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KAIST-UCSD researchers build an enzyme discovering AI
- A joint research team led by Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering and Bernhard Palsson of UCSD developed ‘DeepECtransformer’, an artificial intelligence that can predict Enzyme Commission (EC) number of proteins.
- The AI is tasked to discover new enzymes that have not been discovered yet, which would allow prediction for a total of 5,360 types of Enzyme Commission (EC) numbers
- It is expected to be used in the development of microbial cell factories that produce environmentally friendly chemicals as a core technology for analyzing the metabolic network of a genome.
While E. coli is one of the most studied organisms, the function of 30% of proteins that make up E. coli has not yet been clearly revealed. For this, an artificial intelligence was used to discover 464 types of enzymes from the proteins that were unknown, and the researchers went on to verify the predictions of 3 types of proteins were successfully identified through in vitro enzyme assay.
KAIST (President Kwang-Hyung Lee) announced on the 24th that a joint research team comprised of Gi Bae Kim, Ji Yeon Kim, Dr. Jong An Lee and Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at KAIST, and Dr. Charles J. Norsigian and Professor Bernhard O. Palsson of the Department of Bioengineering at UCSD has developed DeepECtransformer, an artificial intelligence that can predict the enzyme functions from the protein sequence, and has established a prediction system by utilizing the AI to quickly and accurately identify the enzyme function.
Enzymes are proteins that catalyze biological reactions, and identifying the function of each enzyme is essential to understanding the various chemical reactions that exist in living organisms and the metabolic characteristics of those organisms. Enzyme Commission (EC) number is an enzyme function classification system designed by the International Union of Biochemistry and Molecular Biology, and in order to understand the metabolic characteristics of various organisms, it is necessary to develop a technology that can quickly analyze enzymes and EC numbers of the enzymes present in the genome.
Various methodologies based on deep learning have been developed to analyze the features of biological sequences, including protein function prediction, but most of them have a problem of a black box, where the inference process of AI cannot be interpreted. Various prediction systems that utilize AI for enzyme function prediction have also been reported, but they do not solve this black box problem, or cannot interpret the reasoning process in fine-grained level (e.g., the level of amino acid residues in the enzyme sequence).
The joint team developed DeepECtransformer, an AI that utilizes deep learning and a protein homology analysis module to predict the enzyme function of a given protein sequence. To better understand the features of protein sequences, the transformer architecture, which is commonly used in natural language processing, was additionally used to extract important features about enzyme functions in the context of the entire protein sequence, which enabled the team to accurately predict the EC number of the enzyme. The developed DeepECtransformer can predict a total of 5360 EC numbers.
The joint team further analyzed the transformer architecture to understand the inference process of DeepECtransformer, and found that in the inference process, the AI utilizes information on catalytic active sites and/or the cofactor binding sites which are important for enzyme function. By analyzing the black box of DeepECtransformer, it was confirmed that the AI was able to identify the features that are important for enzyme function on its own during the learning process.
"By utilizing the prediction system we developed, we were able to predict the functions of enzymes that had not yet been identified and verify them experimentally," said Gi Bae Kim, the first author of the paper. "By using DeepECtransformer to identify previously unknown enzymes in living organisms, we will be able to more accurately analyze various facets involved in the metabolic processes of organisms, such as the enzymes needed to biosynthesize various useful compounds or the enzymes needed to biodegrade plastics." he added.
"DeepECtransformer, which quickly and accurately predicts enzyme functions, is a key technology in functional genomics, enabling us to analyze the function of entire enzymes at the systems level," said Professor Sang Yup Lee. He added, “We will be able to use it to develop eco-friendly microbial factories based on comprehensive genome-scale metabolic models, potentially minimizing missing information of metabolism.”
The joint team’s work on DeepECtransformer is described in the paper titled "Functional annotation of enzyme-encoding genes using deep learning with transformer layers" written by Gi Bae Kim, Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering of KAIST and their colleagues. The paper was published via peer-review on the 14th of November on “Nature Communications”.
This research was conducted with the support by “the Development of next-generation biorefinery platform technologies for leading bio-based chemicals industry project (2022M3J5A1056072)” and by “Development of platform technologies of microbial cell factories for the next-generation biorefineries project (2022M3J5A1056117)” from National Research Foundation supported by the Korean Ministry of Science and ICT (Project Leader: Distinguished Professor Sang Yup Lee, KAIST).
< Figure 1. The structure of DeepECtransformer's artificial neural network >
2023.11.24 View 3122 -
KAIST presents a fundamental technology to remove metastatic traits from lung cancer cells
KAIST (President Kwang Hyung Lee) announced on January 30th that a research team led by Professor Kwang-Hyun Cho from the Department of Bio and Brain Engineering succeeded in using systems biology research to change the properties of carcinogenic cells in the lungs and eliminate both drug resistance and their ability to proliferate out to other areas of the body.
As the incidences of cancer increase within aging populations, cancer has become the most lethal disease threatening healthy life. Fatality rates are especially high when early detection does not happen in time and metastasis has occurred in various organs. In order to resolve this problem, a series of attempts were made to remove or lower the ability of cancer cells to spread, but they resulted in cancer cells in the intermediate state becoming more unstable and even more malignant, which created serious treatment challenges.
Professor Kwang-Hyun Cho's research team simulated various cancer cell states in the Epithelial-to-Mesenchymal Transition (EMT) of lung cancer cells, between epithelial cells without metastatic ability and mesenchymal cells with metastatic ability. A mathematical model of molecular network was established, and key regulators that could reverse the state of invasive and drug resistant mesenchymal cells back to the epithelial state were discovered through computer simulation analysis and molecular cell experiments. In particular, this process succeeded in properly reverting the mesenchymal lung cancer cells to a state where they were sensitive to chemotherapy treatment while avoiding the unstable EMT hybrid cell state in the middle process, which had remained a difficult problem.
The results of this research, in which KAIST Ph.D. student Namhee Kim, Dr. Chae Young Hwang, Researcher Taeyoung Kim, and Ph.D. student Hyunjin Kim participated, were published as an online paper in the international journal “Cancer Research” published by the American Association for Cancer Research (AACR) on January 30th. (Paper title: A cell fate reprogramming strategy reverses epithelial-to-mesenchymal transition of lung cancer cells while avoiding hybrid states)
Cells in an EMT hybrid state, which are caused by incomplete transitions during the EMT process in cancer cells, have the characteristics of both epithelial cells and mesenchymal cells, and are known to have high drug resistance and metastatic potential by acquiring high stem cell capacity. In particular, EMT is further enhanced through factors such as transforming growth factor-beta (TGF-β) secreted from the tumor microenvironment (TME) and, as a result, various cell states with high plasticity appear. Due to the complexity of EMT, it has been very difficult to completely reverse the transitional process of the mesenchymal cancer cells to an epithelial cell state in which metastatic ability and drug resistance are eliminated while avoiding the EMT hybrid cell state with high metastatic ability and drug resistance.
Professor Kwang-Hyun Cho's research team established a mathematical model of the gene regulation network that governs the complex process of EMT, and then applied large-scale computer simulation analysis and complex system network control technology to identify and verify 'p53', 'SMAD4', and 'ERK1' and 'ERK 2' (collectively ERKs) through molecular cell experiments as the three key molecular targets that can transform lung cancer cells in the mesenchymal cell state, reversed back to an epithelial cell state that no longer demonstrates the ability to metastasize, while avoiding the EMT hybrid cell state.
In particular, by analyzing the molecular regulatory mechanism of the complex EMT process at the system level, the key pathways were identified that were linked to the positive feedback that plays an important role in completely returning cancer cells to an epithelial cell state in which metastatic ability and drug resistance are removed.
This discovery is significant in that it proved that mesenchymal cells can be reverted to the state of epithelial cells under conditions where TGF-β stimulation are present, like they are in the actual environment where cancer tissue forms in the human body.
Abnormal EMT in cancer cells leads to various malignant traits such as the migration and invasion of cancer cells, changes in responsiveness to chemotherapy treatment, enhanced stem cell function, and the dissemination of cancer. In particular, the acquisition of the metastatic ability of cancer cells is a key determinant factor for the prognosis of cancer patients. The EMT reversal technology in lung cancer cells developed in this research is a new anti-cancer treatment strategy that reprograms cancer cells to eliminate their high plasticity and metastatic potential and increase their responsiveness to chemotherapy.
Professor Kwang-Hyun Cho said, "By succeeding in reversing the state of lung cancer cells that acquired high metastatic traits and resistance to drugs and reverting them to a treatable epithelial cell state with renewed sensitivity to chemotherapy, the research findings propose a new strategy for treatments that can improve the prognosis of cancer patients.”
Professor Kwang-Hyun Cho's research team was the first to present the principle of reversal treatment to revert cancer cells to normal cells, following through with the announcement of the results of their study that reverted colon cancer cells to normal colon cells in January of 2020, and also presenting successful re-programming research where the most malignant basal type breast cancer cells turned into less-malignant luminal type breast cancer cells that were treatable with hormonal therapies in January of 2022. This latest research result is the third in the development of reversal technology where lung cancer cells that had acquired metastatic traits returned to a state in which their metastatic ability was removed and drug sensitivity was enhanced.
This research was carried out with support from the Ministry of Science and ICT and the National Research Foundation of Korea's Basic Research in Science & Engineering Program for Mid-Career Researchers.
< Figure 1. Construction of the mathematical model of the regulatory network to represent the EMT phenotype based on the interaction between various molecules related to EMT.
(A) Professor Kwang-Hyun Cho's research team investigated numerous literatures and databases related to complex EMT, and based on comparative analysis of cell line data showing epithelial and mesenchymal cell conditions, they extracted key signaling pathways related to EMT and built a mathematical model of regulatory network (B) By comparing the results of computer simulation analysis and the molecular cell experiments, it was verified how well the constructed mathematical model simulated the actual cellular phenomena. >
< Figure 2. Understanding of various EMT phenotypes through large-scale computer simulation analysis and complex system network control technology.
(A) Through computer simulation analysis and experiments, Professor Kwang-Hyun Cho's research team found that complete control of EMT is impossible with single-molecule control alone. In particular, through comparison of the relative stability of attractors, it was revealed that the cell state exhibiting EMT hybrid characteristics has unstable properties. (B), (C) Based on these results, Prof. Cho’s team identified two feedbacks (positive feedback consisting of Snail-miR-34 and ZEB1-miR-200) that play an important role in avoiding the EMT hybrid state that appeared in the TGF-β-ON state. It was found through computer simulation analysis that the two feedbacks restore relatively high stability when the excavated p53 and SMAD4 are regulated. In addition, molecular cell experiments demonstrated that the expression levels of E-cad and ZEB1, which are representative phenotypic markers of EMT, changed similarly to the expression profile in the epithelial cell state, despite the TGF-β-ON state. >
< Figure 3. Complex molecular network analysis and discovery of reprogramming molecular targets for intact elimination of EMT hybrid features.
(A) Controlling the expression of p53 and SMAD4 in lung cancer cell lines was expected to overcome drug resistance, but contrary to expectations, chemotherapy responsiveness was not restored. (B) Professor Kwang-Hyun Cho's research team additionally analyzed computer simulations, genome data, and experimental results and found that high expression levels of TWIST1 and EPCAM were related to drug resistance. (C) Prof. Cho’s team identified three key molecular targets: p53, SMAD4 and ERK1 & ERK2. (D), (E) Furthermore, they identified a key pathway that plays an important role in completely reversing into epithelial cells while avoiding EMT hybrid characteristics, and confirmed through network analysis and attractor analysis that high stability of the key pathway was restored when the proposed molecular target was controlled. >
< Figure 4. Verification through experiments with lung cancer cell lines.
When p53 was activated and SMAD4 and ERK1/2 were inhibited in lung cancer cell lines, (A), (B) E-cad protein expression increased and ZEB1 protein expression decreased, and (C) mesenchymal cell status including TWIST1 and EPCAM and gene expression of markers related to stem cell potential characteristics were completely inhibited. In addition, (D) it was confirmed that resistance to chemotherapy treatment was also overcome as the cell state was reversed by the regulated target. >
< Figure 5. A schematic representation of the research results.
Prof. Cho’s research team identified key molecular regulatory pathways to avoid high plasticity formed by abnormal EMT of cancer cells and reverse it to an epithelial cell state through systems biology research. From this analysis, a reprogramming molecular target that can reverse the state of mesenchymal cells with acquired invasiveness and drug resistance to the state of epithelial cells with restored drug responsiveness was discovered.
For lung cancer cells, when a drug that enhances the expression of p53, one of the molecular targets discovered, and inhibits the expression of SMAD4 and ERK1 & ERK2 is administered, the molecular network of genes in the state of mesenchymal cells is modified, eventually eliminating metastatic ability and it is reprogrammed to turn into epithelial cells without the resistance to chemotherapy treatments. >
2023.01.30 View 11767 -
KAIST-NYU Digital Governance Forum Held
KAIST (President Kwang Hyung Lee) held the 'KAIST-NYU Digital Governance Forum' at the Korea Press Center in the morning of October 28th, 2022.
This forum was held in continuation to discuss the objectives of the 'Digital Vision Forum' that was hosted by New York University (NYU) back in September in the United States, and is the first public event to be held through joint efforts by KAIST and NYU since the signage of the 'KAIST-NYU Joint Campus' was presented at the New York forum.
< Signage of KAIST-NYU Joint Campus >
This forum was promoted based on the consensus of the two universities to create an international forum of solidarity to solve global challenges and seek new governance in the era of digital transformation.
Digital innovation technology is expected to bring economic and industrial benefits as well as political, social and ethical risks such as accelerating the digital divide, among others. In particular, in a time of global digital transformation, as the competition for digital and AI supremacy based on technology nationalism catches fire, there is an emergent need for a global governance system in which digital innovation and the value of freedom co-exist. With the consensus formed through this forum with NYU, KAIST plans to focus on detailing the vision for future digital cooperation that encompasses various stakeholders in our society.
To this end, President Kwang Hyung Lee of KAIST and President Andrew Hamilton of NYU led the forum with keynote addresses with President Hamilton taking part virtually, followed by NYU Professor Matthew Liao, a world-renowned scholar specialized in the ethics in the field of science and technology, and Jason Allford, Special Representative of the World Bank Group to Korea, presenting on relevant topics for discussion.
From KAIST, Professor Kyung Ryul Park of the Graduate School of Science and Technology Policy and Director So Young Kim of the Korea Policy Center for the Fourth Industrial Revolution, followed with their presentations. A panel discussion on governance in the period of digital transformation was also held, led by Professor Dongman Lee, the Dean of the College of Engineering.
To kick things off, Professor Matthew Liao of NYU proposed a normative system that can harmonize technology and social ethics while explaining various ethical issues following the technological development of artificial intelligence.
Jason Allford, Special Representative of the World Bank Group to Korea, outlined the changing roles of government in the digital era from the perspective of transparency and government efficiency and explained global development strategies through various cases of digital innovations by international organizations.
Professor Kyung Ryul Park of the Graduate School of Science and Technology Policy at KAIST emphasized that the core of new digital governance is not only innovative technology but also the participation and harmony of various stakeholders at home at abroad and brought up the importance of multi-dimensional international solidarity based on digital transformation that goes beyond the flat ‘technological geopolitics.’
Professor So Young Kim, the Director of the Korea Policy Center for the Fourth Industrial Revolution at KAIST, commented on the current government's digital platform strategy and emphasized the need for a leading digital transformation strategy that goes beyond the governance of the existing government.
Edward Mermelstein, the Commissioner for International Affairs of New York City, said, “The City of New York, shall also provide active support for the cooperative governance initiative organized by KAIST in Korea. As the conversation progresses further, we can draw up plans to organize international organizations to support the effort, likely to be named ‘Digitization for Good’, and we can go on to consider future collaboration,” to express the city’s willingness and anticipation for active cooperation.
Andrew Hamilton, the President of NYU, said "NYU is thrilled by the partnership we are embarking upon with KAIST, which goes hand in hand with our global tradition, and is based upon our bedrock commitment to the free movement of people and ideas.” He added that “As data-driven software, AI, and social networks become even more essential parts of our daily lives, I am confident that today’s discussions will lead to new and promising insights.”
President Kwang Hyung Lee of KAIST said, “It is significant that we are to cooperate with New York University to prepare a venue to assess the changes of the forth coming era at a time in which digital technology, government platforms, and public data are attracting attention as a medium that can create various social and economic value.”
President Lee added, “KAIST and NYU, the two institutions in cross-continental partnership to lead innovations in higher education via the creation of a joint campus, have joined forces to host this forum to create an opportunity to envision the future of a cooperative governance that is inclusive of key players like the government, businesses, the civil societies, academia, and international organizations.”
The 'KAIST-NYU Digital Governance Forum' was broadcast live on KAIST’s Official YouTube Channel from 9:30 am on the 28th of October (Korea Standard Time) with simultaneous interpretation provided in both Korean and English. A recording of the video is available online for everyone to watch free of charge.
KAIST’s YouTube Channel: https://www.youtube.com/c/KAISTofficial
Forum Recording with English interpretation: https://youtu.be/Vs31i7BtfEw
2022.10.28 View 5445 -
KAIST develops biocompatible adhesive applicable to hair transplants
Aside from being used as a new medical adhesive, the new material can be applied to developing a new method of hair transplants, which cannot be repeated multiple times using current method of implanting the wholly intact follicles into the skin.
Medical adhesives are materials that can be applied to various uses such as wound healing, hemostasis, vascular anastomosis, and tissue engineering, and is expected to contribute greatly to the development of minimally invasive surgery and organ transplants. However, adhesives with high adhesion, low toxicity, and capable of decomposing in the body are rare. Adhesives based on natural proteins, such as fibrin and collagen, have high biocompatibility but insufficient adhesive strength. Synthetic polymer adhesives based on urethane or acrylic have greater adhesion but do not decompose well and may cause an inflammatory reaction in the body.
A joint research team led by Professor Myungeun Seo and Professor Haeshin Lee from the KAIST Department of Chemistry developed a bio-friendly adhesive from biocompatible polymers using tannic acid, the source of astringency in wine.
The research team focused on tannic acid, a natural polyphenolic product. Tannic acid is a polyphenol present in large amounts in fruit peels, nuts, and cacao. It has a high affinity and coating ability on other substances, and we sense the astringent taste in wine when tannic acid sticks to the surface of our tongue. When tannic acid is mixed with hydrophilic polymers, they form coacervates, or small droplets of jelly-like fluids that sink. If the polymers used are biocompatible, the mixture can be applied as a medical adhesive with low toxicity. However, coacervates are fundamentally fluid-like and cannot withstand large forces, which limits their adhesive capabilities. Thus, while research to utilize it as an adhesive has been actively discussed, a biodegradable material exhibiting strong adhesion due to its high shear strength has not yet been developed.
The research team figured out a way to enhance adhesion by mixing two biocompatible FDA-approved polymers, polyethylene glycol (PEG) and polylactic acid (PLA). While PEG, which is used widely in eyedrops and cream, is hydrophilic, PLA, a well-known bioplastic derived from lactic acid, is insoluble in water. The team combined the two into a block copolymer, which forms hydrophilic PLA aggregates in water with PEG blocks surrounding them. A coacervate created by mixing the micelles and tannic acid would behave like a solid due to the hard PLA components, and show an elastic modulus improved by a thousand times compared to PEG, enabling it to withstand much greater force as an adhesive.
Figure 1. (Above) Principle of biodegradable adhesive made by mixing poly(ethylene glycol)-poly(lactic acid) diblock copolymer and tannic acid in water. Yellow coacervate is precipitated through hydrogen bonding between the block copolymer micelles and tannic acid, and exhibits adhesion. After heat treatment, hydrogen bonds are rearranged to further improve adhesion. (Bottom) Adhesion comparison. Compared to using poly(ethylene glycol) polymer (d), it can support 10 times more weight when using block copolymer (e) and 60 times more weight after heat treatment (f). The indicated G' values represent the elastic modulus of the material.
Furthermore, the research team observed that the material’s mechanical properties can be improved by over a hundred times through a heating and cooling process that is used to heat-treat metals. They also discovered that this is due to the enforced interactions between micelle and tannic acid arrays.
The research team used the fact that the material shows minimal irritation to the skin and decomposes well in the body to demonstrate its possible application as an adhesive for hair transplantation through an animal experiment. Professor Haeshin Lee, who has pioneered various application fields including medical adhesives, hemostatic agents, and browning shampoo, focused on the adhesive capacities and low toxicity of polyphenols like tannic acid, and now looks forward to it improving the limitations of current hair transplant methods, which still involve follicle transfer and are difficult to be repeated multiple times.
Figure 2. (a) Overview of a hair transplantation method using a biodegradable adhesive (right) compared to a conventional hair transplantation method (left) that transplants hair containing hair follicles. After applying an adhesive to the tip of the hair, it is fixed to the skin by implanting it through a subcutaneous injection, and repeated treatment is possible. (b) Initial animal test results. One day after 15 hair transplantation, 12 strands of hair remain. If you pull the 3 strands of hair, you can see that the whole body is pulled up, indicating that it is firmly implanted into the skin. All strands of hair applied without the new adhesive material fell off, and in the case of adhesive without heat treatment, the efficiency was 1/7.
This research was conducted by first co-authors Dr. Jongmin Park (currently a senior researcher at the Korea Research Institute of Chemical Technology) from Professor Myeongeun Seo’s team and Dr. Eunsook Park from Professor Haeshin Lee’s team in the KAIST Department of Chemistry, and through joint research with the teams led by Professor Hyungjun Kim from the KAIST Department of Chemistry and Professor Siyoung Choi from the Department of Chemical and Biomolecular Engineering. The research was published online on August 22 in the international journal Au (JACS Au) under the title Biodegradable Block Copolymer-Tannic Acid Glue.
This study was funded by the Support Research Under Protection Project of the National Research Foundation (NRF), Leading Research Center Support Project (Research Center for Multiscale Chiral Structure), Biodegradable Plastics Commercialization and Demonstration Project by the Ministry of Trade and Industry, and institutional funding from the Korea Research Institute of Chemical Technology.
2022.10.07 View 7602 -
Industrial Liaison Program to Provide Comprehensive Consultation Services
The ILP’s one-stop solutions target all industrial sectors including conglomerates, small and medium-sized enterprises, venture companies, venture capital (VC) firms, and government-affiliated organizations.
The Industrial Liaison Center at KAIST launched the Industrial Liaison Program (ILP) on September 28, an industry-academic cooperation project to provide comprehensive solutions to industry partners. The Industrial Liaison Center will recruit member companies for this service every year, targeting all industrial sectors including conglomerates, small and medium-sized enterprises, venture companies, venture capital (VC) firms, and government-affiliated organizations.
The program plans to build a one-stop support system that can systematically share and use excellent resource information from KAIST’s research teams, R&D achievements, and infrastructure to provide member companies with much-needed services.
More than 40 KAIST professors with abundant academic-industrial collaboration experience will participate in the program. Experts from various fields with different points of view and experiences will jointly provide solutions to ILP member companies. To actively participate in academic-industrial liaisons and joint consultations, KAIST assigned 10 professors from related fields as program directors.
The program directors will come from four different fields including AI/robots (Professor Alice Oh, School from the School of Computing, Professor Young Jae Jang from the Department of Industrial & Systems Engineering, and Professor Yong-Hwa Park from Department of Mechanical Engineering), bio/medicine (Professor Daesoo Kim from Department of Biological Sciences and Professor YongKeun Park from Department of Physics), materials/electronics (Professor Sang Ouk Kim from the Department of Materials Science and Engineering and Professors Jun-Bo Yoon and Seonghwan Cho from the School of Electrical Engineering), and environment/energy (Professor Hee-Tak Kim from the Department of Biological Sciences and Professor Hoon Sohn from the Department of Civil and Environmental Engineering).
The transdisciplinary board of consulting professors that will lead technology innovation is composed of 30 professors including Professor Min-Soo Kim (School of Computing, AI), Professor Chan Hyuk Kim (Department of Biological Sciences, medicine), Professor Hae-Won Park (Department of Mechanical Engineering, robots), Professor Changho Suh (School of Electrical Engineering, electronics), Professor Haeshin Lee (Department of Chemistry, bio), Professor Il-Doo Kim (Department of Materials Science and Engineering, materials), Professor HyeJin Kim (School of Business Technology and Management), and Professor Byoung Pil Kim (School of Business Technology and Management, technology law)
The Head of the Industrial Liaison Center who is also in charge of the program, Professor Keon Jae Lee, said, “In a science and technology-oriented generation where technological supremacy determines national power, it is indispensable to build a new platform upon which innovative academic-industrial cooperation can be pushed forward in the fields of joint consultation, the development of academic-industrial projects, and the foundation of new industries.
He added, “KAIST professors carry out world-class research in many different fields and faculty members can come together through the ILP to communicate with representatives from industry to improve their corporations’ global competitiveness and further contribute to our nation’s interests by cultivating strong small enterprises
2021.09.30 View 5582 -
KAIST Teams Up with Yozma Group to Nurture Startups
KAIST has joined hands with Israeli venture capital investor Yozma Group to help campus-based startups grow and build success. The two signed a memorandum of understanding (MOU) on joint technology value creation initiatives at the signing ceremony that was held at KAIST’s main campus in Daejeon on April 8.
Under the MOU, Yozma Group will make investments and implement acceleration programs for startups established by KAIST professors, graduates, and students, as well as those invested in by the university.
Yozma Group already launched a $70 million fund to help grow companies in Korea and Israel. Yozma Group will use the fund as well as its global acceleration know-how and network of over 400 R&D centers across Israel to help promising KAIST startups enter overseas markets.
Moreover, Yozma Group also plans to discover and support KAIST startups that need technology from the Weizmann Institute of Science, Israel’s leading multidisciplinary basic research institution in natural and exact sciences.
KAIST is also in talks to locate Yozma Group’s branch office on the university’s campus to ensure seamless collaborations.
KAIST President Kwang Hyung Lee explained to Yozma Group’s Founder and Chairman Yigal Erlich and Head of Asia Pacific Won-Jae Lee at the MOU signing ceremony that “startup and technology commercialization are the crucial areas where KAIST will make innovations.”
“Cooperation with Yozma Group will help KAIST startups transform their ideas and technologies into real businesses and build a global presence,” he added.
Yozma Group started as Yozma Fund, created in conjunction with the Israeli government in 1993 to support the globalization of Israeli startups and to foster the growth of Israel’s venture capital industry. The Fund, which was privatized in 1998, has supported 97 Israeli tech ventures joining the Nasdaq, leading Israel to become a global innovation hub that has the third-most companies listed on the Nasdaq.
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2021.04.20 View 6302 -
KAIST Technology Value Tops in Commercialization Market
KAIST became the first Korean university to achieve 10.183 billion KRW in annual technology royalties, and was also selected as an ‘Institution of Outstanding Patent Quality Management’ and an ‘Institution of Outstanding Public Patent Technology Transfer’ for 2020.
KAIST earns its technology royalties through 56 technology transfer contracts. Following KAIST in the rankings were Seoul National University (SNU) in second place with 8.8 billion KRW from 87 contracts and Korea University (KU) in the third with 5.4 billion KRW from 133 contracts. The data shows the high value of KAIST-created technology in the market.
The Korean Intellectual Property Office (KIPO) started to recognize the Institution of Outstanding Patent Quality Management this year to encourage profit-driven patent management at universities and public research institutes, and KAIST was selected as one of the four first recipients of this distinction.
In addition, KAIST was selected as an Institution of Outstanding Public Patent Technology Transfer, a title given by KIPO to three universities and public research institutes this year with outstanding achievements in technology transfers and commercialization to encourage patent utilization.
Director of the KAIST Institute of Technology Value Creation (ITVC) Professor Kyung-cheol Choi said that KAIST’s achievement in annual technology royalties and technology transfers and commercialization were prime examples of accelerating competitiveness in intellectual property through innovative R&D investment.
In April, KAIST expanded and reorganized its Industry-Academia Collaboration Team into the ITVC to support technology transfers and commercialization. Specialized organizations such as the Intellectual Property and Technology Transfer Center and Industrial Liaison Center have been established under the ITVC, and industry experts have been recruited as special professors focusing on industry-academia collaborations to enhance its specialized functions.
KAIST also operates an enterprise membership system and technology consulting system, aimed at sharing its outstanding intellectual property within domestic industries. In 2019, it secured a technology transfer commercialization fund of 1.2 billion KRW available for three years under KIPO’s Intellectual Property Profit Reinvestment Support Program (formerly the Korean Patent Gap Fund Creation Project).
This program was introduced to bridge the gap between the technology developed in universities and the level of technology required by industry. Under the program, bold investments are made in early-stage technologies at the research paper or experiment phase.
The program encourages enterprises to take active steps for the transfer of technologies by demonstrating their commercial potential through prototype production, testing and certification, and standard patent filing. KAIST is currently funding approximately 20 new technologies under this program as of July 2020.
KAIST’s outstanding intellectual property management has also received international recognition, with its selection as Asia’s leading institution in university R&D intellectual property at the Intellectual Property Business Congress (IPBC) Asia 2019 held in Tokyo, Japan last October.
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2020.08.18 View 8215 -
Every Moment of Ultrafast Chemical Bonding Now Captured on Film
- The emerging moment of bond formation, two separate bonding steps, and subsequent vibrational motions were visualized. -
< Emergence of molecular vibrations and the evolution to covalent bonds observed in the research. Video Credit: KEK IMSS >
A team of South Korean researchers led by Professor Hyotcherl Ihee from the Department of Chemistry at KAIST reported the direct observation of the birthing moment of chemical bonds by tracking real-time atomic positions in the molecule. Professor Ihee, who also serves as Associate Director of the Center for Nanomaterials and Chemical Reactions at the Institute for Basic Science (IBS), conducted this study in collaboration with scientists at the Institute of Materials Structure Science of High Energy Accelerator Research Organization (KEK IMSS, Japan), RIKEN (Japan), and Pohang Accelerator Laboratory (PAL, South Korea). This work was published in Nature on June 24.
Targeted cancer drugs work by striking a tight bond between cancer cell and specific molecular targets that are involved in the growth and spread of cancer. Detailed images of such chemical bonding sites or pathways can provide key information necessary for maximizing the efficacy of oncogene treatments. However, atomic movements in a molecule have never been captured in the middle of the action, not even for an extremely simple molecule such as a triatomic molecule, made of only three atoms.
Professor Ihee's group and their international collaborators finally succeeded in capturing the ongoing reaction process of the chemical bond formation in the gold trimer. "The femtosecond-resolution images revealed that such molecular events took place in two separate stages, not simultaneously as previously assumed," says Professor Ihee, the corresponding author of the study. "The atoms in the gold trimer complex atoms remain in motion even after the chemical bonding is complete. The distance between the atoms increased and decreased periodically, exhibiting the molecular vibration. These visualized molecular vibrations allowed us to name the characteristic motion of each observed vibrational mode." adds Professor Ihee.
Atoms move extremely fast at a scale of femtosecond (fs) ― quadrillionths (or millionths of a billionth) of a second. Its movement is minute in the level of angstrom equal to one ten-billionth of a meter. They are especially elusive during the transition state where reaction intermediates are transitioning from reactants to products in a flash. The KAIST-IBS research team made this experimentally challenging task possible by using femtosecond x-ray liquidography (solution scattering). This experimental technique combines laser photolysis and x-ray scattering techniques. When a laser pulse strikes the sample, X-rays scatter and initiate the chemical bond formation reaction in the gold trimer complex. Femtosecond x-ray pulses obtained from a special light source called an x-ray free-electron laser (XFEL) were used to interrogate the bond-forming process. The experiments were performed at two XFEL facilities (4th generation linear accelerator) that are PAL-XFEL in South Korea and SACLA in Japan, and this study was conducted in collaboration with researchers from KEK IMSS, PAL, RIKEN, and the Japan Synchrotron Radiation Research Institute (JASRI).
Scattered waves from each atom interfere with each other and thus their x-ray scattering images are characterized by specific travel directions. The KAIST-IBS research team traced real-time positions of the three gold atoms over time by analyzing x-ray scattering images, which are determined by a three-dimensional structure of a molecule. Structural changes in the molecule complex resulted in multiple characteristic scattering images over time. When a molecule is excited by a laser pulse, multiple vibrational quantum states are simultaneously excited. The superposition of several excited vibrational quantum states is called a wave packet. The researchers tracked the wave packet in three-dimensional nuclear coordinates and found that the first half round of chemical bonding was formed within 35 fs after photoexcitation. The second half of the reaction followed within 360 fs to complete the entire reaction dynamics.
They also accurately illustrated molecular vibration motions in both temporal- and spatial-wise. This is quite a remarkable feat considering that such an ultrafast speed and a minute length of motion are quite challenging conditions for acquiring precise experimental data.
In this study, the KAIST-IBS research team improved upon their 2015 study published by Nature. In the previous study in 2015, the speed of the x-ray camera (time resolution) was limited to 500 fs, and the molecular structure had already changed to be linear with two chemical bonds within 500 fs. In this study, the progress of the bond formation and bent-to-linear structural transformation could be observed in real time, thanks to the improvement time resolution down to 100 fs. Thereby, the asynchronous bond formation mechanism in which two chemical bonds are formed in 35 fs and 360 fs, respectively, and the bent-to-linear transformation completed in 335 fs were visualized. In short, in addition to observing the beginning and end of chemical reactions, they reported every moment of the intermediate, ongoing rearrangement of nuclear configurations with dramatically improved experimental and analytical methods.
They will push this method of 'real-time tracking of atomic positions in a molecule and molecular vibration using femtosecond x-ray scattering' to reveal the mechanisms of organic and inorganic catalytic reactions and reactions involving proteins in the human body. "By directly tracking the molecular vibrations and real-time positions of all atoms in a molecule in the middle of reaction, we will be able to uncover mechanisms of various unknown organic and inorganic catalytic reactions and biochemical reactions," notes Dr. Jong Goo Kim, the lead author of the study.
Publications:
Kim, J. G., et al. (2020) ‘Mapping the emergence of molecular vibrations mediating bond formation’. Nature. Volume 582. Page 520-524. Available online at https://doi.org/10.1038/s41586-020-2417-3
Profile: Hyotcherl Ihee, Ph.D.
Professor
hyotcherl.ihee@kaist.ac.kr
http://time.kaist.ac.kr/
Ihee Laboratory
Department of Chemistry
KAIST
https://www.kaist.ac.kr
Daejeon 34141, Korea
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2020.06.24 View 14793 -
Transformative Electronics Systems to Broaden Wearable Applications
Imagine a handheld electronic gadget that can soften and deform when attached to our skin. This will be the future of electronics we all dreamed of. A research team at KAIST says their new platform called 'Transformative Electronics Systems' will open a new class of electronics, allowing reconfigurable electronic interfaces to be optimized for a variety of applications.
A team working under Professor Jae-Woong Jeong from the School of Electrical Engineering at KAIST has invented a multifunctional electronic platform that can mechanically transform its shape, flexibility, and stretchability. This platform, which was reported in Science Advances, allows users to seamlessly and precisely tune its stiffness and shape.
"This new class of electronics will not only offer robust, convenient interfaces for use in both tabletop or handheld setups, but also allow seamless integration with the skin when applied onto our bodies," said Professor Jeong.
The transformative electronics consist of a special gallium metal structure, hermetically encapsulated and sealed within a soft silicone material, combined with electronics that are designed to be flexible and stretchable. The mechanical transformation of the electronic systems is specifically triggered by temperature change events controlled by the user.
"Gallium is an interesting key material. It is biocompatible, has high rigidity in solid form, and melts at a temperature comparable to the skin's temperature," said lead author Sang-Hyuk Byun, a researcher at KAIST.
Once the transformative electronic platform comes in contact with a human body, the gallium metal encapsulated inside the silicone changes to a liquid state and softens the whole electronic structure, making it stretchable, flexible, and wearable. The gallium metal then solidifies again once the structure is peeled off the skin, making the electronic circuits stiff and stable. When flexible electronic circuits were integrated onto these transformative platforms, it empowered them with the ability to become either flexible and stretchable or rigid.
"This technology could not have been achieved without interdisciplinary efforts," said co-lead author Joo Yong Sim, who is a researcher with ETRI. "We worked together with electrical, mechanical, and biomedical engineers, as well as material scientists and neuroscientists to make this breakthrough."
This universal electronics platform allowed researchers to demonstrate applications that were highly adaptable and customizable, such as a multi-purpose personal electronics with variable stiffness and stretchability, a pressure sensor with tuneable bandwidth and sensitivity, and a neural probe that softens upon implantation into brain tissue.
Applicable for both traditional and emerging electronics technologies, this breakthrough can potentially reshape the consumer electronics industry, especially in the biomedical and robotic domains. The researchers believe that with further development, this novel electronics technology can significantly impact the way we use electronics in our daily life.
< Transformative electronics in soft mode,which becomes wearable for outdoor applications.>
Video Material:
https://youtu.be/im0J18TfShk
Publication: Sang-Hyuk Byun, Joo Yong Sim, Zhanan Zhou, Juhyun Lee, Raza Qazi, Marie C. Walicki, Kyle E. Parker, Matthew P. Haney, Su Hwan Choi, Ahnsei Shon, Graydon B. Gereau, John Bilbily, Shuo Li, Yuhao Liu, Woon-Hong Yeo, Jordan G. McCall, Jianliang Xiao, and Jae-Woong Jeong. 2019. Mechanically transformative electronics, sensors, and implantable devices. Science Advances. Volume 5. No. 11. 12 pages. https://doi.org/10.1126/sciadv.aay0418
Link to download the full-text paper: https://advances.sciencemag.org/content/advances/5/11/eaay0418.full.pdf
Profile: Prof. Jae-Woong Jeong, PhD jjeong1@kaist.ac.kr
https://www.jeongresearch.org/
Professor
Bio-Integrated Electronics and Systems Laboratory
School of Electrical Engineering
Korea Advanced Institute of Science and Technology (KAIST) https://www.kaist.ac.kr
Daejeon 34141, Korea
Profile: Sang-Hyuk Byun, PhD Candidate
shbun95@kaist.ac.kr
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2020.01.31 View 6275 -
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 24087 -
OUIC Presents the Six Most Promising Techs Transferrable to Local SMEs
KAIST will showcase the six most promising technologies for small and medium enterprises (SMEs) on November 14 in the Academic Cultural Complex. To strengthen the competitive edge of local SMEs in Daejeon, the Office of University-Industry made a survey of their technological needs and came up with the six most promising technologies. Developers will introduce their technologies during the session.Besides the introduction of the promising technologies, the session will also provide a program named University to Business (U2B) to match up technologies according to the SMEs’ needs. SMEs who wish to engage in technology transfers can receive counseling and other support programs during the session.First, Professor Seok-Hyung Bae from the Department of Industrial Design will present a technology for controlling cooperation robots. Professor Bae inserted flexible materials between the controllers to allow robots to use both hands stably and operate more accurately and swiftly. It can be applied to automatic robots, industrial robots, and service robots.Professor Hyun Myung from the Department of Civil & Environmental Engineering will demonstrate a robot navigation system in a dynamic indoor and outdoor environment, which can be applied to robotics in logistics, smart factories, and autonomous vehicles. Providing robust simultaneous localization and mapping systems, this technology shows high-performing navigation with low-cost sensors.Meanwhile, Professor Siyoung Choi from the Department of Chemical and Biomolecular Engineering will introduce a technology for forming stable adhesive emulsions. An emulsion is a stable mixture of water and oil. Conventionally, a small amount of surfactant is added to stabilize an emulsion. Here, Professor Choi developed a stable emulsion system without using any chemical substances. This technology can be applied to various fields, including the cosmetics, pharmaceutical, semiconductor, and painting industries. The session will also present smart IoTs platform technology developed by Professor Jinhong Yang from the KAIST Institute for IT Convergence. His technology minimizes errors occurring when multiple IoT devices are connected simultaneously. Professor Yong Keun Park from the Department of Physics will introduce a technology for measuring glycated hemoglobin by using the optical properties of red blood cells. This technology can be applied to make low-cost, small-sized measuring equipment. It can also be used for vitro diagnoses including diabetes, cardiovascular disorders, tumors, kidney disease, and infectious diseases. Professor Yong Man Ro from the School of Electrical Engineering will show technology for biometric access control. Conventional technologies for face recognition fall behind other biometrics. Professor Ro and his team developed a facial dynamics interpreting network which allows very accurate facial recognition by interpreting the relationships between facial local dynamics and estimating facial traits. This technology can be applied to security and communication in finance, computers, and information system.KAIST President Sung-Chul Shin said, “KAIST will continue to support SMEs to have stronger competitiveness in the market. Through technology transfer, we will drive innovation in technological commercialization where a university’s research and development creates economic value.”
2018.11.13 View 7544 -
In Jin Cho Earned the Best Poster Prize at ME Summit 2017
In Jin Cho, a Ph.D. student in the Department of Chemical and Biomolecular Engineering at KAIST received the best poster prize at the International Metabolic Engineering Summit 2017 held on October 24 in Beijing, China.
The International Metabolic Engineering Summit is a global conference where scientists and corporate researchers in the field of metabolic engineering present their latest research outcomes and build networks.
At this year’s summit, about 500 researchers from around the world participated in active academic exchanges, including giving keynote speeches and presenting posters.
During the poster session, the summit selects one person for the KeAi-synthetic and Systems Biotechnology Poster Award, two for Microbial Cell Factories Poster Awards, and three for Biotechnology Journal Poster Awards among the posters presented by graduate students, post-doctoral fellows and researchers. Cho received the KeAi-synthetic and Systems Biotechnology Poster Award. Her winning poster is on the biotransformation of p-xylene to terephthalic acid using engineered Escherichia coli.
Terephthalic acid is generally produced by p-xylene oxidation; however, this process requires a high temperature and pressure as well as a toxic catalyst during the reaction process.
Cho and Ziwei Luo, a Ph.D. student at KAIST, co-conducted the research and developed a successful biological conversion process. Compared to the existing chemical process, it does not require a high temperature and pressure; and it is environmentally friendly with a relatively high conversion rate of approximately 97%.
Cho’s advisor, Distinguished Professor Sang Yup Lee said, “Further research on glucose-derived terephthalic acid will enable us to produce biomass-based eco-friendly terephthalic acid through engineered Escherichia coli.”
2017.10.31 View 7955