Journal of Physics Communications最新文献

{"title":"Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations","authors":"M. B. Hahn","doi":"10.1088/2399-6528/accb3f","DOIUrl":"https://doi.org/10.1088/2399-6528/accb3f","url":null,"abstract":"Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells and their organelles, the study of linear energy transfer (LET), the relative biological effectiveness (RBE), ion beam cancer therapy, microbeam radiation therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48033720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reply to Comment on: ‘Experimental indications of non-classical brain function’ (2022 Journal of Physics Communications 6 105001)","authors":"C. Kerskens, David López Pérez","doi":"10.1088/2399-6528/acc636","DOIUrl":"https://doi.org/10.1088/2399-6528/acc636","url":null,"abstract":"We have recently suggested a proposal to explore non-classicality in the brain, for which we developed an entanglement witness protocol using MRI. The witness protocol intended to find spin interactions which could not be explained by classical interactions, based on intermolecular multiple quantum coherence (iMQC). As for Warren’s comments, we show in more detail that this was indeed the case; our observations were certainly not generated by interactions based on the iMQC model. Further, we discuss some additional details not present in the original paper.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46400754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comment on: ‘Experimental indications of non-classical brain function’ 2022 Journal of Physics Communications 6 105001","authors":"Warren S. Warren","doi":"10.1088/2399-6528/acc4a8","DOIUrl":"https://doi.org/10.1088/2399-6528/acc4a8","url":null,"abstract":"A recent paper in this journal presents magnetic resonance imaging (MRI) data on humans which are asserted to ‘suggest that we may have witnessed entanglement mediated by consciousness-related brain functions. Those brain functions must then operate non-classically, which would mean that consciousness is non-classical.’ Unfortunately, the article provides no evidence to justify this claim. In fact, the paper only provides evidence for what we already knew: the brain (and any other living tissue) is complex, multicompartmental, and imprecisely characterized by MRI.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48514003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Self-focusing, compression and collapse of ultrashort weakly-relativistic Laguerre–Gaussian lasers in near-critical plasma","authors":"T. Wilson, Z. Sheng, P. McKenna, B. Hidding","doi":"10.1088/2399-6528/acbf05","DOIUrl":"https://doi.org/10.1088/2399-6528/acbf05","url":null,"abstract":"Simultaneous self-focusing and compression of ultrashort weakly-relativistic Laguerre–Gaussian laser pulses in dense plasma is investigated theoretically and numerically. A simple theoretical model is developed and used to identify parameter regimes of interest, and then three-dimensional particle-in-cell simulations are carried out to examine the physics in detail. Rapid self-focusing and compression are observed, leading to pulse collapse even for laser pulse energy at the ten millijoule level. Long-lived ring-shaped post-soliton structures are left at the location of the first collapse, and the residual laser energy is scattered into the plasma. Filamentation and re-focusing occur beyond this point, the structure of which depends on the beam parameters but is observed to be only weakly dependent upon the mode of the laser. Circularly-polarised light is found to produce particulary symmetric plasma density structures. In all cases, bursts of MeV electrons with thermal-like spectra are observed at points of collapse.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41657795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interactions of deposited Ca with TiSe2 and TiTe2 surfaces","authors":"H. Starnberg","doi":"10.1088/2399-6528/acbc65","DOIUrl":"https://doi.org/10.1088/2399-6528/acbc65","url":null,"abstract":"The interaction of evaporated Ca with TiSe2 and TiTe2 surfaces was studied using photoelectron spectroscopy. The surfaces were held at room temperature, and the measured spectra clearly show that the deposited Ca reacted with the substrates, without formation of any Ca overlayers. For depositions on TiSe2 corresponding to less than 2 nm of Ca there were indications of an intercalation reaction taking place, with charge transfer to the TiSe2 layers, but as more Ca was added a layer-breaking reaction dominated. For the case of TiTe2 only a large Ca deposition was studied, resulting in a layer-breaking reaction very similar to that found on the TiSe2 surface for similar amounts of deposited Ca.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42763490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compression and information entropy of binary strings from the collision history of three hard balls","authors":"Matej Vedak, G. Ackland","doi":"10.1088/2399-6528/acd2a3","DOIUrl":"https://doi.org/10.1088/2399-6528/acd2a3","url":null,"abstract":"We investigate how to measure and define the entropy of a simple chaotic system, three hard spheres on a ring. A novel approach is presented, which does not assume the ergodic hypothesis. It consists of transforming the particles’ collision history into a sequence of binary digits. We then investigate three approaches which should demonstrate the non-randomness of these collision-generated strings compared with random number generator created strings: Shannon entropy, diehard randomness tests and compression percentage. We show that the Shannon information entropy is unable to distinguish random from deterministic strings. The Diehard test performs better, but for certain mass-ratios the collision-generated strings are misidentified as random with high confidence. The zlib and bz2 compression algorithms are efficient at detecting non-randomness and low information content, with compression efficiencies that tend to 100% in the limit of infinite strings. Thus ‘compression algorithm entropy’ is non-extensive for this chaotic system, in marked contrast to the extensive entropy determined from phase-space integrals by assuming ergodicity.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48712194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Streamer and leader characterization in HFO1234ze(E) gas, in a divergent electric field","authors":"S. Soulié, N. Bonifaci, O. Lesaint, F. Gentils","doi":"10.1088/2399-6528/acbae3","DOIUrl":"https://doi.org/10.1088/2399-6528/acbae3","url":null,"abstract":"Pre-breakdown phenomena in HFO1234ze-(E) gas, considered as a potential replacement of SF6 for medium voltage insulation, are studied in needle-plane electrode systems versus pressure (0.01 to 0.3 MPa) under positive impulse voltage. Measurements are also carried out in air and SF6 in the same conditions for comparison. At the lowest pressure in HFO, the propagation of fast streamers is observed. Above 0.03 MPa, breakdown is the consequence of the propagation of stepped leaders, with shapes and velocities nearly identical to those observed in SF6. Several leader features (minimum inception voltage, propagation length) show that leader formation and propagation is easier in HFO compared to SF6. In turn, this allow explaining why breakdown voltages in HFO are slightly lower than in SF6.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48260701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dirac impenetrable barrier in the limit point of the Klein energy zone","authors":"S. De Vincenzo","doi":"10.1088/2399-6528/acb8ff","DOIUrl":"https://doi.org/10.1088/2399-6528/acb8ff","url":null,"abstract":"We reanalyze the problem of a 1D Dirac single particle colliding with the electrostatic potential step of height V 0 with a positive incoming energy that tends to the limit point of the so-called Klein energy zone, i.e. E → V 0 − mc 2, for a given V 0. In such a case, the particle is actually colliding with an impenetrable barrier. In fact, V 0 → E + mc 2, for a given relativistic energy E( < V 0), is the maximum value that the height of the step can reach and that ensures the perfect impenetrability of the barrier. Nevertheless, we note that, unlike the nonrelativistic case, the entire eigensolution does not completely vanish, either at the barrier or in the region under the step, but its upper component does satisfy the Dirichlet boundary condition at the barrier. More importantly, by calculating the mean value of the force exerted by the impenetrable wall on the particle in this eigenstate and taking its nonrelativistic limit, we recover the required result. We use two different approaches to obtain the latter two results. In one of these approaches, the corresponding force on the particle is a type of boundary quantum force. Throughout the article, various issues related to the Klein energy zone, the transmitted solutions to this problem, and impenetrable barriers related to boundary conditions are also discussed. In particular, if the negative-energy transmitted solution is used, the lower component of the scattering solution satisfies the Dirichlet boundary condition at the barrier, but the mean value of the external force when V 0 → E + mc 2 does not seem to be compatible with the existence of the impenetrable barrier.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61174272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reinforcing critical links for robust network logistics: A centrality measure for substitutability","authors":"Takahiro Ezaki, Naoto Imura, K. Nishinari","doi":"10.1088/2399-6528/acb7c9","DOIUrl":"https://doi.org/10.1088/2399-6528/acb7c9","url":null,"abstract":"Logistics networks are becoming more complex and interconnected. Guaranteeing the performance of the entire system when a part of the network is disrupted (e.g. due to excessive demands and extreme weather conditions) is one of the important issues. However, how much transportation resources should be allocated to which part of the network while maintaining efficiency is an open question. In this paper, we propose a novel metric, the substitutability centrality, which quantifies how much each transport link in the network contributes to the robustness of the system against disruptions. This metric is compelling in the following aspects: (1) it is intuitively interpretable; (2) it does not require simulation or optimization calculations; and (3) it takes into account changes in transportation routes of delivery due to disruptions. Furthermore, as a proof of concept, we demonstrate a simple case study, in which capacity allocation based on the proposed metric can maintain high performance of the system against various types of disruptions. We also found that this approach might not be effective for further increasing the robustness of networks that have many bypass routes.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48887178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Random error propagation on electron beam dynamics for a 50 MeV S-band linac","authors":"H. Purwar, E. Goutierre, H. Guler, M. Rossetti Conti, S. Chancé, A. Gonnin, H. Monard, A. Bacci, M. Sebag, J. Cohen, C. Bruni","doi":"10.1088/2399-6528/acb415","DOIUrl":"https://doi.org/10.1088/2399-6528/acb415","url":null,"abstract":"The stability and the quality of particle beams are of utmost importance for many emerging linac installations. The impact on beam properties damage of beam electromagnetic element misalignments and jitter/fluctuations in various accelerator sub-systems should be properly known, as usually such shot-to-shot fluctuations cannot be avoided. On top of that, knowing which parameters the machine is most sensitive to is of utmost to take precautionary measures to reduce the beam degradation and thus improve beam stability and quality. This simulation work focuses on a 50 MeV S-band linear accelerator based on RF photoinjector electron source. The sensitivity of the beam parameters towards several errors has been studied collectively as well as individually for each accelerator element. While the emittance at the end of the linac is dominated by the laminar behavior in the accelerating section, the main emittance degradation comes mainly from orbit errors located at the linac entrance.","PeriodicalId":47089,"journal":{"name":"Journal of Physics Communications","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43519391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}