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1. Pushing single atoms near an optical cavity

Author

Lee, Dowon, Ha, Taegyu, Kim, Donggeon, Kim, Keumhyun, An, Kyungwon, and Lee, Moonjoo

Subjects
Quantum Physics, Physics - Atomic Physics, Physics - Optics
Abstract

Optical scattering force is used to reduce the loading time of single atoms to a cavity mode. Releasing a cold atomic ensemble above the resonator, we apply a push beam along the direction of gravity, offering fast atomic transport with narrow velocity distribution. We also observe in real time that, when the push beam is illuminated against gravity, single atoms slow down and even turn around in the mode, through the cavity-transmission measurement. Our method can be employed to make atom-cavity experiments more efficient., Comment: 11 pages, 6 figures

Published
2024

3. Third-order exceptional point in an ion-cavity system

Author

Kim, Jinuk, Ha, Taegyu, Kim, Donggeon, Lee, Dowon, Lee, Ki-Se, Won, Jongcheol, Moon, Youngil, and Lee, Moonjoo

Subjects
Quantum Physics, Physics - Atomic Physics
Abstract

We investigate a scheme for observing the third-order exceptional point (EP3) in an ion-cavity setting. In the lambda-type level configuration, the ion is driven by a pump field, and the resonator is probed with another weak laser field. We exploit the highly asymmetric branching ratio of an ion's excited state to satisfy the weak-excitation limit, which allows us to construct the non-Hermitian Hamiltonian $(H_{\textrm{nH}})$. Via fitting the cavity-transmission spectrum, the eigenvalues of $H_{\textrm{nH}}$ are obtained. The EP3 appears at a point where the Rabi frequency of the pump laser and the atom-cavity coupling constant balance the loss rates of the system. Feasible experimental parameters are provided., Comment: 9 pages, 6 figures

Published
2023
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5. Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

Author

Nam, Yoonhee, Koo, Harim, Yang, Yingxi, Shin, Sang, Zhu, Zhihan, Kim, Donggeon, Cho, Hee Jin, Mu, Quanhua, Choi, Seung Won, Sa, Jason K., Seo, Yun Jee, Kim, Yejin, Lee, Kyoungmin, Oh, Jeong-Woo, Kwon, Yong-Jun, Park, Woong-Yang, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Park, Chul-Kee, Lee, Hye Won, Yoon, Yeup, and Wang, Jiguang

Published
2023
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7. A Loop-Break Decision Feedback Equalizer for DAC/ADC-DSP-Based Wireline Transceivers

Author

Kim, Donggeon, Choi, Yujin, Lee, Jaewon, Jang, Seoyoung, Song, Sungyu, Braendli, Matthias, Morf, Thomas, Kossel, Marcel, Francese, Pier-Andrea, and Kim, Gain

Abstract

This paper presents a novel digital decision feedback equalizer (DFE) design that can relax the feedback timing constraints for analog-to-digital converter (ADC)-based high-speed wireline receivers. The proposed technique breaks the loop-unrolled DFE (LU-DFE) chain by computing multiple LU-DFE chains in parallel with all possible seed symbols, and selecting the appropriate output by the post-processing selection logic. The proposed loop-break DFE (LB-DFE) is functionally equivalent to the conventional DFE with any other implementation techniques such as LU-DFE, look-ahead DFE (LA-DFE), or direct DFE. With topographical synthesis in 28nm CMOS process, the proposed LB-DFE achieved up to 54% of DFE area saving as compared to LA-DFE with look-ahead factor (LF) of 16 for 112Gb/s PAM-4 with 875MHz DSP clock speed. The implementation feasibility and functionality are verified using ZCU111 RFSoC platform at 6Gb/s (3GS/s ADC conversion rate) with a channel exhibiting 25dB loss at 1.5GHz, demonstrating the same bit error rate (BER) performance between the LB-DFE and the LA-DFE. Equipment-based measurements using arbitrary waveform generator (AWG) and real-time oscilloscope transmitting/receiving 40GBaud PAM-4 (80Gb/s) to/from the differential cables with software 21-tap feed-forward equalizer (FFE) and LB-DFE on PC was also conducted.

Published
2024
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10. MODL-06. THE GUT MICROBIOTA OF BRAIN TUMOR PATIENTS CAN IMPACT IMMUNOTHERAPY EFFICACY IN A PRECLINICAL MODEL OF GLIOMA

Author

Kim, Donggeon, primary, Sarvesh, Sujith, additional, Valbak, Olivia, additional, Backan, Olivia, additional, Chen, Dongquan, additional, Morrow, Casey, additional, Benvensite, Etty, additional, Nabors, Burt, additional, Bekal, Mahesh, additional, Dono, Antonio, additional, Esquenazi, Yoshua, additional, Forsyth, Peter, additional, Yu, Hsiang-Hsuan Michael, additional, Khushalani, Nikhil, additional, Egan, Kathleen, additional, and McFarand, Braden, additional

Published
2023
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13. Hybrid Bionic Nerve Interface for Application in Bionic Limbs

Author

Cho, Youngjun, primary, Jeong, Hyung Hwa, additional, Shin, Heejae, additional, Pak, Changsik John, additional, Cho, Jeongmok, additional, Kim, Yongwoo, additional, Kim, Donggeon, additional, Kim, Taehyeon, additional, Kim, Hoijun, additional, Kim, Sohee, additional, Kwon, Soonchul, additional, Hong, Joon Pio, additional, Suh, Hyunsuk Peter, additional, and Lee, Sanghoon, additional

Published
2023
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15. Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma

Author

Sa, Jason K., Chang, Nakho, Lee, Hye Won, Cho, Hee Jin, Ceccarelli, Michele, Cerulo, Luigi, Yin, Jinlong, Kim, Sung Soo, Caruso, Francesca P., Lee, Mijeong, Kim, Donggeon, Oh, Young Taek, Lee, Yeri, Her, Nam-Gu, Min, Byeongkwi, Kim, Hye-Jin, Jeong, Da Eun, Kim, Hye-Mi, Kim, Hyunho, Chung, Seok, Woo, Hyun Goo, Lee, Jeongwu, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Kim, Jinho, Park, Woong-Yang, Wang, Qianghu, Sulman, Erik P., Heimberger, Amy B., Lim, Michael, Park, Jong Bae, Iavarone, Antonio, Verhaak, Roel G. W., and Nam, Do-Hyun

Published
2020
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16. Effect of choosing coordinate systems on computationally predicting nonradiative transition rates of flexible thermally activated delayed fluorescence molecules.

Author

Min, Byeong Ki, Kim, Donggeon, Kim, Dongwook, and Rhee, Young Min

Subjects
*DELAYED fluorescence, *CARTESIAN coordinates, *PHOTON emission, *STATISTICAL correlation, *LIGHT emitting diodes, *HARMONIC oscillators
Abstract

Understanding nonradiative transition mechanisms is important in various situations. However, compared with radiative processes where temporal profiles of photon emission can be monitored in a straightforward manner, experimentally accessing the rate information may not be an easy task with nonradiative transitions. Hence, applying theoretical tools toward predicting the rates can be a useful tactic. Such predictions become very useful in designing optoelectronic materials as in the molecules adopted for constructing organic light‐emitting diodes (OLEDs). The correlation function formalism is a method that can fulfill the purpose of designing OLED materials. The formalism requires information regarding the vibrational normal modes of the two electronic states before and after the transition. Because the method is also based on harmonic oscillator approximation, it can actually fail to provide high reliability when there is a large geometric distortion between the initial and the final states. In fact, the harmonic normal mode picture is more prone to lose reliability in the Cartesian coordinates than in the internal ones even at a small distortion, and hence adopting internal coordinates may be more preferable for practical calculations. This is because normal mode mixing becomes less severe when molecular coordinates are described with internal degrees of freedom such as bond stretching, bending, and torsion. In this regard, how much more reliable the nonradiative rate predictions in OLED materials become with the use of internal coordinate system deserves a close inspection. In this account, we review on the derivation of the correlation function formalism and provide how it can be adapted toward the use of the internal coordinates. As a demonstration, we evaluate the intersystem crossing and the internal conversion rates of a series of thermally activated delayed fluorescence (TADF) molecules with both Cartesian and internal coordinate systems. Overall, handling transitions involving substantial structural changes is improved indeed with the internal coordinates. However, limitations are still apparent for the TADF systems with a flexible donor–acceptor type construct especially when the inevitable inter‐domain twisting takes place with the electronic transition. Future prospect for handling the issue is commented as a concluding remark. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy

Author

Lee, Jin-Ku, Liu, Zhaoqi, Sa, Jason K., Shin, Sang, Wang, Jiguang, Bordyuh, Mykola, Cho, Hee Jin, Elliott, Oliver, Chu, Timothy, Choi, Seung Won, Rosenbloom, Daniel I. S., Lee, In-Hee, Shin, Yong Jae, Kang, Hyun Ju, Kim, Donggeon, Kim, Sun Young, Sim, Moon-Hee, Kim, Jusun, Lee, Taehyang, Seo, Yun Jee, Shin, Hyemi, Lee, Mijeong, Kim, Sung Heon, Kwon, Yong-Jun, Oh, Jeong-Woo, Song, Minsuk, Kim, Misuk, Kong, Doo-Sik, Choi, Jung Won, Seol, Ho Jun, Lee, Jung-Il, Kim, Seung Tae, Park, Joon Oh, Kim, Kyoung-Mee, Song, Sang-Yong, Lee, Jeong-Won, Kim, Hee-Cheol, Lee, Jeong Eon, Choi, Min Gew, Seo, Sung Wook, Shim, Young Mog, Zo, Jae Ill, Jeong, Byong Chang, Yoon, Yeup, Ryu, Gyu Ha, Kim, Nayoung K. D., Bae, Joon Seol, Park, Woong-Yang, Lee, Jeongwu, Verhaak, Roel G. W., Iavarone, Antonio, Lee, Jeeyun, Rabadan, Raul, and Nam, Do-Hyun

Published
2018
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20. HFGCN: High-speed and Fully-optimized GCN Accelerator

Author

Han, MinSeok, primary, Kim, Jiwan, additional, Kim, Donggeon, additional, Jeong, Hyunuk, additional, Jung, Gilho, additional, Oh, Myeongwon, additional, Lee, Hyundong, additional, Go, Yunjeong, additional, Kim, HyunWoo, additional, Kim, Jongbeom, additional, and Song, Taigon, additional

Published
2023
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22. Abstract 3234: OCT-598, a novel EP2/EP4 dual antagonist, promotes anti-tumor immune responses in syngeneic mouse tumor models in combination with standard-of-care chemo- and immunotherapies

Author

Lee, Youngrae, primary, Baek, Sujeong, additional, Kim, Dong Kwon, additional, Lee, Yeri, additional, Kim, Donggeon, additional, Jo, Seongin, additional, Lim, Sang Kyun, additional, Shin, Young Sook, additional, Kwon, Soonsang, additional, Yang, Seung Min, additional, Kim, Young Taek, additional, Kang, Seong-San, additional, Synn, Chun-Bong, additional, Na, Kwangmin, additional, Kim, Mi Hyun, additional, Han, Heekyung, additional, Han, Yu Jin, additional, Lee, Sungwoo, additional, Kim, Jae Hwan, additional, Yun, Mi Ran, additional, Byeon, Youngseon, additional, Kim, Young Seob, additional, Lee, Ji Yun, additional, Lee, Jii Bum, additional, Kim, Chang Gon, additional, Hong, Min Hee, additional, Lim, Sun Min, additional, Pyo, Kyoung-Ho, additional, Cho, Byoung Chul, additional, and Yoon, Taeyoung, additional

Published
2023
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23. Abstract 515: Discovery of potent and orally available small molecule inhibitors of the SOS1-KRAS interaction

Author

Yu, Ha Na, primary, Ki, Dong Hyuk, additional, Nam, Joonwoo, additional, Kim, Eun-Jung, additional, Kim, Sungeun, additional, Choi, Hunmi, additional, Kim, Jieun, additional, Yu, Jihyun, additional, Kim, Donggeon, additional, Park, Dohyun, additional, Yoon, Kyeong Jin, additional, Jo, Seongin, additional, Hwang, So-Hyeon, additional, Lim, Sang Kyun, additional, Shin, Young Sook, additional, and Han, Wooseok, additional

Published
2023
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24. Diffraction-Angle Filtering-Based Two-Step Acoustic Full-Waveform Inversion for 3-D Seismic Reflection Data

Author

Kim, Donggeon, Min, Dong-Joo, and Oh, Ju-Won

Abstract

Full-waveform inversion (FWI) aims at building a high-resolution velocity model by fitting numerically computed seismic data to observed one. Considering both the kinematic and dynamic properties of all waves in seismic data makes FWI highly non-linear. To mitigate its non-linearity, one can preferentially build low-wavenumber background velocity first, and then retrieve high-wavenumber reflectivity. However, in the early stage of FWI, the low-wavenumber velocity update is hardly derived from the reflected waves and mainly relies on the diving waves. To secure a wider coverage of low-wavenumber velocity updates from the reflected waves in addition to the diving waves, we propose two-step FWI based on diffraction-angle filtering (DAF) for 3-D seismic reflection data. In our method, DAF, which imitates the amplitude variations of the PP partial derivative wavefields with respect to the model parameters in elastic FWI to control small, intermediate, or large diffraction-angle energy, is adopted for the scale separation of a given velocity model into a background velocity and reflectivity model. The prior reflectivity provides information on reflection wavepaths. Then, the low-wavenumber update generated along the full wavepaths can build a background velocity model with improved wavenumber coverage. In addition, DAF can be implemented without a large increase in computational effort, which enables practical applications of our method to large-scale 3-D seismic field data. Applications of DAF-based two-step FWI to 3-D synthetic and field seismic data demonstrate that DAF-based two-step FWI can build a reliable background velocity model, which leads to stable convergence toward the global minimum.

Published
2024
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25. Additional file 2 of Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

Author

Nam, Yoonhee, Koo, Harim, Yang, Yingxi, Shin, Sang, Zhu, Zhihan, Kim, Donggeon, Cho, Hee Jin, Mu, Quanhua, Choi, Seung Won, Sa, Jason K., Seo, Yun Jee, Kim, Yejin, Lee, Kyoungmin, Oh, Jeong-Woo, Kwon, Yong-Jun, Park, Woong-Yang, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Park, Chul-Kee, Lee, Hye Won, Yoon, Yeup, and Wang, Jiguang

Abstract

Additional file 2: Fig. S1. Timeline of sample acquisition, sequencing, in vitro culture and TMZ screening. Fig. S2. Gaussian Mixture Model used to identify genes with the same expression profile between patient-derived cells (PDCs) and tumor tissues. Fig. S3. Principal Component Analysis and differentially expressed gene analysis on 34 tissue RNA-seq samples. Fig. S4. Association of MGMT promoter methylation status to survival and in vitro TMZ screening in the main cohort. Fig. S5. Copy number estimation by GliomaSCAN. Fig. S6. Copy number estimation by RNA-seq. Fig. S7. Machine learning model feature importance. Fig. S8. Correlations between GBM subtypes and TMZ response. Fig. S9. Comparison of survival prediction in TCGA cohort. Fig. S10. Genomic landscape of multi-sector samples. Fig. S11. TMZ-resistant marker expression and CNV comparison in patient M13 and M14. Fig. S12. Progression free survival difference in patients with multi-sector samples.

Published
2023
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26. Additional file 3 of Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

Author

Nam, Yoonhee, Koo, Harim, Yang, Yingxi, Shin, Sang, Zhu, Zhihan, Kim, Donggeon, Cho, Hee Jin, Mu, Quanhua, Choi, Seung Won, Sa, Jason K., Seo, Yun Jee, Kim, Yejin, Lee, Kyoungmin, Oh, Jeong-Woo, Kwon, Yong-Jun, Park, Woong-Yang, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Park, Chul-Kee, Lee, Hye Won, Yoon, Yeup, and Wang, Jiguang

Abstract

Additional file 3. Supplementary methods.

Published
2023
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27. Generation of Tag-Based User Profiles for Clustering Users in a Social Music Site

Author

Kim, Hyon Hee, Jo, Jinnam, Kim, Donggeon, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Pan, Jeng-Shyang, editor, Chen, Shyi-Ming, editor, and Nguyen, Ngoc Thanh, editor

Published
2012
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38. Two-step full waveform inversion of diving and reflected waves with the diffraction-angle-filtering-based scale-separation technique.

Author

Kim, Donggeon, Hwang, Jongha, Min, Dong-Joo, Oh, Ju-Won, and Alkhalifah, Tariq

Subjects
*INVERSION (Geophysics), *DIVING, *NONLINEAR equations, *WAVE diffraction, *SEISMIC tomography, *DIFFRACTIVE scattering
Abstract

Full waveform inversion (FWI) is a highly non-linear optimization problem that aims to reconstruct high-resolution subsurface structures. The success of FWI in reflection seismology relies on appropriate updates of low-wavenumber background velocity structures, which are generally driven by the diving waves in conventional FWI. On the other hand, the reflected waves mainly contribute to updating high-wavenumber components rather than low-wavenumber components. To extract low-wavenumber information from the reflected waves in addition to the diving waves, we propose a two-step FWI strategy that separates a given model into the reflectivity and background velocity models and then alternately update them using the scale-separation technique based on diffraction-angle filtering (DAF; which was proposed to effectively control wavenumber components of the FWI gradient). Our strategy first inverts the high-wavenumber reflectivity model by suppressing energy at large diffraction angles, which are necessary to compute the reflection wave paths (i.e. the rabbit-ears-shaped kernels) for low-wavenumber updates in the subsequent stage. Then, we extract low-wavenumber components due to the diving (banana-shaped kernels) and reflected waves (rabbit-ears-shaped kernels) from the gradient by suppressing energy at small diffraction angles. Our strategy is similar to reflection waveform inversion (RWI) in that it separates a given model into high- and low-wavenumber components and uses the rabbit-ears-shaped kernels for low-wavenumber updates. The main difference between our strategy and RWI is that our strategy adopts the DAF-based scale-separation technique in the space domain, which makes our algorithm of using both the banana-shaped and rabbit-ears-shaped kernels computationally attractive. By applying our two-step inversion strategy to the synthetic data for the Marmousi-II model and the real ocean-bottom cable data from the North sea, we demonstrate that our method properly reconstructs low-wavenumber structures even if initial models deviate from the true models. [ABSTRACT FROM AUTHOR]

Published
2022
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39. 572 Fibroblast activating protein (FAP)-targeting IL-12 (anti-FAP/IL-12) TMEkine™ potentiates anti-cancer effects in preclinical cancer models

Author

Kim, Donggeon, primary, Lee, Dahea, additional, Ryu, Soomin, additional, Byeon, Yeongseon, additional, Pyo, Kyoung-Ho, additional, Kim, Jae-Hwan, additional, Lee, Seul, additional, Kim, Dong Kwon, additional, Lee, Eun Ji, additional, Oh, Seung Yeon, additional, Cho, Byoung Chul, additional, and Lee, Byoung Chul, additional

Published
2020
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40. 707 Discovery of a novel EP2 and EP4 dual antagonist

Author

Lee, Yeri, primary, Kim, Hyun Jin, additional, Kim, Donggeon, additional, Lee, Joo Youn, additional, Yun, Chang Soo, additional, Lee, Hyuk, additional, Shin, Young Sook, additional, Han, Soo Bong, additional, and Lim, Sang Kyun, additional

Published
2020
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44. cIRCR201-dPBD, a Novel Pyrrolobenzodiazepine Dimer-Containing Site-Specific Antibody–Drug Conjugate Targeting c-Met Overexpression Tumors

Author

Min, Byeongkwi, primary, Jin, Jonghwa, additional, Kim, Hyeree, additional, Her, Nam-Gu, additional, Park, Changsik, additional, Kim, Donggeon, additional, Yang, Jehoon, additional, Hwang, Juhyeon, additional, Kim, Eunmi, additional, Choi, Minji, additional, Song, Ho Young, additional, Nam, Do-Hyun, additional, and Yoon, Yeup, additional

Published
2020
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45. Sphere-Forming Culture for Expanding Genetically Distinct Patient-Derived Glioma Stem Cells by Cellular Growth Rate Screening

Author

Shin, Kayoung, primary, Shin, Hyemi, additional, Cho, Hee Jin, additional, Kang, Hyunju, additional, Lee, Jin-Ku, additional, Seo, Yun Jee, additional, Shin, Yong Jae, additional, Kim, Donggeon, additional, Koo, Harim, additional, Kong, Doo-Sik, additional, Seol, Ho Jun, additional, Lee, Jung-Il, additional, Lee, Hye Won, additional, and Nam, Do-Hyun, additional

Published
2020
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47. Full-waveform inversion strategies using common-receiver gathers for ocean-bottom cable data.

Author

Hwang, Jongha, Oh, Ju-Won, Kim, Donggeon, and Min, Dong-Joo

Subjects
RECIPROCITY theorems, GAUSS-Newton method, INVERSION (Geophysics), CABLES, ELECTRONIC data processing, VELOCITY
Abstract

Full-waveform inversion (FWI), which is among the most powerful seismic data processing techniques for imaging subsurface geological structures, has a huge computational cost in proportion to the number of sources. To increase the speed of FWI, we explored the use of common-receiver gathers (CRGs) as an alternative to common-shot gathers (CSGs) as observed data. This approach has the potential to reduce the computational cost of FWI significantly, particularly for ocean-bottom cable (OBC) acquisition. As we match modelled and observed CSGs in CSG-based FWI, we match observed CRGs with modelled CSGs of switched source–receiver geometry in CRG-based FWI. According to the reciprocity principle, CRG FWI based on the steepest descent or Gauss–Newton method yields the same inverted velocity models as CSG FWI for an identical and known source signature applied over whole source positions. However, when the source wavelet is unknown, and changes from one source position to another, each trace of a CRG contains a different source signature, making it difficult to apply conventional source estimation or source-independent methods to CRG FWI. Therefore, in this study, we proposed inversion strategies for CRG FWI in both the time and frequency domains to deal with errors arising from different source wavelets between CRG traces. Then, we used a synthetic example for the Marmousi-II model and a real data example from the North Sea to demonstrate that our strategies for CRG FWI provide very similar inverted velocity models to those obtained from CSG FWI, at a lower computational cost. [ABSTRACT FROM AUTHOR]

Published
2022
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50. PIP4K2A as a negative regulator of PI3K in PTEN-deficient glioblastoma

Author

Shin, Yong Jae, primary, Sa, Jason K., additional, Lee, Yeri, additional, Kim, Donggeon, additional, Chang, Nakho, additional, Cho, Hee Jin, additional, Son, Miseol, additional, Oh, Michael Y.T., additional, Shin, Kayoung, additional, Lee, Jin-Ku, additional, Park, Jiwon, additional, Jo, Yoon Kyung, additional, Kim, Misuk, additional, Paddison, Patrick J., additional, Tergaonkar, Vinay, additional, Lee, Jeongwu, additional, and Nam, Do-Hyun, additional

Published
2019
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