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Seminar Series | Center for Chemical Dynamics in Living Cells



Surprises and Open Questions in Soft Materials Physics


Steve Granick


Steve Granick is Founding Director of the Center for Soft and Living Matter. He is a member of the U.S. National Academy of Sciences and of the American Academy of Arts and Sciences. Among his other major awards are APS Fellow (1992), Paris-Sciences Medal (2002), APS national Polymer Physics Prize (2009), NSF Special Creativity Award (2012), and ACS national Colloid and Surface Chemistry Prize (2013). He served as Chair of the DOE Council on Materials Panel on Polymers at Interfaces (2002) and Chair of the APS Division of Polymer Physics (2006). He holds and has held Honorary or Visiting Positions at numerous universities in Europe and Asia.
Before joining the IBS (Institute for Basic Science), Granick spent 30 years at the University of Illinois at Urbana-Champaign (USA), most recently as the Racheff Chair of Materials Science and Engineering, Professor of Chemistry, Professor of Chemical and Biomolecular Engineering, and Professor of Physics and Biophysics. His education was at Princeton University (B.A. 1978) and the University of Wisconsin (Ph.D. 1982). His doctoral study was with J.D. Ferry, the most prominent polymer scientist of his generation. His postdoctoral study was with P.-G. de Gennes (Nobel Prize, 1991).

Director, IBS Center for Soft and Living Matter and UNIST

www.softmatt.ibs.re.kr

Abstract

A fundamental challenge of modern fundamental and applied science is to form structure that is not frozen in place but instead reconfigures internally driven by energy throughput and adapts to its environment robustly. Predicated on fluorescence imaging at the single-particle level, this talk describes quantitative studies of how this can happen. With Janus colloidal clusters, we show the powerful role of synchronized motion in self-assembly. In living cells, we find that transportation efficiency problems bear a provocative parallel with polymer chain trajectories with their spatial extent, and with jammed matter in their time evolution. A picture emerges in which simple experiments, performed at single-particle and single-molecule resolution, can dissect macroscopic phenomena in ways that surprise.

Thursday, April 13, 5-6 p.m.

Room # 106, Building # 102



Alternative Antibacterial Strategies against Drug Resistant Bacteria


Kyeong Kyu Kim

Professor, Sungkyunkwan University School of Medicine

Abstract

Emergence of bacteria resistance to antibiotics is the serious threat to human health in hospitals and communities. Therefore new antibiotics that can effectively control multi-drug resistant pathogens is urgently needed. However, only limited numbers of new antibiotics are available or under development. Moreover, occurrence of drug-resistance is inevitable as a consequence of evolutionary selection following indiscriminate antibiotic usage. Under these situations, it is necessary not only to develop new antibiotics but also to establish a novel strategy by which pathogenic bacteria can be eliminated without triggering resistance. We propose several alternative antibacterial strategies to overcome these serious problems: (1) a magnetic nanoparticle-based physical treatment against pathogenic bacteria, which blocks biofilm formation and kills bacteria by physicochemical forces, (2) an antivirulence strategy in which suppression of virulence gene expression or inhibition of virulence factors eventually makes pathogenic bacteria eliminated by host innate immune system with less selective pressure for the development of bacterial resistance, and (3) a drug repositioning strategy to identify a novel adjuvant that can make antibiotics effective against multidrug resistant bacteria. These alternative antibacterial strategies can be used for many purposes including environmental and therapeutic applications since the drug-resistance occurs not only in the hospital but also because of the antibiotic abuse in the fields. In this seminar, the detailed strategies and results will be discuss.

Thursday, May 11, 5-6 p.m.

Room # 106, Building # 102



On the process of solving biological puzzles in collaboration between biologists and mathematicians


Jae Kyoung Kim

Professor, Department of Mathematical Sciences, KAIST

Abstract

The revolution of molecular biology in the early 1980s has revealed complex biochemical interactions underlying biological systems. To understand this complex system, collaborations between biologists and mathematician have played important roles. The collaboration, however, is not always successful, and it is even difficult to resume or maintain the collaboration. In this talk, I will share my experience of successful collaboration involving various puzzles of circadian (~24hr) rhythms, including 60 years old one. Specifically, I will present how the combination of mathematical modeling and experiments have successfully identified molecular mechanisms underlying robust circadian timekeeping and circadian regulation of disease (e.g. Cancer).

Friday, May 19, 4:30-6 p.m.

Room # 106, Building # 102



Realization of a Brownian information engine and verification of nonequilibrium equalities under error-free and real time feedback control


Hyuk Kyu Pak

Professor, IBS Center for Soft and Living Matter and Department of Physics, UNIST

Abstract

In the presence of a feedback control, there are several studies about the relation between information and thermodynamics in describing non-equilibrium dynamics of fluctuating systems. Here, we have designed an information engine that consists of a colloidal particle in a single heat bath. The engine is capable of transporting the particle along one direction by utilizing the information about the microscopic state of the system. This one way transportation of the particle behaves as a Brownian information motor. We measured the average extracted work for various feedback period and found that the average extracted work per engine cycle increases with increasing the period, and for large period, our system is capable of achieving an upper bound of the extractable work. We have also investigated the relation between the average transport velocity and the extracted work. For a given period, the average transport velocity is limited by the amount of extracted work or the net available information. We have also demonstrated that the generalized Jarzynski equalities are satisfied in this engine.

Monday, June 5, 5-6 p.m.

Room # 108, Building # 102



Genome-wide Target Specificities of CRISPR Nucleases and Deaminases


Jin-Soo Kim

Director, IBS Center for Genome Engineering and Seoul National University

http://cge.ibs.re.kr/html/cge_en/

Abstract

Despite broad interest in RNA-guided genome editing, Cas9 and Cpf1 are limited by off-target mutations. We developed nuclease-digested whole genome sequencing (Digenome-seq) to profile genome-wide specificities of these nucleases in an unbiased manner. Digenome-seq captured nuclease cleavage sites at single nucleotide resolution and identified off-target sites at which indels were induced with frequencies below 0.1%. We also showed that these off-target effects could be avoided by using purified Cas9/Cpf1 ribonucleoproteins (RNPs) and modified guide RNAs. Digenome-seq is a robust, sensitive, unbiased, and cost-effective (< USD 1,500) method for profiling genome-wide off-target effects of programmable nucleases.

Thursday, June 8, 5-6 p.m.

Room # 106, Building # 102



Live-cell imaging with upconverting nanoparticles (UCNPs): 3D single particle tracking and super-resolution imaging


Kang Taek Lee

Professor, Department of Chemistry, Gwangju Institute of Science and Technology (GIST)

Abstract

Lanthanide ion-doped upconverting nanoparticles (UCNPs), which emit in the visible range upon absorption of NIR photons, have attracted great attention in the area of biological imaging owing to their advantageous properties. First, two-photon upconversion of NIR to the emission of a visible photon is so efficient that a tiny CW laser with the output of tens of milliwatts is sufficient as the excitation source even for single-particle detection. Therefore, “inexpensive” “wide-field” two-photon imaging can easily be achieved with UCNPs, which is not feasible with organic fluorophores and femtosecond laser systems used in conventional two-photon microscopy. Second, by employing NIR excitation, one can suppress cellular autofluorescence, hardly induce photo-damage to cells, and achieve deep penetration into tissues. In addition, UCNPs are extremely photo-stable without photoblinking and photobleaching, and finally, their cytotoxicity turns out to be very low. All these aspects strongly suggest that the UCNP-based imaging should provide an excellent platform for “non-scanning” wide-field two-photon microscopy, which is capable of high-speed, high-contrast, biocompatible, uninterrupted, long-term, live-cell imaging. These advanced concepts in microscopy were fully demonstrated in our recent studies on single-particle 3D imaging and tracking. Currently, we are focusing on the chemical functionalization of UCNPs to specifically bind biomolecules or organelles (mitochondria, nuclei, and cell membrane) to reveal the dynamics of cellular compartments in live cells with high temporal and spatial resolution for a long period of time. Finally, we recently found that UCNPs might be an excellent probe for super-resolution microscopy by inducing intermediate state STED (stimulated emission depletion).

Friday, June 16, 5-6 p.m.

Room # 325, Building # 104



Mass Spectrometry Imaging in Metabolomics Scale


Young Jin Lee

Associate Professor, Department of Chemistry, Iowa State University

Abstract

Metabolomics has become an essential tool for functional genomics and systems biology. In spite of recent progresses, there are fundamental limitations in current protocols of metabolomics, especially in terms of localization information of the metabolites. Mass spectrometry imaging (MSI) is one of the fast growing technological science that can directly explore the fine details of endogeneous molecular distributions. With matrix-assisted laser desorption ionization (MALDI) as an ionization method, it is particularly powerful to unveil cell-specific heterogeneous metabolite distributions. Because of the lack in chromatographic separation, however, it is very difficult to confidently identify metabolites. Additionally, the chemical diversity it can cover is very limited due to the matrix-dependent selectivity of ionization efficiencies. We have overcome the former issue by developing "multiplex mass spectrometry imaging" technique that acquires high-resolution mass spectra and tandem mass spectra simultaneously in a single MSI data acquisition. In this approach, chemical composition is determined from accurate mass information and structural information is obtained from MS/MS spectra for each of the mass peaks. We have expanded this technology to include polarity switching so that both positive and negative ion mass spectrometric images can be acquired in a single data acquisition, and also demonstrated that sampling pixels can be overlapped to avoid the sacrifice of spatial resolution. To overcome the latter issue, we have adopted the use of multiple matrices and dual polarity on consecutive tissue sections. When this approach was applied for germinating maize embryos, we could obtain over five hundreds of unique ions based on accurate mass, and over one hundred of them shows high-quality MS/MS spectra. Systematic adoption of this approach on various germination time points and two different genotypes, along with in-parallel global metabolomics, made many new unprecedented discoveries involved in the germination metabolism of maize seeds. Also discussed will be the use of nanoparticles as a new type of matrices. Nanoparticles have shown a great potential for small molecule analysis, because of no or minimal matrix backgrounds, high laser absorptivity, vacuum stability, and homogeneous application. Because there is a lack of understanding in nanoparticle-analyte correlation, we have performed a large-scale nanoparticle screening which has become a useful guideline in nanoparticle selection.

Wednesday, November 22, 2017, 4-6 p.m.

Room # 106, Building # 102

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