device structure but features high speeds and density.
Professor Park said, “I feel rewarded to have forwarded the feasibility and applicability of MRAM. I will continue devoting myself to studying further on the development of new materials that can help enhance the performance of memory devices."
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2019.10.10 View 10012 -
Object Identification and Interaction with a Smartphone Knock
(Professor Lee (far right) demonstrate 'Knocker' with his students.)
A KAIST team has featured a new technology, “Knocker”, which identifies objects and executes actions just by knocking on it with the smartphone. Software powered by machine learning of sounds, vibrations, and other reactions will perform the users’ directions.
What separates Knocker from existing technology is the sensor fusion of sound and motion. Previously, object identification used either computer vision technology with cameras or hardware such as RFID (Radio Frequency Identification) tags. These solutions all have their limitations. For computer vision technology, users need to take pictures of every item. Even worse, the technology will not work well in poor lighting situations. Using hardware leads to additional costs and labor burdens.
Knocker, on the other hand, can identify objects even in dark environments only with a smartphone, without requiring any specialized hardware or using a camera. Knocker utilizes the smartphone’s built-in sensors such as a microphone, an accelerometer, and a gyroscope to capture a unique set of responses generated when a smartphone is knocked against an object. Machine learning is used to analyze these responses and classify and identify objects.
The research team under Professor Sung-Ju Lee from the School of Computing confirmed the applicability of Knocker technology using 23 everyday objects such as books, laptop computers, water bottles, and bicycles. In noisy environments such as a busy café or on the side of a road, it achieved 83% identification accuracy. In a quiet indoor environment, the accuracy rose to 98%.
The team believes Knocker will open a new paradigm of object interaction. For instance, by knocking on an empty water bottle, a smartphone can automatically order new water bottles from a merchant app. When integrated with IoT devices, knocking on a bed’s headboard before going to sleep could turn off the lights and set an alarm. The team suggested and implemented 15 application cases in the paper, presented during the 2019 ACM International Joint Conference on Pervasive and Ubiquitous Computing (UbiComp 2019) held in London last month.
Professor Sung-Ju Lee said, “This new technology does not require any specialized sensor or hardware. It simply uses the built-in sensors on smartphones and takes advantage of the power of machine learning. It’s a software solution that everyday smartphone users could immediately benefit from.” He continued, “This technology enables users to conveniently interact with their favorite objects.”
The research was supported in part by the Next-Generation Information Computing Development Program through the National Research Foundation of Korea funded by the Ministry of Science and ICT and an Institute for Information & Communications Technology Promotion (IITP) grant funded by the Ministry of Science and ICT.
Figure: An example knock on a bottle. Knocker identifies the object by analyzing a unique set of responses from the knock, and automatically launches a proper application or service.
2019.10.02 View 27946 -
Professor Hyun Gyu Park Appointed as Associate Editor for Biosensors and Bioelectronics
Professor Hyun Gyu Park from the Department of Chemical and Biomolecular Engineering was appointed as an associate editor for Biosensors and Bioelectronics, an international journal published by Elsevier.
Biosensors and Bioelectronics is one of the top SCI journals in the fields of chemistry and analytical science (IF 9.518 as of 2018). Professor Park was recognized and appointed as the associate editor for this journal due to his outstanding research achievements in the fields of nucleic acid engineering, biosensors, and nanobiotechnology.
Professor Park will serve as the associate editor from this October until December 2021.
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2019.10.01 View 7562 -
Professor Ki-Jun Yoon selected as the 2019 SUHF Young Investigator
< Professor Ki-Jun Yoon >
Professor Ki-Jun Yoon from the Department of Biological Sciences was named one of four recipients of the 2019 Suh Kyung-Bae Science Foundation (SUHF) Young Investigator Awards.
The SUHF is a non-profit organization established in 2016 and funded by a personal donation of 300 billion KRW in shares from Chairman and CEO Kyung-Bae Suh of the Amorepacific Group. The primary purpose of the foundation is to serve as a platform to nurture and provide comprehensive long-term support for creative and passionate young Korean scientists committed to pursuing research in the field of life sciences. The SUHF selects three to five scientists through an open recruiting process every year, and grants each scientist a maximum of 2.5 billion KRW over a period of up to five years.
Since January this year, the foundation received 83 research proposals from scientists across the nation, especially from those who had less than five years of experience as professors, and selected the four recipients, including Professor Yoon.
Professor Yoon was recognized for his contributions to the advancement of research on how post-transcriptional mechanisms may modulate stem cell properties. His research project involves deciphering the molecular mechanisms controlling RNA metabolism in neural stem cells during normal development, and how alterations in RNA regulatory programs lead to human brain disorders.
< (From left) Professor Joo-Hong Park, Professor Yuree Lee, Chairman and CEO Kyung-Bae Suh, Professor Eunjung Lee, Professor Ki-Jun Yoon, ⓒ Amorepacific Group >
The other awards were given to Professor Joo-Hong Park and Professor Yuree Lee of Seoul National University, and Professor Eunjung Lee of Boston Children's Hospital and Harvard Medical School.
The awards ceremony was held on September 18 at the Amorepacific Headquarters in Seoul.
With these four new awardees, a total of 14 scientists have been named as SUHF Young Investigators to date.
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2019.09.23 View 9120 -
Chair Professor Jo-Won Lee Named Sixth President of National Nano Fab Center
< President Jo-Won Lee >
Chair professor Jo-Won Lee from Hanyang University was appointed as the sixth president of the National Nano Fab Center (NNFC). President Lee will serve his term for three years from September 16.
The NNFC is an affiliated institution of KAIST, established in 2002 to foster qualified manpower in the field of nanotechnology (NT) in Korea. The NNFC features cutting-edge NT-related research equipment and fabrication services, and provides students and researchers quality education and training. The NNFC seeks to become a world-leading institute by performing extensive business operations including the commercialization of NT research results and conducting various multidisciplinary projects.
President Lee received his BS degree from Hanyang University and his MS and PhD degrees in metals science from the Pennsylvania State University. He taught nano-conversion science at his alma mater, Hanyang University, while serving as the director of the National Program for Tera-level Nanodevices. President Lee also guided the governmental planning committee for the 10-year Korea Nanotechnology Initiative as secretary general.
President Lee said, “The NNFC has been striving to develop Korea as the world’s strongest nation in nanotechnology thus far. All of the members of the NNFC will continue giving our best effort for the improvement of our nation’s nanotechnology.”
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2019.09.17 View 4023 -
Sungjoon Park Named Google PhD Fellow
PhD candidate Sungjoon Park from the School of Computing was named a 2019 Google PhD Fellow in the field of natural language processing. The Google PhD fellowship program has recognized and supported outstanding graduate students in computer science and related fields since 2009. Park is one of three Korean students chosen as the recipients of Google Fellowships this year. A total of 54 students across the world in 12 fields were awarded this fellowship.
Park’s research on computational psychotherapy using natural language processing (NLP) powered by machine learning earned him this year’s fellowship. He presented of learning distributed representations in Korean and their interpretations during the 2017 Annual Conference of the Association for Computational Linguistics and the 2018 Conference on Empirical Methods in Natural Language Processing. He also applied machine learning-based natural language processing into computational psychotherapy so that a trained machine learning model could categorize client's verbal responses in a counseling dialogue. This was presented at the Annual Conference of the North American Chapter of the Association for Computational Linguistics.
More recently, he has been developing on neural response generation model and the prediction and extraction of complex emotion in text, and computational psychotherapy applications.
2019.09.17 View 8878 -
Two More Cross-generation Collaborative Labs Open
< President Sung-Chul Shin (sixth from the left) and Professor Sun Chang Kim (seventh from the left) at the signboard ceremony of KAIST BioDesigneering Laboratory >
KAIST opened two more cross-generation collaborative labs last month. KAIST BioDesigneering Laboratory headed by Professor Sun Chang Kim from the Department of Biological Sciences and Nanophotonics Laboratory led by Professor Yong-Hee Lee from the Department of Physics have been selected to receive 500 million KRW funding for five years.
A four-member selection committee including the former President of ETH Zürich Professor Emeritus Ralph Eichler and Professor Kwang-Soo Kim of Harvard Medical School conducted a three-month review and evaluation for this selection to be made. With these two new labs onboard, a total of six cross-generation collaborative labs will be operated on campus.
The operation of cross-generation collaborative labs has been in trial since March last year, as one of the KAIST’s Vision 2031 research innovation initiatives. This novel approach is to pair up senior and junior faculty members for sustaining research and academic achievements even after the senior researcher retires, so that the spectrum of knowledge and research competitiveness can be extended to future generations. The selected labs will be funded for five years, and the funding will be extended if necessary. KAIST will continue to select new labs every year.
One of this year’s selectees Professor Sun Chang Kim will be teamed up with Professor Byung-Kwan Cho from the same department and Professor Jung Kyoon Choi from the Department of Bio and Brain Engineering to collaborate in the fields of synthetic biology, systems biology, and genetic engineering. This group mainly aims at designing and synthesizing optimal genomes that can efficiently manufacture protein drug and biomedical active materials. They will also strive to secure large amounts of high-functioning natural active substances, new adhesive antibacterial peptides, and eco-friendly ecological restoration materials. It is expected that collaboration between these three multigenerational professors will help innovate their bio-convergence technology and further strengthen their international competitiveness in the global bio-market.
Another world-renowned scholar Professor Yong-Hee Lee of photonic crystal laser study will be joined by Professor Minkyo Seo from the same department and Professor Hansuek Lee from the Graduate School of Nanoscience and Technology. They will explore the extreme limits of light-material interaction based on optical micro/nano resonators, with the goal of developing future nonlinear optoelectronic and quantum optical devices. The knowledge and technology newly gained from the research are expected to provide an important platform for a diverse range of fields from quantum communications to biophysics.
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2019.09.06 View 10581 -
Algorithm Identifies Optimal Pairs for Composing Metal-Organic Frameworks
The integration of metal-organic frameworks (MOFs) and other metal nanoparticles has increasingly led to the creation of new multifunctional materials. Many researchers have integrated MOFs with other classes of materials to produce new structures with synergetic properties.
Despite there being over 70,000 collections of synthesized MOFs that can be used as building blocks, the precise nature of the interaction and the bonding at the interface between the two materials still remains unknown. The question is how to sort out the right matching pairs out of 70,000 MOFs.
An algorithmic study published in Nature Communications by a KAIST research team presents a clue for finding the perfect pairs. The team, led by Professor Ji-Han Kim from the Department of Chemical and Biomolecular Engineering, developed a joint computational and experimental approach to rationally design MOF@MOFs, a composite of MOFs where an MOF is grown on a different MOF.
Professor Kim’s team, in collaboration with UNIST, noted that the metal node of one MOF can coordinately bond with the linker of a different MOF and the precisely matched interface configurations at atomic and molecular levels can enhance the likelihood of synthesizing MOF@MOFs.
They screened thousands of MOFs and identified optimal MOF pairs that can seamlessly connect to one another by taking advantage of the fact that the metal node of one MOF can form coordination bonds with the linkers of the second MOF. Six pairs predicted from the computational algorithm successfully grew into single crystals.
This computational workflow can readily extend into other classes of materials and can lead to the rapid exploration of the composite MOFs arena for accelerated materials development. Even more, the workflow can enhance the likelihood of synthesizing MOF@MOFs in the form of large single crystals, and thereby demonstrated the utility of rationally designing the MOF@MOFs.
This study is the first algorithm for predicting the synthesis of composite MOFs, to the best of their knowledge. Professor Kim said, “The number of predicted pairs can increase even more with the more general 2D lattice matching, and it is worth investigating in the future.”
This study was supported by Samsung Research Funding & Incubation Center of Samsung Electronics.
(Figure: An example of a rationally synthesized MOF@MOFs (cubic HKUST-1@MOF-5 ))
2019.08.30 View 16765 -
Researchers Describe a Mechanism Inducing Self-Killing of Cancer Cells
(Professor Kim (left) and lead author Lee)
Researchers have described a new mechanism which induces the self-killing of cancer cells by perturbing ion homeostasis. A research team from the Department of Biochemical Engineering has developed helical polypeptide potassium ionophores that lead to the onset of programmed cell death. The ionophores increase the active oxygen concentration to stress endoplasmic reticulum to the point of cellular death.
The electrochemical gradient between extracellular and intracellular conditions plays an important role in cell growth and metabolism. When a cell’s ion homeostasis is disturbed, critical functions accelerating the activation of apoptosis are inhibited in the cell.
Although ionophores have been intensively used as an ion homeostasis disturber, the mechanisms of cell death have been unclear and the bio-applicability has been limited. In the study featured at Advanced Science, the team presented an alpha helical peptide-based anticancer agent that is capable of transporting potassium ions with water solubility. The cationic, hydrophilic, and potassium ionic groups were combined at the end of the peptide side chain to provide both ion transport and hydrophilic properties.
These peptide-based ionophores reduce the intracellular potassium concentration and at the same time increase the intracellular calcium concentration. Increased intracellular calcium concentrations produce intracellular reactive oxygen species, causing endoplasmic reticulum stress, and ultimately leading to apoptosis.
Anticancer effects were evaluated using tumor-bearing mice to confirm the therapeutic effect, even in animal models. It was found that tumor growth was strongly inhibited by endoplasmic stress-mediated apoptosis.
Lead author Dr. Dae-Yong Lee said, “A peptide-based ionophore is more effective than conventional chemotherapeutic agents because it induces apoptosis via elevated reactive oxygen species levels. Professor Yeu-Chun Kim said he expects this new mechanism to be widely used as a new chemotherapeutic strategy. This research was funded by the National Research Foundation.
2019.08.28 View 20324 -
Distinguished Professor Sukbok Chang Donates His Prize Money
The honoree of the 2019 Korea Best Scientist and Technologist Award, Distinguished Professor Sukbok Chang donated his prize money of one hundred million KRW to the Chemistry Department Scholarship Fund and the Lyu Keun-Chul Sports Complex Management Fund during a donation ceremony last week.
Professor Chang won the award last month in recognition of his pioneering achievements and lifetime contributions to the development of carbon-hydrogen activation strategies, especially for carbon-carbon, carbon-nitrogen, and carbon-oxygen formations. Professor Chang, a world renowned chemist, has been recognized for his highly selective catalytic systems, allowing the controlled defunctionalization of bio-derived platform substrates under mild conditions and opening a new avenue for the utilization of biomass-derived platform chemicals.
“All my achievements are the results of my students’ hard work and dedication. I feel very fortunate to have such talented team members. I want to express my sincere gratitude for such a great research environment that we have worked together in so far,” said Professor Chang at the ceremony.
KAIST President Sung-Chul Shin said, “Not only will Professor Chang’s donation make a significant contribution to the Department of Chemistry, but also to the improvement of the Lyu Keun-Chul Sports Complex’s management, which directly links to the health and welfare of the KAIST community.”
Professor Chang currently holds the position of distinguished professor at KAIST and director of the Center for Catalytic Hydrocarbon Functionalizations in the Institute for Basic Science (IBS). He previously received the Kyung-Ahm Academic Award in 2013 and the Korea Toray Science Award in 2018. All these prize money also went to the school.
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2019.08.26 View 8352