1
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Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. Am J Physiol Lung Cell Mol Physiol 2022; 322:L822-L841. [PMID: 35438006 PMCID: PMC9142163 DOI: 10.1152/ajplung.00254.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis is controversial. Recently, aberrant basaloid cells were identified in fibrotic lung tissue as a novel epithelial cell type displaying a partial EMT phenotype. The developmental origin of these cells remains unknown. To elucidate the role of EMT in the development of aberrant basaloid cells from the bronchial epithelium, we mapped EMT-induced transcriptional changes at the population and single-cell levels. Human bronchial epithelial cells grown as submerged or air-liquid interface (ALI) cultures with or without EMT induction were analyzed by bulk and single-cell RNA-Sequencing. Comparison of submerged and ALI cultures revealed differential expression of 8,247 protein coding (PC) and 1,621 long noncoding RNA (lncRNA) genes and revealed epithelial cell-type-specific lncRNAs. Similarly, EMT induction in ALI cultures resulted in robust transcriptional reprogramming of 6,020 PC and 907 lncRNA genes. Although there was no evidence for fibroblast/myofibroblast conversion following EMT induction, cells displayed a partial EMT gene signature and an aberrant basaloid-like cell phenotype. The substantial transcriptional differences between submerged and ALI cultures highlight that care must be taken when interpreting data from submerged cultures. This work supports that lung epithelial EMT does not generate fibroblasts/myofibroblasts and confirms ALI cultures provide a physiologically relevant system to study aberrant basaloid-like cells and mechanisms of EMT. We provide a catalog of PC and lncRNA genes and an interactive browser (https://bronc-epi-in-vitro.cells.ucsc.edu/) of single-cell RNA-Seq data for further exploration of potential roles in the lung epithelium in health and lung disease.
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Affiliation(s)
- Dinesh Babu Uthaya Kumar
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
| | - Efthymios Motakis
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Te-Chia Wu
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Johad Khoury
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jessica Grassmann
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, Massachusetts
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jonathan L Koff
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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2
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Kohar V, Gordin D, Katebi A, Levine H, Onuchic JN, Lu M. Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics 2021; 37:1327-1329. [PMID: 33279968 PMCID: PMC8599779 DOI: 10.1093/bioinformatics/btaa785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/08/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY GeneEx is an interactive web-app that uses an ODE-based mathematical modeling approach to simulate, visualize and analyze gene regulatory circuits (GRCs) for an explicit kinetic parameter set or for a large ensemble of random parameter sets. GeneEx offers users the freedom to modify many aspects of the simulation such as the parameter ranges, the levels of gene expression noise and the GRC network topology itself. This degree of flexibility allows users to explore a variety of hypotheses by providing insight into the number and stability of attractors for a given GRC. Moreover, users have the option to upload, and subsequently compare, experimental gene expression data to simulated data generated from the analysis of a built or uploaded custom circuit. Finally, GeneEx offers a curated database that contains circuit motifs and known biological GRCs to facilitate further inquiry into these. Overall, GeneEx enables users to investigate the effects of parameter variation, stochasticity and/or topological changes on gene expression for GRCs using a systems-biology approach. AVAILABILITY AND IMPLEMENTATION GeneEx is available at https://geneex.jax.org. This web-app is released under the MIT license and is free and open to all users and there is no mandatory login requirement. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vivek Kohar
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Danya Gordin
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.,Center for Theoretical Biological Physics.,Department of Bioengineering
| | - Ataur Katebi
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.,Center for Theoretical Biological Physics.,Department of Bioengineering
| | - Herbert Levine
- Center for Theoretical Biological Physics.,Department of Bioengineering.,Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics.,Department of Physics and Astronomy.,Department of Chemistry.,Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Mingyang Lu
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.,Center for Theoretical Biological Physics.,Department of Bioengineering
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Murali K, Rajasekar S, Aravind MV, Kohar V, Ditto WL, Sinha S. Construction of logic gates exploiting resonance phenomena in nonlinear systems. Philos Trans A Math Phys Eng Sci 2021; 379:20200238. [PMID: 33455552 DOI: 10.1098/rsta.2020.0238] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 05/22/2023]
Abstract
A two-state system driven by two inputs has been found to consistently produce a response mirroring a logic function of the two inputs, in an optimal window of moderate noise. This phenomenon is called logical stochastic resonance (LSR). We extend the conventional LSR paradigm to implement higher-level logic architecture or typical digital electronic structures via carefully crafted coupling schemes. Further, we examine the intriguing possibility of obtaining reliable logic outputs from a noise-free bistable system, subject only to periodic forcing, and show that this system also yields a phenomenon analogous to LSR, termed Logical Vibrational Resonance (LVR), in an appropriate window of frequency and amplitude of the periodic forcing. Lastly, this approach is extended to realize morphable logic gates through the Logical Coherence Resonance (LCR) in excitable systems under the influence of noise. The results are verified with suitable circuit experiments, demonstrating the robustness of the LSR, LVR and LCR phenomena. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 1)'.
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Affiliation(s)
- K Murali
- Department of Physics, Anna University, Chennai 600 025, India
| | - S Rajasekar
- Department of Physics, Bharathidasan University, Tiruchirapalli 620 024, India
| | - Manaoj V Aravind
- Indian Institute of Science Education and Research Mohali, Sector 81, Manauli PO 140 306, Punjab, India
| | - Vivek Kohar
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - W L Ditto
- Nonlinear Artificial Intelligence Lab, Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Sudeshna Sinha
- Indian Institute of Science Education and Research Mohali, Sector 81, Manauli PO 140 306, Punjab, India
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4
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Hosur V, Low BE, Li D, Stafford GA, Kohar V, Shultz LD, Wiles MV. Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation. Genome Biol 2020; 21:168. [PMID: 32646486 PMCID: PMC7350591 DOI: 10.1186/s13059-020-02086-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Gene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function in vivo. However, because different gene disruption strategies use different mechanisms to disrupt genes, the strategies can result in diverse phenotypes in the resulting mouse model. To determine whether different gene disruption strategies affect the phenotype of resulting mutant mice, we characterized Rhbdf1 mouse mutant strains generated by three commonly used strategies-definitive-null, targeted knockout (KO)-first, and CRISPR/Cas9. RESULTS We find that Rhbdf1 responds differently to distinct KO strategies, for example, by skipping exons and reinitiating translation to potentially yield gain-of-function alleles rather than the expected null or severe hypomorphic alleles. Our analysis also revealed that at least 4% of mice generated using the KO-first strategy show conflicting phenotypes. CONCLUSIONS Exon skipping is a widespread phenomenon occurring across the genome. These findings have significant implications for the application of genome editing in both basic research and clinical practice.
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Affiliation(s)
- Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Benjamin E. Low
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Daniel Li
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery at Weill Cornell Medicine, New York, NY 10021 USA
| | | | - Vivek Kohar
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | | | - Michael V. Wiles
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
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5
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Katebi A, Kohar V, Lu M. Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience 2020; 23:101150. [PMID: 32450514 PMCID: PMC7251928 DOI: 10.1016/j.isci.2020.101150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 02/03/2023] Open
Abstract
Many biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how a gene regulatory circuit encodes essential information of state transitions. We present a generalized random circuit perturbation method for circuits containing heterogeneous regulation types and its usage to analyze both steady and oscillatory states from an ensemble of circuit models with random kinetic parameters. The stable steady states form robust clusters with a circular structure that are associated with cell cycle phases. This circular structure in the clusters is consistent with single-cell RNA sequencing data. The oscillatory states specify the irreversible state transitions along cell cycle progression. Furthermore, we identify possible mechanisms to understand the irreversible state transitions from the steady states. We expect this approach to be robust and generally applicable to unbiasedly predict dynamical transitions of a gene regulatory circuit.
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Affiliation(s)
- Ataur Katebi
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Vivek Kohar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mingyang Lu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA.
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6
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Hosur V, Skelly DA, Francis C, Low BE, Kohar V, Burzenski LM, Amiji MM, Shultz LD, Wiles MV. Improved mouse models and advanced genetic and genomic technologies for the study of neutrophils. Drug Discov Today 2020; 25:1013-1025. [PMID: 32387410 DOI: 10.1016/j.drudis.2020.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 12/31/2022]
Abstract
Mice have been excellent surrogates for studying neutrophil biology and, furthermore, murine models of human disease have provided fundamental insights into the roles of human neutrophils in innate immunity. The emergence of novel humanized mice and high-diversity mouse populations offers the research community innovative and powerful platforms for better understanding, respectively, the mechanisms by which human neutrophils drive pathogenicity, and how genetic differences underpin the variation in neutrophil biology observed among humans. Here, we review key examples of these new resources. Additionally, we provide an overview of advanced genetic engineering tools available to further improve such murine model systems, of sophisticated neutrophil-profiling technologies, and of multifunctional nanoparticle (NP)-based neutrophil-targeting strategies.
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Affiliation(s)
- Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA.
| | - Daniel A Skelly
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Christopher Francis
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - Benjamin E Low
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Vivek Kohar
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Lisa M Burzenski
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Mansoor M Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - Leonard D Shultz
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Michael V Wiles
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME 04609 USA
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7
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Ramirez D, Kohar V, Lu M. Toward Modeling Context-Specific EMT Regulatory Networks Using Temporal Single Cell RNA-Seq Data. Front Mol Biosci 2020; 7:54. [PMID: 32391378 PMCID: PMC7190801 DOI: 10.3389/fmolb.2020.00054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/17/2020] [Indexed: 01/02/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is well established as playing a crucial role in cancer progression and being a potential therapeutic target. To elucidate the gene regulation that drives the decision making of EMT, many previous studies have been conducted to model EMT gene regulatory circuits (GRCs) using interactions from the literature. While this approach can depict the generic regulatory interactions, it falls short of capturing context-specific features. Here, we explore the effectiveness of a combined bioinformatics and mathematical modeling approach to construct context-specific EMT GRCs directly from transcriptomics data. Using time-series single cell RNA-sequencing data from four different cancer cell lines treated with three EMT-inducing signals, we identify context-specific activity dynamics of common EMT transcription factors. In particular, we observe distinct paths during the forward and backward transitions, as is evident from the dynamics of major regulators such as NF-KB (e.g., NFKB2 and RELB) and AP-1 (e.g., FOSL1 and JUNB). For each experimental condition, we systematically sample a large set of network models and identify the optimal GRC capturing context-specific EMT states using a mathematical modeling method named Random Circuit Perturbation (RACIPE). The results demonstrate that the approach can build high quality GRCs in certain cases, but not others and, meanwhile, elucidate the role of common bioinformatics parameters and properties of network structures in determining the quality of GRCs. We expect the integration of top-down bioinformatics and bottom-up systems biology modeling to be a powerful and generally applicable approach to elucidate gene regulatory mechanisms of cellular state transitions.
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Affiliation(s)
- Daniel Ramirez
- College of Health Solutions, Arizona State University, Tempe, AZ, United States
| | - Vivek Kohar
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, United States
| | - Mingyang Lu
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, United States
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8
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Abstract
Certain nonlinear systems can switch between dynamical attractors occupying different regions of phase space, under variation of parameters or initial states. In this work we exploit this feature to obtain reliable logic operations. With logic output 0/1 mapped to dynamical attractors bounded in distinct regions of phase space, and logic inputs encoded by a very small bias parameter, we explicitly demonstrate that the system hops consistently in response to an external input stream, operating effectively as a reliable logic gate. This system offers the advantage that very low-amplitude inputs yield highly amplified outputs. Additionally, different dynamical variables in the system yield complementary logic operations in parallel. Further, we show that in certain parameter regions noise aids the reliability of logic operations, and is actually necessary for obtaining consistent outputs. This leads us to a generalization of the concept of Logical Stochastic Resonance to attractors more complex than fixed point states, such as periodic or chaotic attractors. Lastly, the results are verified in electronic circuit experiments, demonstrating the robustness of the phenomena. So we have combined the research directions of Chaos Computing and Logical Stochastic Resonance here, and this approach has potential to be realized in wide-ranging systems.
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Affiliation(s)
- K Murali
- Department of Physics, Anna University, Chennai, India
| | - Sudeshna Sinha
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli, Punjab, India
| | - Vivek Kohar
- Nonlinear Artificial Intelligence Lab, Department of Physics, North Carolina State University, Raleigh, NC, United States of America.,The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Behnam Kia
- Nonlinear Artificial Intelligence Lab, Department of Physics, North Carolina State University, Raleigh, NC, United States of America
| | - William L Ditto
- Nonlinear Artificial Intelligence Lab, Department of Physics, North Carolina State University, Raleigh, NC, United States of America
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9
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Abstract
We report the phenomenon of temporally intermittently synchronized and desynchronized dynamics in Watts-Strogatz networks of chaotic Rössler oscillators. We consider topologies for which the master stability function (MSF) predicts stable synchronized behaviour, as the rewiring probability (p) is tuned from 0 to 1. MSF essentially utilizes the largest non-zero Lyapunov exponent transversal to the synchronization manifold in making stability considerations, thereby ignoring the other Lyapunov exponents. However, for an N-node networked dynamical system, we observe that the difference in its Lyapunov spectra (corresponding to the N - 1 directions transversal to the synchronization manifold) is crucial and serves as an indicator of the presence of intermittently synchronized behaviour. In addition to the linear stability-based (MSF) analysis, we further provide global stability estimate in terms of the fraction of state-space volume shared by the intermittently synchronized state, as p is varied from 0 to 1. This fraction becomes appreciably large in the small-world regime, which is surprising, since this limit has been otherwise considered optimal for synchronized dynamics. Finally, we characterize the nature of the observed intermittency and its dominance in state-space as network rewiring probability (p) is varied.
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Affiliation(s)
- Anshul Choudhary
- Theoretical Physics/Complex Systems, ICBM, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Chiranjit Mitra
- Research Domain IV - Transdisciplinary Concepts & Methods, Potsdam Institute for Climate Impact Research, 14473 Potsdam, Germany
| | - Vivek Kohar
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Sudeshna Sinha
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
| | - Jürgen Kurths
- Research Domain IV - Transdisciplinary Concepts & Methods, Potsdam Institute for Climate Impact Research, 14473 Potsdam, Germany
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10
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Kohar V, Kia B, Lindner JF, Ditto WL. Superlinearly scalable noise robustness of redundant coupled dynamical systems. Phys Rev E 2016; 93:032213. [PMID: 27078350 DOI: 10.1103/physreve.93.032213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 06/05/2023]
Abstract
We illustrate through theory and numerical simulations that redundant coupled dynamical systems can be extremely robust against local noise in comparison to uncoupled dynamical systems evolving in the same noisy environment. Previous studies have shown that the noise robustness of redundant coupled dynamical systems is linearly scalable and deviations due to noise can be minimized by increasing the number of coupled units. Here, we demonstrate that the noise robustness can actually be scaled superlinearly if some conditions are met and very high noise robustness can be realized with very few coupled units. We discuss these conditions and show that this superlinear scalability depends on the nonlinearity of the individual dynamical units. The phenomenon is demonstrated in discrete as well as continuous dynamical systems. This superlinear scalability not only provides us an opportunity to exploit the nonlinearity of physical systems without being bogged down by noise but may also help us in understanding the functional role of coupled redundancy found in many biological systems. Moreover, engineers can exploit superlinear noise suppression by starting a coupled system near (not necessarily at) the appropriate initial condition.
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Affiliation(s)
- Vivek Kohar
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Behnam Kia
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - John F Lindner
- Physics Department, The College of Wooster, Wooster, Ohio 44691, USA
| | - William L Ditto
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
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11
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Abstract
The unprecedented light curves of the Kepler space telescope document how the brightness of some stars pulsates at primary and secondary frequencies whose ratios are near the golden mean, the most irrational number. A nonlinear dynamical system driven by an irrational ratio of frequencies generically exhibits a strange but nonchaotic attractor. For Kepler's "golden" stars, we present evidence of the first observation of strange nonchaotic dynamics in nature outside the laboratory. This discovery could aid the classification and detailed modeling of variable stars.
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Affiliation(s)
- John F Lindner
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA and Physics Department, The College of Wooster, Wooster, Ohio 44691, USA
| | - Vivek Kohar
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
| | - Behnam Kia
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
| | - Michael Hippke
- Institute for Data Analysis, Luiter Straße 21b, 47506 Neukirchen-Vluyn, Germany
| | - John G Learned
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
| | - William L Ditto
- Department of Physics and Astronomy, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
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Kohar V, Ji P, Choudhary A, Sinha S, Kurths J. Synchronization in time-varying networks. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 90:022812. [PMID: 25215786 DOI: 10.1103/physreve.90.022812] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Indexed: 06/03/2023]
Abstract
We study the stability of the synchronized state in time-varying complex networks using the concept of basin stability, which is a nonlocal and nonlinear measure of stability that can be easily applied to high-dimensional systems [P. J. Menck, J. Heitzig, N. Marwan, and J. Kurths, Nature Phys. 9, 89 (2013)]. The time-varying character is included by stochastically rewiring each link with the average frequency f. We find that the time taken to reach synchronization is lowered and the stability range of the synchronized state increases considerably in dynamic networks. Further we uncover that small-world networks are much more sensitive to link changes than random ones, with the time-varying character of the network having a significant effect at much lower rewiring frequencies. At very high rewiring frequencies, random networks perform better than small-world networks and the synchronized state is stable over a much wider window of coupling strengths. Lastly we show that the stability range of the synchronized state may be quite different for small and large perturbations, and so the linear stability analysis and the basin stability criterion provide complementary indicators of stability.
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Affiliation(s)
- Vivek Kohar
- Potsdam Institute for Climate Impact Research (PIK), 14473 Potsdam, Germany and Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
| | - Peng Ji
- Potsdam Institute for Climate Impact Research (PIK), 14473 Potsdam, Germany and Department of Physics, Humboldt University, 12489 Berlin, Germany
| | - Anshul Choudhary
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
| | - Sudeshna Sinha
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
| | - Jüergen Kurths
- Potsdam Institute for Climate Impact Research (PIK), 14473 Potsdam, Germany and Department of Physics, Humboldt University, 12489 Berlin, Germany and Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom and Department of Control Theory, Nizhny Novgorod State University, Gagarin Avenue 23, 606950 Nizhny Novgorod, Russia
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Abstract
We study the dynamics of a collection of nonlinearly coupled limit cycle oscillators relevant to a wide class of systems, ranging from neuronal populations to electrical circuits, over network topologies varying from a regular ring to a random network. We find that for sufficiently strong coupling strengths the trajectories of the system escape to infinity in the regular ring network. However when a fraction of the regular connections are dynamically randomized, the unbounded growth is suppressed and the system remains bounded. Further, we find a scaling relation between the critical fraction of random links necessary for successful prevention of explosive behavior and the network rewiring time-scale. These results suggest a mechanism by which blow-ups may be controlled in extended oscillator systems.
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Affiliation(s)
- Anshul Choudhary
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
| | - Vivek Kohar
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
| | - Sudeshna Sinha
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO 140 306, Punjab, India
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14
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Gupta A, Sohane A, Kohar V, Murali K, Sinha S. Noise-free logical stochastic resonance. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 84:055201. [PMID: 22181464 DOI: 10.1103/physreve.84.055201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Indexed: 05/31/2023]
Abstract
The phenomena of logical stochastic resonance (LSR) was demonstrated recently [Phys. Rev. Lett. 102, 104101 (2009)]: namely, when a bistable system is driven by two inputs it consistently yields a response mirroring a logic function of the two inputs in an optimal window of moderate noise. Here we examine the intriguing possibility of obtaining dynamical behavior equivalent to LSR in a noise-free bistable system, subjected only to periodic forcing, such as sinusoidal driving or rectangular pulse trains. We find that such a system, despite having no stochastic influence, also yields phenomena analogous to LSR, in an appropriate window of frequency and amplitude of the periodic forcing. The results are corroborated by circuit experiments.
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Affiliation(s)
- Animesh Gupta
- Indian Institute of Technology Bombay, Powai, Mumbai, India
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