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Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations 通过粒子散射模拟在纳米尺度上获取对生物分子的辐射损伤
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-04-06 DOI: 10.1088/2399-6528/accb3f
M. B. Hahn
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.
辐射对DNA的损伤在治疗癌症的放射治疗中起着核心作用。所涉及的物理化学和生物过程涵盖了巨大的时间和空间尺度。对实验技术而言,全面了解纳米和宏观尺度是一项非常具有挑战性的任务。因此,粒子散射模拟通常用于补充测量和辅助解释,帮助规划实验,预测结果和测试损伤模型。近年来,基于蒙特卡罗模拟(MCS)方法的强大的多用途粒子散射框架,如Geant4和Geant4- dna,通过友好的用户界面如TOPAS和TOPAS- nbio进行了扩展。这使得它们的适用性从专门的专家领域扩展到更广泛的科学家领域。在本综述中,我们旨在概述基于MCS的方法来理解辐射相互作用的广泛范围,从癌组织、细胞及其细胞器(包括细胞核、线粒体和膜),到放射增敏剂(如金属纳米颗粒)和含有额外自由基清除剂的水,再到以DNA、RNA、蛋白质和DNA-蛋白质复合物形式存在的分离生物分子。从而涵盖了生物分子在物理阶段由非弹性散射过程的直接损伤引起的降解,以及化学阶段由自由基引起的间接损伤以及早期生物反应的某些部分。由于它们的高丰度,羟基自由基(•OH)和次级低能电子(LEE)以及预水合电子的作用将被详细介绍。本文综述了辐射敏化剂在预测DNA损伤、DNA修复过程、细胞存活和凋亡、辐射敏化剂对细胞及其细胞器内剂量分布的影响、线性能量传递(LET)研究、相对生物效应(RBE)、离子束癌症治疗、微束放射治疗(MRT)、FLASH效应和辐射诱导旁观者效应等方面的应用。
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引用次数: 1
Reply to Comment on: ‘Experimental indications of non-classical brain function’ (2022 Journal of Physics Communications 6 105001) 回复关于“非经典脑功能的实验适应症”的评论(2022物理通讯6 105001)
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-03-21 DOI: 10.1088/2399-6528/acc636
C. Kerskens, David López Pérez
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.
我们最近提出了一项探索大脑非经典性的建议,为此我们开发了一种使用MRI的纠缠见证协议。基于分子间多重量子相干(iMQC)的见证协议旨在寻找经典相互作用无法解释的自旋相互作用。至于沃伦的评论,我们更详细地说明了事实确实如此;我们的观察结果当然不是基于iMQC模型的相互作用产生的。此外,我们还讨论了一些原始论文中没有出现的其他细节。
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引用次数: 0
Comment on: ‘Experimental indications of non-classical brain function’ 2022 Journal of Physics Communications 6 105001 评论:“非经典脑功能的实验迹象”,2022年物理通讯杂志6 105001
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-03-01 DOI: 10.1088/2399-6528/acc4a8
Warren S. Warren
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.
该杂志最近发表的一篇论文展示了人类的磁共振成像(MRI)数据,这些数据声称“表明我们可能已经目睹了由意识相关的大脑功能介导的纠缠”。这些大脑功能必须是非经典的,这就意味着意识是非经典的。不幸的是,这篇文章没有提供任何证据来证明这一说法。事实上,这篇论文只是为我们已经知道的东西提供了证据:大脑(和任何其他活组织)是复杂的,多室的,并且通过MRI无法精确表征。
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引用次数: 0
Self-focusing, compression and collapse of ultrashort weakly-relativistic Laguerre–Gaussian lasers in near-critical plasma 超短弱相对论拉盖尔-高斯激光在近临界等离子体中的自聚焦、压缩和坍缩
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-02-24 DOI: 10.1088/2399-6528/acbf05
T. Wilson, Z. Sheng, P. McKenna, B. Hidding
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.
从理论和数值上研究了超短弱相对论性拉盖尔-高斯激光脉冲在稠密等离子体中的同时自聚焦和压缩。开发了一个简单的理论模型,并用于识别感兴趣的参数状态,然后进行了三维粒子细胞模拟,以详细检查物理。观察到快速的自聚焦和压缩,即使在10毫焦耳水平的激光脉冲能量下也会导致脉冲坍塌。在第一次坍塌的位置留下了长寿命的环形后孤立子结构,剩余的激光能量被散射到等离子体中。灯丝化和再聚焦发生在该点之外,其结构取决于光束参数,但观察到仅微弱地取决于激光器的模式。发现圆偏振光产生了粒子对称的等离子体密度结构。在所有情况下,在坍缩点都可以观察到具有类热光谱的MeV电子爆发。
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引用次数: 0
Interactions of deposited Ca with TiSe2 and TiTe2 surfaces 沉积Ca与TiSe2和TiTe2表面的相互作用
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-02-15 DOI: 10.1088/2399-6528/acbc65
H. Starnberg
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.
利用光电子能谱研究了蒸发后的Ca与TiSe2和TiTe2表面的相互作用。在室温下,测量的光谱清楚地表明,沉积的Ca与衬底反应,没有形成任何Ca覆盖层。对于小于2 nm Ca的TiSe2上的沉积,有迹象表明发生了插层反应,电荷向TiSe2层转移,但随着Ca的加入,层破溃反应占主导地位。对于TiTe2,只研究了大量的Ca沉积,导致的破层反应非常类似于在TiSe2表面发现的相同数量的Ca沉积。
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引用次数: 0
Compression and information entropy of binary strings from the collision history of three hard balls 三个硬球碰撞历史中二进制字符串的压缩和信息熵
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-02-14 DOI: 10.1088/2399-6528/acd2a3
Matej Vedak, G. Ackland
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.
我们研究了如何测量和定义一个简单混沌系统的熵,即一个环上的三个硬球。提出了一种新的方法,它不假设遍历假设。它包括将粒子的碰撞历史转换为二进制数字序列。然后,我们研究了三种方法,与随机数生成器创建的字符串相比,这些方法应该证明这些碰撞生成的字符串的非随机性:香农熵、顽固随机性测试和压缩百分比。我们证明了香农信息熵不能区分随机字符串和确定性字符串。Diehard测试表现更好,但对于某些质量比,碰撞产生的字符串被错误地识别为具有高置信度的随机字符串。zlib和bz2压缩算法在检测非随机性和低信息含量方面非常有效,在无限字符串的限制下,压缩效率往往达到100%。因此,对于这个混沌系统,“压缩算法熵”是非扩展的,这与通过假设遍历性从相空间积分确定的扩展熵形成了鲜明对比。
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引用次数: 0
Streamer and leader characterization in HFO1234ze(E) gas, in a divergent electric field 发散电场条件下HFO1234ze(E)气体中拖缆和引线的表征
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-02-09 DOI: 10.1088/2399-6528/acbae3
S. Soulié, N. Bonifaci, O. Lesaint, F. Gentils
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.
在针平面电极系统中,研究了HFO1234ze-(E)气体在正脉冲电压下对压力(0.01至0.3MPa)的预击穿现象,该气体被认为是中压绝缘SF6的潜在替代品。在相同的条件下,也在空气和SF6中进行了测量以进行比较。在HFO的最低压力下,可以观察到快速拖缆的传播。在0.03MPa以上,击穿是阶梯状引线传播的结果,其形状和速度几乎与SF6中观察到的形状和速度相同。几个先导特征(最小起始电压、传播长度)表明,与SF6相比,HFO中的先导形成和传播更容易。反过来,这可以解释为什么HFO中的击穿电压略低于SF6。
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引用次数: 0
The Dirac impenetrable barrier in the limit point of the Klein energy zone 克莱因能区极限点的狄拉克不可穿透障壁
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-02-03 DOI: 10.1088/2399-6528/acb8ff
S. De Vincenzo
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.
我们重新分析了一维狄拉克单粒子与高度为v0的静电势阶跃的碰撞问题,对于给定的v0,入射能量趋向于所谓的克莱因能区的极限点,即E→v0−mc2。在这种情况下,粒子实际上是在与一个不可穿透的屏障碰撞。事实上,对于给定的相对论能量E(< v0), V 0→E + mc 2是台阶高度所能达到的最大值,并且保证了障壁的完全不可穿透性。然而,我们注意到,与非相对论情况不同,整个特征解在势垒处或阶跃下的区域内并不完全消失,但其上分量在势垒处确实满足狄利克雷边界条件。更重要的是,通过计算在本征态下不可穿透壁对粒子施加的力的平均值,并取其非相对论性极限,我们恢复了所需的结果。我们使用两种不同的方法来获得后两种结果。在其中一种方法中,作用在粒子上的相应力是一种边界量子力。在整篇文章中,还讨论了与克莱因能区有关的各种问题,该问题的传输解,以及与边界条件有关的不可穿透障碍。特别是,当采用负能量透射解时,散射解的下分量在势垒处满足Dirichlet边界条件,但当V 0→E + mc 2时的外力平均值似乎与不可穿透势垒的存在不相容。
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引用次数: 0
Reinforcing critical links for robust network logistics: A centrality measure for substitutability 加强健全网络物流的关键环节:可替代性的中心性措施
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-01-31 DOI: 10.1088/2399-6528/acb7c9
Takahiro Ezaki, Naoto Imura, K. Nishinari
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.
物流网络正变得越来越复杂和相互关联。当部分网络中断时(例如,由于过度需求和极端天气条件),保证整个系统的性能是重要问题之一。然而,在保持效率的情况下,应该将多少运输资源分配到网络的哪个部分是一个悬而未决的问题。在本文中,我们提出了一个新的度量,可替代性中心性,它量化了网络中的每个传输链路对系统抗中断的鲁棒性的贡献。这个指标在以下几个方面是引人注目的:(1)它是直观的可解释的;(二)不需要模拟、优化计算的;(3)考虑到中断造成的运输路线的变化。此外,作为概念的证明,我们展示了一个简单的案例研究,其中基于所提议的度量的容量分配可以在各种类型的中断下保持系统的高性能。我们还发现,这种方法可能无法有效地进一步提高具有许多旁路路由的网络的鲁棒性。
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引用次数: 0
Random error propagation on electron beam dynamics for a 50 MeV S-band linac 50 MeV s波段直线加速器电子束动力学中的随机误差传播
IF 1.2 Q3 Physics and Astronomy Pub Date : 2023-01-17 DOI: 10.1088/2399-6528/acb415
H. Purwar, E. Goutierre, H. Guler, M. Rossetti Conti, S. Chancé, A. Gonnin, H. Monard, A. Bacci, M. Sebag, J. Cohen, C. Bruni
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.
粒子束的稳定性和质量对许多新兴的直线装置至关重要。对于各种加速器子系统中波束电磁元件的错位和抖动/波动对波束性能的影响和损伤应该有充分的了解,因为通常这种弹间波动是无法避免的。最重要的是,了解机器对哪些参数最敏感,采取预防措施以减少光束退化,从而提高光束的稳定性和质量。本文研究了基于射频光注入电子源的50 MeV s波段直线加速器。研究了光束参数对若干误差的敏感性,并对每个加速器元件分别进行了研究。直线加速器末端的发射度主要受加速段的层流行为影响,而直线加速器入口的轨道误差是导致发射度下降的主要原因。
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引用次数: 0
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Journal of Physics Communications
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