Tsvi Tlusty – C.V
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Catalytic Enzymes Are Active Matter
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by IBS Publications Repository Catalytic enzymes are active matter Ah-Young Jeea, Yoon-Kyoung Choa,b, Steve Granicka,c,d,1, and Tsvi Tlustya,c,1 aCenter for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, South Korea; bDepartment of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea; cDepartment of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea; and dDepartment of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea Contributed by Steve Granick, September 27, 2018 (sent for review August 17, 2018; reviewed by Changbong Hyeon and Elisha Moses) Using a microscopic theory to analyze experiments, we demon- All this signaled a paradigm shift in our understanding of en- strate that enzymes are active matter. Superresolution fluores- zymes. Large-scale internal mobility, such as hinge-like rotations, cence measurements—performed across four orders of magnitude twists, or shear-like sliding, was already linked to the function of of substrate concentration, with emphasis on the biologically enzymes (9–13) in the classical mechanisms of allostery (14) and relevant regime around or below the Michaelis–Menten constant— induced fit (15). However, energetically driven translational mo- show that catalysis boosts the motion of enzymes to be superdif- tion was considered the exclusive realm of molecular motors (16). fusive for a few microseconds, enhancing their effective diffusiv- In light of the evidence for boosted enzymatic mobility, this dis- ity over longer timescales. Occurring at the catalytic turnover tinction appears rather artificial, and one should see enzymes as rate, these fast ballistic leaps maintain direction over a duration nanomotors whose dynamic profile influences their function and limited by rotational diffusion, driving enzymes to execute worm- spatiotemporal organization (3, 17–19). -
Diffusing Wave Microrheology of Highly Scattering Concentrated Monodisperse Emulsions
Diffusing wave microrheology of highly scattering concentrated monodisperse emulsions Ha Seong Kima, Nesrin S¸enbilb, Chi Zhangb, Frank Scheffoldb,1, and Thomas G. Masona,c,1 aDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095; bDepartment of Physics, University of Fribourg, CH-1700 Fribourg, Switzerland; and cDepartment of Physics and Astronomy, University of California, Los Angeles, CA 90095 Edited by Steve Granick, IBS Center for Soft and Living Matter, Ulju-gun, Ulsan, Republic of Korea, and approved February 27, 2019 (received for review October 3, 2018) Motivated by improvements in diffusing wave spectroscopy nating light (4). Because the standard analytical framework of (DWS) for nonergodic, highly optically scattering soft matter and DWS neglects collective scattering of colloidal probes at high by cursory treatment of collective scattering effects in prior DWS densities, DWS MSDs extracted for such dense colloidal sys- microrheology experiments, we investigate the low-frequency tems do not necessarily represent the true self-motion of the 0 plateau elastic shear moduli Gp of concentrated, monodisperse, probes. Consequently, using DWS MSDs for thermal-entropic disordered oil-in-water emulsions as droplets jam. In such exper- passive microrheology (6, 7) of dense dispersions, including con- iments, the droplets play dual roles both as optical probes and centrated emulsions, would likely lead to inaccurate predictions as the jammed objects that impart shear elasticity. Here, we of their linear viscoelastic moduli, since passive microrheol- demonstrate that collective scattering significantly affects DWS ogy requires accurate self-motion MSDs in the generalized mean-square displacements (MSDs) in dense colloidal emulsions. Stokes–Einstein relation (GSER) (6, 8). -
Mechanistic Mathematical Modeling of Spatiotemporal Microtubule Dynamics and Regulation in Vivo
Research Collection Doctoral Thesis Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo Author(s): Widmer, Lukas A. Publication Date: 2018 Permanent Link: https://doi.org/10.3929/ethz-b-000328562 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library diss. eth no. 25588 MECHANISTICMATHEMATICAL MODELINGOFSPATIOTEMPORAL MICROTUBULEDYNAMICSAND REGULATION INVIVO A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (dr. sc. eth zurich) presented by LUKASANDREASWIDMER msc. eth cbb born on 11. 03. 1987 citizen of luzern and ruswil lu, switzerland accepted on the recommendation of Prof. Dr. Jörg Stelling, examiner Prof. Dr. Yves Barral, co-examiner Prof. Dr. François Nédélec, co-examiner Prof. Dr. Linda Petzold, co-examiner 2018 Lukas Andreas Widmer Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo © 2018 ACKNOWLEDGEMENTS We are all much more than the sum of our work, and there is a great many whom I would like to thank for their support and encouragement, without which this thesis would not exist. I would like to thank my supervisor, Prof. Jörg Stelling, for giving me the opportunity to conduct my PhD research in his group. Jörg, you have been a great scientific mentor, and the scientific freedom you give your students is something I enjoyed a lot – you made it possible for me to develop my own theories, and put them to the test. I thank you for the trust you put into me, giving me a challenge to rise up to, and for always having an open door, whether in times of excitement or despair. -
Causal Queries from Observational Data in Biological Systems Via Bayesian Networks: an Empirical Study in Small Networks
Causal Queries from Observational Data in Biological Systems via Bayesian Networks: An Empirical Study in Small Networks Alex White and Matthieu Vignes Abstract Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and post- genomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the con- sideration of causal representations of the interactions in living systems. We present the causal formalism and bring it out in the context of biological networks, when the data is observational. We also discuss its ability to decipher the causal infor- mation flow as observed in gene expression. We also illustrate our exploration by experiments on small simulated networks as well as on a real biological data set. Key words: Causal biological networks, Gene regulatory network reconstruction, Direct Acyclic Graph inference, Bayesian networks 1 Introduction Throughout their lifetime, organisms express their genetic program, i.e. the instruc- tion manual for molecular actions in every cell. The products of the expression of this program are messenger RNA (mRNA); the blueprints to produce proteins, the cornerstones of the living world. The diversity of shapes and the fate of cells is a re- sult of different readings of the genetic material, probably because of environmental factors, but also because of epigenetic organisational capacities. The genetic mate- rial appears regulated to produce what the organism needs in a specific situation. We now have access to rich genomics data sets. We see them as instantaneous images of cell activity from varied angles, through different filters. -
Multiscale Modeling in Systems Biology
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2051 Multiscale Modeling in Systems Biology Methods and Perspectives ADRIEN COULIER ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1225-5 UPPSALA URN urn:nbn:se:uu:diva-442412 2021 Dissertation presented at Uppsala University to be publicly examined in 2446 ITC, Lägerhyddsvägen 2, Uppsala, Friday, 10 September 2021 at 10:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Mark Chaplain (University of St Andrews). Abstract Coulier, A. 2021. Multiscale Modeling in Systems Biology. Methods and Perspectives. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2051. 60 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1225-5. In the last decades, mathematical and computational models have become ubiquitous to the field of systems biology. Specifically, the multiscale nature of biological processes makes the design and simulation of such models challenging. In this thesis we offer a perspective on available methods to study and simulate such models and how they can be combined to handle biological processes evolving at different scales. The contribution of this thesis is threefold. First, we introduce Orchestral, a multiscale modular framework to simulate multicellular models. By decoupling intracellular chemical kinetics, cell-cell signaling, and cellular mechanics by means of operator-splitting, it is able to combine existing software into one massively parallel simulation. Its modular structure makes it easy to replace its components, e.g. to adjust the level of modeling details. We demonstrate the scalability of our framework on both high performance clusters and in a cloud environment. -
Advancing a Systems Cell-Free Metabolic Engineering Approach to Natural Product Synthesis and Discovery
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2020 Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery Benjamin Mohr University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Mohr, Benjamin, "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery. " PhD diss., University of Tennessee, 2020. https://trace.tennessee.edu/utk_graddiss/6837 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Mohr entitled "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Energy Science and Engineering. Mitchel Doktycz, Major Professor We have read this dissertation and recommend its acceptance: Jennifer Morrell-Falvey, Dale Pelletier, Michael Simpson, Robert Hettich Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Benjamin Pintz Mohr December 2019 c by Benjamin Pintz Mohr, 2019 All Rights Reserved. -
About the Authors
1845 About the Authors Chong H. Ahn Chapter B.19 Authors University of Cincinnati Dr. Chong Ahn is a Professor of Electrical and Computer Engineering at the Department of Electrical University of Cincinnati. He obtained his Ph.D. degree in Electrical Engineering from and Computer Engineering the Georgia Institute of Technology in 1993 and then worked as a postdoctoral fellow and Computer Science at IBM T.J. Watson Research Center. His research interests include all aspects of Cincinnati, OH, USA [email protected] design, fabrication, and characterization of magnetic MEMS devices, microfluidic devices, protein chips, lab-on-a-chips, nano biosensors, point-of-care testing and BioMEMS systems. He is an associate editor of the IEEE Sensors Journal. Boris Anczykowski Chapter C.27 nanoAnalytics GmbH Dr. Boris Anczykowski is a physicist with an extensive research background in the Münster, Germany field of dynamic Scanning Force Microscopy. He co-invented the Q-Control technique [email protected] and received the Innovation Award Münsterland for Science and Economy in 2001 for this achievement. He is a managing director and co-founder of nanoAnalytics GmbH, a company specialized in the characterization of surfaces and interfaces on the micro- and nanometer scale. Massood Z. Atashbar Chapter A.7 Western Michigan University Professor Massood Z. Atashbar received the B.Sc. degree in electrical Department of Electrical engineering from the Isfahan University of Technology, Tehran, Iran, and Computer Engineering the M.Sc. degree in electrical engineering from the Sharif University of Kalamazoo, MI, USA Technology, Tehran, and the Ph.D. degree from the Department of [email protected] Communication and Electronic Engineering, RMIT University, Melbourne, Australia, in 1998. -
Bioengineering Professor Trey Ideker Wins 2009 Overton Prize
Bioengineering Professor Trey Ideker Wins 2009 Overton Prize March 13, 2009 Daniel Kane University of California, San Diego bioengineering professor Trey Ideker-a network and systems biology pioneer-has won the International Society for Computational Biology's Overton Prize. The Overton prize is awarded each year to an early-to-mid-career scientist who has already made a significant contribution to the field of computational biology. Trey Ideker is an Associate Professor of Bioengineering at UC San Diego's Jacobs School of Engineering, Adjunct Professor of Computer Science, and member of the Moores UCSD Cancer Center. He is a pioneer in using genome-scale measurements to construct network models of cellular processes and disease. His recent research activities include development of software and algorithms for protein network analysis, network-level comparison of pathogens, and genome-scale models of the response to DNA-damaging agents. "Receiving this award is a wonderful honor and helps to confirm that the work we have been doing for the past several years has been useful to people," said Ideker. "This award also provides great recognition to UC San Diego which has fantastic bioinformatics programs both at the undergraduate and graduate level. I could never have done it without the help of some really first-rate bioinformatics and bioengineering graduate students," said Ideker. Ideker is on the faculty of the Jacobs School of Engineering's Department of Bioengineering, which ranks 2nd in the nationfor biomedical engineering, according to the latest US News rankings. The bioengineering department has ranked among the top five programs in the nation every year for the past decade. -
The Myth of Junk DNA
The Myth of Junk DNA JoATN h A N W ells s eattle Discovery Institute Press 2011 Description According to a number of leading proponents of Darwin’s theory, “junk DNA”—the non-protein coding portion of DNA—provides decisive evidence for Darwinian evolution and against intelligent design, since an intelligent designer would presumably not have filled our genome with so much garbage. But in this provocative book, biologist Jonathan Wells exposes the claim that most of the genome is little more than junk as an anti-scientific myth that ignores the evidence, impedes research, and is based more on theological speculation than good science. Copyright Notice Copyright © 2011 by Jonathan Wells. All Rights Reserved. Publisher’s Note This book is part of a series published by the Center for Science & Culture at Discovery Institute in Seattle. Previous books include The Deniable Darwin by David Berlinski, In the Beginning and Other Essays on Intelligent Design by Granville Sewell, God and Evolution: Protestants, Catholics, and Jews Explore Darwin’s Challenge to Faith, edited by Jay Richards, and Darwin’s Conservatives: The Misguided Questby John G. West. Library Cataloging Data The Myth of Junk DNA by Jonathan Wells (1942– ) Illustrations by Ray Braun 174 pages, 6 x 9 x 0.4 inches & 0.6 lb, 229 x 152 x 10 mm. & 0.26 kg Library of Congress Control Number: 2011925471 BISAC: SCI029000 SCIENCE / Life Sciences / Genetics & Genomics BISAC: SCI027000 SCIENCE / Life Sciences / Evolution ISBN-13: 978-1-9365990-0-4 (paperback) Publisher Information Discovery Institute Press, 208 Columbia Street, Seattle, WA 98104 Internet: http://www.discoveryinstitutepress.com/ Published in the United States of America on acid-free paper. -
Snapshot: Network Motifs Oren Shoval and Uri Alon Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
SnapShot: Network Motifs Oren Shoval and Uri Alon Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel 326 Cell 143, October 15, 2010 ©2010 Elsevier Inc. DOI 10.1016/j.cell.2010.09.050 See online version for legend and references. SnapShot: Network Motifs Oren Shoval and Uri Alon Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel Transcription regulation and signaling networks are composed of recurring patterns called network motifs. Network motifs are much more prevalent in biological networks than would be expected by comparison to random networks and comprise almost the entire network structure. The same small set of network motifs has been found in diverse organ- isms ranging from bacteria to plants to humans. Experiments show that each network motif can carry out specific dynamic functions in the computation done by the cell. Here we review the main classes of network motifs and their biological functions. Autoregulation Negative autoregulation (NAR) occurs when a transcription factor represses the transcription of its own gene. (We use transcription to help make examples concrete; all circuits described here could operate also in other regulatory modes, e.g., a protein inhibiting its own activity by autophosphorylation.) This occurs in about half of the repressors in E. coli and can speed up the response time of gene circuits and reduce cell–cell variation in protein levels that are due to fluctuations in production rate. Positive autoregulation occurs when a transcription factor enhances its own rate of production. Response times are slowed and variation is usually enhanced. This motif, given sufficient cooperativity, can lead to bimodal (all-or-none) distributions, where the concentration of X is low in some cells but high in others. -
Instructions for Preparation of Abstracts for UFO-HFSW 2009
复旦大学物理系 物质科学报告 Time:2:00pm, Tuesday, 2020.01.14 Location: Room C108, Jiangwan Physics Building Title: Some Puzzles and Research Opportunities in Soft Matter Science Speaker: Steve Granick Director, Center for Soft and Living Matter Institute for Basic Science, South Korea Abstract: A fundamental challenge of modern physical 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 and on liquid-cell TEM, 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. With catalytic enzymes, we find problems of mechanobiology. A picture emerges in which simple experiments, performed at single-particle and single-molecule resolution, can dissect macroscopic phenomena in ways that surprise. Steve Granick Member of the U.S. National Academy of Sciences Member of American Academy of Arts and Sciences. He received his PhD degree in University of Wisconsin in 1982. In 1982, he joined the French University of France and University of Minnesota for postdoctoral research. He became an professor in University of Illinois at Urbana-Champaigns. Since 2015, he became the director of the Laboratory at the Korea Institute of Basic Science in Soft Materials and Life Materials. Among his other major awards are the Paris-Sciences Medal, APS national Polymer Physics Prize, and ACS national Colloid and Surface Chemistry Prize.. -
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[Attachment 1-5] List of IBS Research Centers (As of Dec. 21, 2020) □ Total 31 Centers (30 Directors and 3 CIs) ○ Nine HQ, thirteen Campus(five at KAIST alliance campus, seven at DUP alliance campus, one at GIST), and nine Extramural Centers Field (number of Center name Director·CI Photo Center type Research area centers) Center for Correlated External Condensed NOH Tae Won Electron Systems (Seoul Nat. Univ.) matter physics Center for Integrated External Nanostructure LEE Young Hee Nanostructure Physics (Sungkyunkwan Univ.) physics Center for Relativistic Campus NAM Chang Hee Optics Laser Science (GIST) Center for Axion and Yannis Campus Elementary Precision Physics Research SEMERTZIDIS (KAIST) particle physics Center for Artificial YEOM Han Campus Condensed Low Dimensional Woong (POSTECH) matter physics Physics Electronic Systems (10) Center for KIM Yeongduk HQ Particle physics Underground Physics Ceter for Theoretical HQ Theoretical CHOI Kiwoon Physics of the Universe (Co-director) physics Center for Theoretical HQ Theoretical Physics of Complex Sergej FLACH (Co-director) physics Systems Center for Quantum Andreas External Quantum Nanoscience HEINRICH (Ewha W. Univ.) nanoscience Center for Exotic Rare Isotope HAHN Kevin Insik HQ Nuclear Studies Sciences SHIN Hee-Sup Center for Cognition HQ Brain science and Sociality LEE Changjoon (Co-director) Justin Center for Synaptic Campus KIM Eunjoon Brain science Brain Dysfunctions (KAIST) Life Center for RNA External Molecular cell KIM V. Narry Sciences Research (Seoul Nat. Univ.) biology (6)