Article
Physics, Multidisciplinary
Liat Nemirovsky, Moshe-Ishay Cohen, Yaakov Lumer, Eran Lustig, Mordechai Segev
Summary: Synthetic-space topological insulators are topological systems where at least one spatial dimension is replaced by a periodic arrangement of modes. These systems can enrich the physics of topological insulators by enabling higher dimensions and nonlocal coupling. This new mechanism can be realized in photonics and cold atoms, showcasing robust unidirectional propagation in the presence of defects and disorder.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Kunwei Wu, Wenyan Han, Wei Lu
Summary: Sleep is an essential process for memory consolidation, and this study reveals the daily rhythmic alterations of GABAergic synapses in hippocampal CA1 pyramidal neurons. Wake promotes tonic inhibition and inhibits phasic inhibition compared to sleep. The study also demonstrates that inhibitory inputs from parvalbumin-expressing interneurons contribute to dynamic iLTP during sleep and wake. Additionally, synaptic insertion of alpha 5-GABA(A) receptors is found to underlie the wake-specific enhancement of iLTP at parvalbumin synapses, independent of the time of the day.
Article
Physics, Fluids & Plasmas
Edem Kossi Akakpo, Marc Haelterman, Francois Leo, Pedro Parra-Rivas
Summary: In this paper, we theoretically investigate the dynamics, bifurcation structure, and stability of dark localized states in Kerr cavities with positive second- and fourth-order dispersion. We found that dark states form through the locking of uniform wave fronts, or domain walls, and undergo a bifurcation structure known as collapsed homoclinic snaking. We also showed that increasing the dispersion of fourth order can stabilize bright localized states.
Article
Astronomy & Astrophysics
Vaclav Pavlik, Steven N. Shore
Summary: This study aims to investigate the consequences of a fast massive stellar remnant encountering a planetary system. By modeling close encounters between the Solar System and a neutron star or a black hole, the distribution of possible outcomes is presented, including the potential for captured planets to form new systems.
ASTRONOMY & ASTROPHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Tianhong Huang, Jiawei Chang, Lin Ma, Andrew J. Fisher, Nicholas M. Harrison, Taoyu Zou, Hai Wang, Wei Wu
Summary: This study explores the potential of optically controlling molecular spin quantum bits, and calculates exchange interactions and spin dynamics mediated by optically driven triplet state. By proposing a technological blueprint that combines two-dimensional molecular networks and programmable nanophotonics, computational exploration of chemical databases could be realized, advancing molecular quantum technology.
NPG ASIA MATERIALS
(2023)
Article
Multidisciplinary Sciences
Ece Sakalar, Thomas Klausberger, Balint Lasztoczi
Summary: Effective communication across brain areas requires distributed neuronal networks to synchronize or decouple their activity. GABAergic interneurons not only lock the ensembles to oscillations, but also synchronize the firing of pyramidal cells with cortical inputs without reducing their activity. The temporary disengagement of synchrony allows for new communication partners.
Article
Biology
Lewis Macdonald, Gillian C. Taylor, Jennifer Margaret Brisbane, Ersi Christodoulou, Lucy Scott, Alex von Kriegsheim, Janet Rossant, Bin Gu, Andrew J. Wood
Summary: Researchers have developed a genetic engineering method using CRISPR technology to efficiently degrade endogenous proteins in vivo, and found that degradation kinetics depend on the dosage of the protein, ligand, and substrate receptor. Applying this method to the study of key regulators of cell division, they discovered that these regulators are essential for cell division in precursor lymphocytes.
Article
Multidisciplinary Sciences
Ebu Bekir Aygar
Summary: Tunnels excavated under high cover in graphitic schists face various problems depending on the squeezing mechanism. Long-term squeezing mechanisms can cause failures in the support systems, and excavating tunnels simultaneously may result in excessive deformations. The excavation method directly affects the stability of the tunnel.
SCIENTIFIC REPORTS
(2022)
Article
Optics
Luqi Yuan, Avik Dutt, Shanhui Fan
Summary: The concept of synthetic dimensions in photonics has attracted growing interest, with a focus on the ring resonator system under dynamic modulation as a powerful method to build synthetic frequency dimensions. Important physical phenomena in synthetic dimensions, including nontrivial topological physics, are discussed in this Tutorial.
Article
Mathematics, Interdisciplinary Applications
Stelios Bekiros, Guessas Laarem, Jun Mou, Abdullah A. Al-Barakati, Hadi Jahanshahi
Summary: In this study, we use a heterogeneous agent-based modeling approach to explore boom-bust cycles in stock markets. We focus on the dynamics of market participants switching between contrarian and fundamental strategies. Our numerical simulations and analysis of phase portraits, bifurcation diagrams, and Lyapunov exponents reveal that chaotic dynamics emerge when the system adjusts with at least one positive Lyapunov exponent. These findings are valuable for traders, arbitrageurs, investors, speculators, and institutional market makers.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Multidisciplinary Sciences
Marie-France Langelier, Ramya Billur, Aleksandr Sverzhinsky, Ben E. Black, John M. Pascal
Summary: HPF1 dynamically regulates the ADP-ribosylation activity of PARP1/2 by accelerating the initiation rate on serine residues; HPF1 efficiently modulates the catalytic output of PARP1/2 to ensure it does not interfere with PAR chain elongation; The study provides evidence for the prevalence of serine-ADP-ribose modification in cells and its importance in an acute DNA damage response.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Takashi Mori, Tatsuhiko Shirai
Summary: Markovian open quantum systems exhibit complex relaxation dynamics. The spectral gap of the Liouvillian characterizes the decay rate towards the steady state, but it may not accurately estimate the relaxation time due to a long crossover time. We introduce the symmetrized Liouvillian gap to provide a rigorous upper bound on the transient decay of autocorrelation functions in the steady state. Numerical results show that the symmetrized Liouvillian gap always gives a correct upper bound, while the standard Liouvillian gap does not.
PHYSICAL REVIEW LETTERS
(2023)
Review
Biochemistry & Molecular Biology
Qianqian Zheng, Liangwei Duan, Yang Zhang, Jiaoyang Li, Shiyu Zhang, Hui Wang
Summary: Autophagy is a cellular degradation process that maintains cellular homeostasis and protects organisms from environmental stress. Pathogens have evolved strategies to interfere with autophagy and utilize autophagic degradation for their own proliferation and reproduction.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2022)
Article
Oceanography
Yunhai Fang, Tianyuan Zheng, Huan Wang, Xilai Zheng, Marc Walther
Summary: This study investigated the influence of seasonal inland freshwater input on the stability of the tide-induced upper saline plume (USP) and the behavior of seawater intrusion (SWI) and submarine groundwater discharge (SGD). It was found that USP experienced a dynamically stable-unstable process as the seasonal inland freshwater input varied. The extent of SWI and SGD showed a dual response to the seasonal inland freshwater input. Moreover, the response of saline SGD and total SGD to the seasonal fluctuation in the inland freshwater input was nonlinear.
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2022)
Article
Geosciences, Multidisciplinary
Brenton Hirao, Heather Savage, Emily E. Brodsky
Summary: The study found shallow triggered creep events along the northern edge of the San Andreas Fault's central creeping section following the 2003 and 2004 earthquakes, with significant changes in creep rate between regional earthquakes. This suggests that triggering connects behavior in the northern San Andreas Fault to the southern section and other regional faults.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Michel Bengtson, Mitasha Bharadwaj, Oskar Franch, Jaco van der Torre, Veronique Meerdink, Henk Schallig, Cees Dekker
Summary: This article presents an isothermal DNA detection scheme for diagnosing pathogenic DNA in resource-limited settings. The scheme uses instrument-free DNA extraction methods and Recombinase Polymerase Amplification for amplification. A colorimetric readout visible to the naked eye is produced through two amplification steps. The method has been successfully applied for detecting DNA from parasites causing leishmaniasis and has potential for detecting any DNA with minimal means.
Article
Biochemical Research Methods
Kevin D. Whitley, Stuart Middlemiss, Calum Jukes, Cees Dekker, Seamus Holden
Summary: Light microscopy is crucial for analyzing bacterial spatial organization, but the sizes and shapes of bacterial cells present unique challenges for imaging. This article introduces a pair of newly developed methods, VerCINI and mu VerCINI, which greatly improve spatial resolution and image quality for microscopy of the short axes of bacteria.
Article
Biochemistry & Molecular Biology
Je-Kyung Ryu, Sang-Hyun Rah, Richard Janissen, Jacob W. J. Kerssemakers, Andrea Bonato, Davide Michieletto, Cees Dekker
Summary: The condensin SMC protein complex is responsible for organizing chromosomal structure by extruding loops of DNA. This study reveals that the condensin reels in DNA in large amounts, with an average of approximately 200 base pairs per extrusion step at low force. ATP binding is found to be the primary step-generating stage underlying DNA loop extrusion.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Alberto Blanch Jover, Nicola De Franceschi, Daphna Fenel, Winfried Weissenhorn, Cees Dekker
Summary: In this study, using TEM imaging and biochemical assays, the researchers investigated CdvB1, a major component of the cell division system in Crenarchaea. They found that CdvB1 self-assembles into filaments and can be detached from lipid membranes by the action of CdvC.
Article
Multidisciplinary Sciences
Indra A. Shaltiel, Sumanjit Datta, Lea Lecomte, Markus Hassler, Marc Kschonsak, Sol Bravo, Catherine Stober, Jenny Ormanns, Sebastian Eustermann, Christian H. Haering
Summary: This study reveals the molecular mechanism underlying the activity of the active condensin complex in shaping chromosome structure by extruding DNA loops. The study shows that the condensin complex entraps the bases of a DNA loop in two separate chambers, with a power-stroke movement feeding DNA into the SMC-kleisin ring and the second chamber holding on upstream of the same DNA double helix.
Article
Biochemistry & Molecular Biology
Eugene Kim, Alejandro Martin Gonzalez, Biswajit Pradhan, Jaco van der Torre, Cees Dekker
Summary: Condensin is a motor protein that organizes chromosomes by extruding loops of DNA. This study investigates how DNA supercoiling affects loop extrusion and provides insights into the loading and formation of supercoiled loops by SMC complexes.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Review
Nanoscience & Nanotechnology
Yi-Lun Ying, Zheng-Li Hu, Shengli Zhang, Yujia Qing, Alessio Fragasso, Giovanni Maglia, Amit Meller, Hagan Bayley, Cees Dekker, Yi-Tao Long
Summary: This Review discusses the latest advancements in nanopore technologies beyond DNA sequencing. Nanopore techniques have evolved as ultrasensitive analytical tools for individual molecules, enabling applications in molecular sensing and sequencing, chemical catalysis, and biophysical characterization. The prospects of single-protein analysis and sequencing, clinical sensing applications, and synthetic biomimetic nanopores are highlighted. Further exploration of nanopore technologies is expected as control over pore design improves.
NATURE NANOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Nicola De Franceschi, Weria Pezeshkian, Alessio Fragasso, Bart M. H. Bruininks, Sean Tsai, Siewert J. Marrink, Cees Dekker
Summary: The shape of cellular membranes determines their structure and function. A DNA-nanotechnology-based approach, called the synthetic membrane shaper (SMS), can stabilize the shape of cellular membranes and is compatible with protein reconstitution. This method provides a general tool for studying protein binding to complex membrane geometries.
Article
Chemistry, Multidisciplinary
Chenyu Wen, Eva Bertosin, Xin Shi, Cees Dekker, Sonja Schmid
Summary: In this study, we achieved strong trapping and extended observation of single proteins using site specific cholesterol functionalization on a lipid-coated nanopore. This greatly enhances the trapping capacity and extends the observation time.
Article
Multidisciplinary Sciences
Sabrina Meindlhumer, Fridtjof Brauns, Jernej Rudi Finzgar, Jacob Kerssemakers, Cees Dekker, Erwin Frey
Summary: Meindlhumer et al. have conducted a combined theoretical and experimental study on how the propagation direction of Min protein patterns can be changed by a bulk flow of solution. They demonstrate that the direction of in vitro Min protein patterns can be controlled by hydrodynamic flow, with downstream propagation for low concentration ratios of MinE:MinD, upstream propagation for large ratios, and multistability in between. Their study reveals the potential of using flow to probe molecular features and constrain mathematical models for pattern formation systems.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Iain F. Davidson, Roman Barth, Maciej Zaczek, Jaco van der Torre, Wen Tang, Kota Nagasaka, Richard Janissen, Jacob Kerssemakers, Gordana Wutz, Cees Dekker, Jan-Michael Peters
Summary: CTCF is a DNA-binding protein that establishes topologically associating domains (TADs) by blocking the diffusion and loop extrusion of cohesin. CTCF functions asymmetrically and is dependent on DNA tension. Moreover, CTCF regulates cohesin's loop-extrusion activity by changing its direction and inducing loop shrinkage. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.
Article
Biotechnology & Applied Microbiology
Ian C. C. Nova, Justas Ritmejeris, Henry Brinkerhoff, Theo J. R. Koenig, Jens H. H. Gundlach, Cees Dekker
Summary: Drawing peptides through a nanopore allows for the detection of individual phosphorylation sites; Current methods cannot measure single molecules or differentiate between closely spaced phosphorylation sites; We can detect cancer-associated post-translational modifications at the single-molecule level by controlling the peptide's movement through a nanopore; With individual reads of single molecules, we can discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre, Cees Dekker
Summary: Transcription-coupled supercoiling of DNA plays a crucial role in chromosome compaction and the regulation of genetic processes. This study experimentally validates the twin-supercoiled-domain model and demonstrates that RNA polymerase can generate up- and downstream supercoils simultaneously during transcription. These findings provide insight into the mechanistic cause of supercoil generation by RNA polymerase in transcription.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Pauline J. Kolbeck, Milos Tisma, Brian T. Analikwu, Willem Vanderlinden, Cees Dekker, Jan Lipfert
Summary: In this article, the authors propose a quantitative model for the modulation of DNA binding by DNA topology and demonstrate its accuracy through experiments. They focus on the binding of fluorescent intercalators to DNA and directly observe the impact of different intercalator densities on DNA through single-molecule assays. The model has wide implications for the detection and quantification of DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Martin Holub, Anthony Birnie, Aleksandre Japaridze, Jaco van der Torre, Maxime den Ridder, Carol de Ram, Martin Pabst, Cees Dekker
Summary: Chromosome structure and function were studied through various cell-based methods and in vitro single-molecule techniques. The researchers developed a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. By isolating chromosomes from bacterial cells and enzymatically digesting native proteins, they removed DNA-binding proteins and observed DNA compaction and motion. The study suggests the feasibility of a "genome-in-a-box" approach to study chromosome organization.
CELL REPORTS METHODS
(2022)
