1
|
Kültz D, Gardell AM, DeTomaso A, Stoney G, Rinkevich B, Rinkevich Y, Qarri A, Dong W, Luu B, Lin M. Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri). Proteomics 2024:e2300628. [PMID: 38400697 DOI: 10.1002/pmic.202300628] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.
Collapse
Affiliation(s)
- Dietmar Kültz
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Alison M Gardell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington, USA
| | - Anthony DeTomaso
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Greg Stoney
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Baruch Rinkevich
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Yuval Rinkevich
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Andy Qarri
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Weizhen Dong
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Brenda Luu
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Mandy Lin
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| |
Collapse
|
2
|
Voss G, Rosenthal JJC. High-level RNA editing diversifies the coleoid cephalopod brain proteome. Brief Funct Genomics 2023; 22:525-532. [PMID: 37981860 DOI: 10.1093/bfgp/elad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/11/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.
Collapse
Affiliation(s)
- Gjendine Voss
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| |
Collapse
|
3
|
Ofek T, Izhaki I, Halpern M. Aeromonashydrophila infection in tilapia triggers changes in the microbiota composition of fish internal organs. FEMS Microbiol Ecol 2023; 99:fiad137. [PMID: 37881004 DOI: 10.1093/femsec/fiad137] [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: 05/08/2023] [Revised: 08/30/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
Aeromonas hydrophila is a major pathogenic species that causes mass mortality in various freshwater fish species including hybrid tilapia, the main fish species in Israeli aquaculture. Our hypothesis was that A. hydrophila infection may cause changes in the microbiota composition of fish internal organs, and therefore we aimed to study the effect of A. hydrophila infection by injection or by net handling on the microbiota compositions of fish intestine, spleen, and liver. Significant differences in the microbiota composition were found between the internal organs of the diseased and the healthy fish in both experimental setups. Fusobacteriota was the most dominant phylum in the microbiota of healthy fish (∼70%, liver). Cetobacterium was the most abundant genus and relatively more abundant in healthy, compared to diseased fish. When A. hydrophila was inoculated by injection, it was the only pathogenic genus in the spleen and liver of the diseased fish. However, in the handling experiment, Vibrio was also detected in the diseased fish, demonstrating coinfection interactions. Based on these experiments, we conclude that indeed, A. hydrophila infection in tilapia causes changes in the microbiota composition of fish internal organs, and that fish net handling may trigger bacterial infection in freshwater aquaculture.
Collapse
Affiliation(s)
- Tamir Ofek
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, 199 Abba Khoushi Ave. Mt. Carmel, Haifa 3498838, Israel
- Central Fish Health Laboratory, Fishery and Aquaculture Department, Ministry of Agriculture and Rural Development, 1 Havazelet St. Nir David 1080300, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, 199 Abba Khoushi Ave. Mt. Carmel, Haifa 3498838, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, 199 Abba Khoushi Ave. Mt. Carmel, Haifa 3498838, Israel
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Derech Kiryat Amal, Tivon 3600600, Israel
| |
Collapse
|
4
|
Fonseca N, Thummalapalli SV, Jambhulkar S, Ravichandran D, Zhu Y, Patil D, Thippanna V, Ramanathan A, Xu W, Guo S, Ko H, Fagade M, Kannan AM, Nian Q, Asadi A, Miquelard-Garnier G, Dmochowska A, Hassan MK, Al-Ejji M, El-Dessouky HM, Stan F, Song K. 3D Printing-Enabled Design and Manufacturing Strategies for Batteries: A Review. Small 2023:e2302718. [PMID: 37501325 DOI: 10.1002/smll.202302718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/08/2023] [Indexed: 07/29/2023]
Abstract
Lithium-ion batteries (LIBs) have significantly impacted the daily lives, finding broad applications in various industries such as consumer electronics, electric vehicles, medical devices, aerospace, and power tools. However, they still face issues (i.e., safety due to dendrite propagation, manufacturing cost, random porosities, and basic & planar geometries) that hinder their widespread applications as the demand for LIBs rapidly increases in all sectors due to their high energy and power density values compared to other batteries. Additive manufacturing (AM) is a promising technique for creating precise and programmable structures in energy storage devices. This review first summarizes light, filament, powder, and jetting-based 3D printing methods with the status on current trends and limitations for each AM technology. The paper also delves into 3D printing-enabled electrodes (both anodes and cathodes) and solid-state electrolytes for LIBs, emphasizing the current state-of-the-art materials, manufacturing methods, and properties/performance. Additionally, the current challenges in the AM for electrochemical energy storage (EES) applications, including limited materials, low processing precision, codesign/comanufacturing concepts for complete battery printing, machine learning (ML)/artificial intelligence (AI) for processing optimization and data analysis, environmental risks, and the potential of 4D printing in advanced battery applications, are also presented.
Collapse
Affiliation(s)
- Nathan Fonseca
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Sri Vaishnavi Thummalapalli
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Sayli Jambhulkar
- Systems Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Dharneedar Ravichandran
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Yuxiang Zhu
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Dhanush Patil
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Varunkumar Thippanna
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Arunachalam Ramanathan
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Weiheng Xu
- Systems Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Shenghan Guo
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
- Systems Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Hyunwoong Ko
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
- Systems Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
| | - Mofe Fagade
- Mechanical Engineering, School of Engineering for Matter, Transport and Energy (SEMTE), Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Arunchala M Kannan
- Fuel Cell Laboratory, The Polytechnic School (TPS), Ira A. Fulton Schools of Engineering, Arizona State University, Mesa, AZ, 85212, USA
| | - Qiong Nian
- School of Engineering for Matter, Transport and Energy (SEMTE), Arizona State University, Tempe, AZ, 85287, USA
| | - Amir Asadi
- Department of Engineering Technology and Industrial Distribution (ETID), Texas A&M University, College Station, TX, 77843, USA
| | - Guillaume Miquelard-Garnier
- Laboratoire PIMM, Arts et Métiers Institute of Technology, CNRS, Cnam, HESAM Universite, 151 Boulevard de l'Hopital, Paris, 75013, France
| | - Anna Dmochowska
- Laboratoire PIMM, Arts et Métiers Institute of Technology, CNRS, Cnam, HESAM Universite, 151 Boulevard de l'Hopital, Paris, 75013, France
| | - Mohammad K Hassan
- Center for Advanced Materials, Qatar University, P.O. BOX 2713, Doha, Qatar
| | - Maryam Al-Ejji
- Center for Advanced Materials, Qatar University, P.O. BOX 2713, Doha, Qatar
| | - Hassan M El-Dessouky
- Physics Department, Faculty of Science, Galala University, Galala City, 43511, Egypt
- Physics Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Felicia Stan
- Center of Excellence Polymer Processing & Faculty of Engineering, Dunarea de Jos University of Galati, 47 Domneasca Street, Galati, 800008, Romania
| | - Kenan Song
- Manufacturing Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
- Systems Engineering, School of Manufacturing Systems and Networks (MSN), Ira A. Fulton Schools of Engineering, Arizona State University (ASU), Mesa, AZ, 85212, USA
- Mechanical Engineering, University of Georgia, 302 E. Campus Rd, Athens, Georgia, 30602, United States
| |
Collapse
|
5
|
Apostolova S, Oreshkova T, Uzunova V, Georgieva I, Maslenkova L, Tzoneva R. A Standardized Extract of Petasites hybridus L., Containing the Active Ingredients Petasins, Acts as a Pro-Oxidant and Triggers Apoptosis through Elevating of NF-κB in a Highly Invasive Human Breast Cancer Cell Line. FRONT BIOSCI-LANDMRK 2023; 28:111. [PMID: 37395030 DOI: 10.31083/j.fbl2806111] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Common butterbur (Petasites hybridus L.) is a traditional medicinal plant with numerous therapeutic properties among which is its recently uncovered anti-tumor activity. The present study aims to examine the activity of a standardized Bulgarian Petasites hybridus L. root extract, containing the active ingredients petasins, on the human breast cancer cell line MDA-MB-231 and non-cancerous MCF-10A cells. Specifically, we examined cell death, oxidative stress, and nuclear factor kappa-B (NF-κB) signaling. METHODS A standardized butterbur powdered extract containing a minimum of 15% petasins was used. A lipophilic extract was obtained from subterranean portion of the plant of Bulgarian populations of Petasites hybridus using liquid-liquid extraction after completely removing pyrrolizidine alkaloids. The induction of apoptosis and necrosis was analyzed by flow cytometry, and oxidative stress biomarkers and NF-κB were measured using enzyme-linked immunosorbent assay (ELISA). RESULTS Petasites hybridus L. root extract triggered apoptosis in a cancer-specific fashion and induced a moderate oxidative stress characterized by diminished glutathione (GSH) levels and elevated malondialdehyde (MDA) levels in MDA-MB-231 72 h after treatment. NF-κB levels were higher in cancer cells after treatment with IC50 and IC75 doses, this suggested that the NF-κB pathway was activated in response to oxidative stress leading to the induction of apoptosis. MCF-10A cells were affected to a lesser extent by the Petasites hybridus extract, and the adaptive response of their antioxidant defense system halted oxidative stress. CONCLUSIONS Overall, these results indicate that Petasites hybridus L. root extract selectively acts as a pro-oxidant in breast cancer cells and thus represents a potential therapeutic option for cancer treatment with fewer side effects.
Collapse
Affiliation(s)
- Sonia Apostolova
- Laboratory of Transmembrane Signaling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Tsvetelina Oreshkova
- Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov'', Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Veselina Uzunova
- Laboratory of Transmembrane Signaling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Irina Georgieva
- Laboratory of Transmembrane Signaling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Liliana Maslenkova
- Laboratory of Transmembrane Signaling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Rumiana Tzoneva
- Laboratory of Transmembrane Signaling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| |
Collapse
|
6
|
Mor M, Werbner M, Alter J, Safra M, Chomsky E, Lee JC, Hada-Neeman S, Polonsky K, Nowell CJ, Clark AE, Roitburd-Berman A, Ben-Shalom N, Navon M, Rafael D, Sharim H, Kiner E, Griffis ER, Gershoni JM, Kobiler O, Leibel SL, Zimhony O, Carlin AF, Yaari G, Dessau M, Gal-Tanamy M, Hagin D, Croker BA, Freund NT. Multi-clonal SARS-CoV-2 neutralization by antibodies isolated from severe COVID-19 convalescent donors. PLoS Pathog 2021; 17:e1009165. [PMID: 33571304 PMCID: PMC7877634 DOI: 10.1371/journal.ppat.1009165] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mild versus severe cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe, and not mild, infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of ACE2:RBD inhibition. B cell receptor (BCR) sequencing revealed that VH3-53 was enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against authentic SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and mutagenesis of RBD, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.
Collapse
Affiliation(s)
- Michael Mor
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michal Werbner
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Joel Alter
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Modi Safra
- Alexander Kofkin Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Elad Chomsky
- ImmunAi, New York, New York, United States of America
| | - Jamie C. Lee
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Smadar Hada-Neeman
- George S. Wise Life sciences Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Ksenia Polonsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Alex E. Clark
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | | - Noam Ben-Shalom
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michal Navon
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Dor Rafael
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Hila Sharim
- ImmunAi, New York, New York, United States of America
| | - Evgeny Kiner
- ImmunAi, New York, New York, United States of America
| | - Eric R. Griffis
- Nikon Imaging Center, University of California San Diego, California, United States of America
| | | | - Oren Kobiler
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Sandra Lawrynowicz Leibel
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | | - Aaron F. Carlin
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Gur Yaari
- Alexander Kofkin Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Moshe Dessau
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | | | - Ben A. Croker
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | |
Collapse
|
7
|
Morini L, Gokay Tetik Z, Shmuel G, Gei M. On the universality of the frequency spectrum and band-gap optimization of quasicrystalline-generated structured rods. Philos Trans A Math Phys Eng Sci 2020; 378:20190240. [PMID: 31760899 PMCID: PMC6894518 DOI: 10.1098/rsta.2019.0240] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
The dynamical properties of periodic two-component phononic rods, whose elementary cells are generated adopting the Fibonacci substitution rules, are studied through the recently introduced method of the toroidal manifold. The method allows all band gaps and pass bands featuring the frequency spectrum to be represented in a compact form with a frequency-dependent flow line on the surface describing their ordered sequence. The flow lines on the torus can be either closed or open: in the former case, (i) the frequency spectrum is periodic and the elementary cell corresponds to a canonical configuration, (ii) the band gap density depends on the lengths of the two phases; in the latter, the flow lines cover ergodically the torus and the band gap density is independent of those lengths. It is then shown how the proposed compact description of the spectrum can be exploited (i) to find the widest band gap for a given configuration and (ii) to optimize the layout of the elementary cell in order to maximize the low-frequency band gap. The scaling property of the frequency spectrum, that is a distinctive feature of quasicrystalline-generated phononic media, is also confirmed by inspecting band-gap/pass-band regions on the torus for the elementary cells of different Fibonacci orders. This article is part of the theme issue 'Modelling of dynamic phenomena and localization in structured media (part 2)'.
Collapse
Affiliation(s)
- Lorenzo Morini
- School of Engineering, Cardiff University, The Parade, Cardiff CF24 3AA, Wales, UK
| | - Zafar Gokay Tetik
- School of Engineering, Cardiff University, The Parade, Cardiff CF24 3AA, Wales, UK
| | - Gal Shmuel
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Massimiliano Gei
- School of Engineering, Cardiff University, The Parade, Cardiff CF24 3AA, Wales, UK
| |
Collapse
|
8
|
Bury M, van Hameren A, Jung H, Kutak K, Sapeta S, Serino M. Calculations with off-shell matrix elements, TMD parton densities and TMD parton showers. Eur Phys J C Part Fields 2018; 78:137. [PMID: 29497349 PMCID: PMC5816828 DOI: 10.1140/epjc/s10052-018-5642-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
A new calculation using off-shell matrix elements with TMD parton densities supplemented with a newly developed initial state TMD parton shower is described. The calculation is based on the KaTie package for an automated calculation of the partonic process in high-energy factorization, making use of TMD parton densities implemented in TMDlib. The partonic events are stored in an LHE file, similar to the conventional LHE files, but now containing the transverse momenta of the initial partons. The LHE files are read in by the Cascade package for the full TMD parton shower, final state shower and hadronization from Pythia where events in HEPMC format are produced. We have determined a full set of TMD parton densities and developed an initial state TMD parton shower, including all flavors following the TMD distribution. As an example of application we have calculated the azimuthal de-correlation of high [Formula: see text] dijets as measured at the LHC and found very good agreement with the measurement when including initial state TMD parton showers together with conventional final state parton showers and hadronization.
Collapse
Affiliation(s)
- Marcin Bury
- Institute of Nuclear Physics, Polish Academy of Sciences, Cracow, Poland
| | | | - Hannes Jung
- Institute of Nuclear Physics, Polish Academy of Sciences, Cracow, Poland
- DESY, Hamburg, Germany
| | - Krzysztof Kutak
- Institute of Nuclear Physics, Polish Academy of Sciences, Cracow, Poland
| | - Sebastian Sapeta
- Institute of Nuclear Physics, Polish Academy of Sciences, Cracow, Poland
| | - Mirko Serino
- Institute of Nuclear Physics, Polish Academy of Sciences, Cracow, Poland
- Department of Physics, Ben Gurion University of the Negev, Beersheba, Israel
| |
Collapse
|