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arXiv 2023年

作者： Chen, Benzheng Ren, Jieru Deng, Zhigang Qi, Wei Hu, Zhongmin Ma, Bubo Wang, Xing Yin, Shuai Feng, Jianhua Liu, Wei Xu, Zhongfeng Hoffmann, Dieter H.H. Wang, Shaoyi Fan, Quanping Cui, Bo He, Shukai Cao, Zhurong Zhao, Zongqing Cao, Leifeng Gu, Yuqiu Zhu, Shaoping Cheng, Rui Zhou, Xianming Xiao, Guoqing Zhao, Hongwei Zhang, Yihang Zhang, Zhe Li, Yutong Zhou, Weimin Zhao, Yongtao MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter School of Physics Xi’an Jiaotong University Xi’an710049 China Science and Technology on Plasma Physics Laboratory Laser Fusion Research Center China Academy of Engineering Physics Mianyang621900 China Xi’an Technological University Xi’an710021 China Institute of Applied Physics and Computational Mathematics Beijing100094 China Graduate School China Academy of Engineering Physics Beijing100088 China Institute of Modern Physics Chinese Academy of Sciences Lanzhou710049 China Xianyang Normal University Xianyang712000 China Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing100190 China School of Physical Sciences University of Chinese Academy of Sciences Beijing100049 China

Thoroughly understanding the transport and energy loss of intense ion beams in dense matter is essential for high-energy-density physics and inertial confinement fusion. Here, we report a stopping power experiment with a high-intensity laser-driven proton beam in cold, dense matter. The measured energy loss is one order of magnitude higher than the expectation of individual particle stopping models. We attribute this finding to the proximity of beam ions to each other, which is usually insignificant for relatively-low-current beams from classical accelerators. The ionization of the cold target by the intense ion beam is important for the stopping power calculation and has been considered using proper ionization cross section data. Final theoretical values agree well with the experimental results. Additionally, we extend the stopping power calculation for intense ion beams to plasma scenario based on Ohm’s law. Both the proximity- and the Ohmic effect can enhance the energy loss of intense beams in dense matter, which are also summarized as the beam-density effect. This finding is useful for the stopping power estimation of intense beams and significant to fast ignition fusion driven by intense ion beams. Copyright © 2023, The Authors. All rights reserved.

关键词： Energy dissipation

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Casimir preserving stochastic Lie-Poisson integrators

arXiv

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arXiv 2021年

作者： Luesink, Erwin Ephrati, Sagy Cifani, Paolo Geurts, Bernard Multiscale Modelling and Simulation Department of Applied Mathematics Faculty EEMCS University of Twente PO Box 217 Enschede7500 AE Netherlands Gran Sasso Science Institute Viale F. Crispi 7 L’Aquila67100 Italy Multiscale Physics Center for Computational Energy Research Department of Applied Physics Eindhoven University of Technology PO Box 513 Eindhoven5600 MB Netherlands

Casimir preserving integrators for stochastic Lie-Poisson equations with Stratonovich noise are developed extending Runge-Kutta Munthe-Kaas methods. The underlying Lie-Poisson structure is preserved along stochastic trajectories. A related stochastic differential equation on the Lie algebra is derived. The solution of this differential equation updates the evolution of the Lie-Poisson dynamics by means of the exponential map. The constructed numerical method conserves Casimir-invariants exactly, which is important for long time integration. This is illustrated numerically for the case of the stochastic heavy top and the stochastic sine-Euler equations. Copyright © 2021, The Authors. All rights reserved.

关键词： Integration

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Modeling the extracellular matrix in cell migration and morphogenesis: A guide for the curious biologist

arXiv

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arXiv 2023年

作者： Crossley, Rebecca M. Johnson, Samuel Tsingos, Erika Bell, Zoe Berardi, Massimiliano Botticelli, Margherita Braat, Quirine J.S. Metzcar, John Ruscone, Marco Yin, Yuan Shuttleworth, Robyn Wolfson Centre for Mathematical Biology Mathematical Institute University of Oxford United Kingdom Computational Developmental Biology Group Institute of Biodynamics and Biocomplexity Utrecht University Utrecht Netherlands Northern Institute for Cancer Research Newcastle University United Kingdom LaserLab department of Physics and Astronomy Vrije Universiteit Amsterdam Amsterdam Netherlands Optics11 life Amsterdam Netherlands Watson School of Mathematics University of Birmingham United Kingdom Department of Applied Physics and Science Education Eindhoven University of Technology Netherlands Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States Department of Informatics Indiana University BloomingtonIN United States Institut Curie Université PSL ParisF-75005 France Altos Labs Redwood CityCA United States

The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as points of potential attachment. Although the ECM is a well-studied structure, its role in many biological processes remains difficult to investigate comprehensively due to its complexity and structural variation within an organism. In tandem with experiments, mathematical models are helpful in refining and testing hypotheses, generating predictions, and exploring conditions outside the scope of experiments. Such models can be combined and calibrated with in vivo and in vitro data to identify critical cell-ECM interactions that drive developmental and homeostatic processes, or the progression of diseases. In this review, we focus on mathematical and computational models of the ECM in processes such as cell migration including cancer metastasis, and in tissue structure and morphogenesis. By highlighting the predictive power of these models, we aim to help bridge the gap between experimental and computational approaches to studying the ECM and to provide guidance on selecting an appropriate model framework to complement corresponding experimental studies. © 2023, CC BY.

关键词： Tissue

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X-ray transient absorption spectroscopy by an ultrashort x-ray-laser pulse in a continuous-wave IR field

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Physical Review A 2020年第2期101卷 023401-023401页

作者： Xin Shi Yong Wu Jian Guo Wang Victor Kimberg Song Bin Zhang School of Physics and Information Technology Shaanxi Normal University Xi’an 710119 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China Center for Applied Physics and Technology Peking University Beijing 100084 China Theoretical Chemistry and Biology Royal Institute of Technology Stockholm 10691 Sweden Siberian Federal University 660041 Krasnoyarsk Russia Kirensky Institute of Physics Federal Research Center KSC SB RAS 660036 Krasnoyarsk Russia

X-ray transient absorption spectra (XTAS) of molecules are theoretically investigated in a femtosecond x-ray pump and continuous-wave (cw) infrared (IR)-control scenario. The scheme is exemplified by a CO molecule resonantly pumped into carbon and oxygen core-excited 1s→π* states by a weak femtosecond x-ray pulse, while dynamic Stark shifts are induced by the cw IR-control radiation. As a result, significant shoulder structures appear in XTAS showing strong dependence on the phase of IR radiation relative to the envelope of the x-ray pulse. Due to a significant difference in the frequencies of the two pulses, the present XTAS scheme provides much clear interpretation of the dynamic Stark effects as compared to the attosecond UV transient absorption scenario. Within the suggested two-level model, where the total spectrum is decomposed as incoherent superposition of contributions from different vibrational excitations weighted by the Franck-Condon Factors, all spectral structures can be well identified and interpreted in a good agreement with the full-scale molecular simulations. Well-characterized XTAS in the proposed IR-control scheme can be applied for fine phase synchronization between IR and x-ray pulses, highly demanded in modern experiments on x-ray free-electron lasers.

关键词： Atomic & molecular processes in external fields

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Dynamics and structure of monolayer polymer crystallites on graphene

arXiv

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arXiv 2020年

作者： Gulde, Max Rissanou, Anastassia N. Harmandaris, Vagelis Müller, Marcus Schäfer, Sascha Ropers, Claus 4th Physical Institute - Solids and Nanostructures University of Göttingen Göttingen37077 Germany Institute of Applied and Computational Mathematics Foundation for Research and Technology Hellas HeraklionCrete71110 Greece Department of Mathematics and Applied Mathematics University of Crete HeraklionCrete71409 Greece Institute for Theoretical Physics University of Göttingen Göttingen37077 Germany Fraunhofer Institute for High-Speed Dynamics Ernst-Mach-Institut Freiburg79104 Germany

Graphene-based nanostructured systems and van-der-Waals heterostructures comprise a material class of growing technological and scientific importance. Joining materials with vastly different properties, polymer-graphene heterosystems promise diverse applications in surface- and nanotechnology, including photovoltaics or nanotribology. Fundamentally, molecular adsorbates are prototypical systems to study confinement-induced phase transitions exhibiting intricate dynamics, which require a comprehensive understanding of the dynamical and static properties on molecular time and length scales. Here, we investigate the dynamics and the structure of a single polyethylene chain on free-standing graphene by means of molecular dynamics simulations. In equilibrium, the adsorbed polymer is orientationally linked to the graphene as two-dimensional folded-chain crystallites or, at elevated temperatures, as a floating solid. The associated superstructure can be reversibly melted on a picosecond time scale upon quasi-instantaneous substrate heating, involving ultrafast heterogeneous melting via a transient floating phase. Our findings elucidate time-resolved molecular-scale ordering and disordering phenomena in individual polymers interacting with solids, yielding complementary information to collective friction and viscosity, and linking to recent experimental observables from ultrafast electron diffraction. We anticipate that the approach will help in resolving non-equilibrium phenomena of hybrid polymeric systems over a broad range of time and length scales. Copyright © 2020, The Authors. All rights reserved.

关键词： Graphene

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Renyi divergence and non-deterministic subsampling in Rigid Image Registration

Renyi divergence and non-deterministic subsampling in Rigid ...

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IEEE International Workshop on Imaging Systems and Techniques (IST)

作者： C. Spanakis E. Mathioudakis N. Kampanis N. Tsiknakis K. Marias Computational BioMedicine Lab (CBML) Institute of Computer Science Foundation for Research and Technology-Hellas School of Mineral Resources Engineering Technical University of Crete Institute of Applied and Computational Mathematics Foundation for Research and Technology-Hellas Hellenic Mediterranean University

ISBN: (数字)9781728138688

ISBN: (纸本)9781728138695

The successful application and reported robustness of Mutual Information both in rigid and nonrigid image registration over the last decades gave rise to an ongoing research on other information based similarity metrics emanating from Renyi Divergence. To the best of our knowledge however, this is the first paper studying the effects of Renyi parameter in combination with a subsampling factor in image registration accuracy. To this end, a series of experiments are presented with respect to the effect of Renyi's parameter and the subsampling factor in registration accuracy. Our results show that the increase of the Renyi parameter and the percentage of the pixels used leads, on average, to the reduction of the registration error.

关键词： Image registration Mutual information Random variables Biomedical imaging Biomedical measurement Robustness Entropy

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Thermal conductivity of CaSiO3 perovskite at lower mantle conditions

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Physical Review B 2021年第18期104卷 184101-184101页

作者： Zhen Zhang Dong-Bo Zhang Kotaro Onga Akira Hasegawa Kenji Ohta Kei Hirose Renata M. Wentzcovitch Department of Applied Physics and Applied Mathematics Columbia University New York New York 10027 USA College of Nuclear Science and Technology Beijing Normal University Beijing 100875 People's Republic of China Beijing Computational Science Research Center Beijing 100193 People's Republic of China Department of Earth and Planetary Sciences Tokyo Institute of Technology Meguro Tokyo 152-8551 Japan National Metrology Institute of Japan National Institute of Advanced Industrial Science and Technology Tsukuba Ibaraki 305-8563 Japan Department of Earth and Planetary Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan Earth-Life Science Institute Tokyo Institute of Technology Meguro Tokyo 152-8550 Japan Department of Earth and Environmental Sciences Columbia University New York New York 10027 USA Lamont–Doherty Earth Observatory Columbia University Palisades New York 10964 USA

Thermal conductivity (κ) of mantle minerals is key to understanding dynamics in the deep Earth. It controls the style of mantle convection and the timescale of cooling both the mantle and the core. Cubic CaSiO3 perovskite (CaPv) is the third most abundant mineral in the lower mantle (7vol%). Despite its importance, no theoretical or experimental estimate of CaPv's κ is available. Theoretical investigations of its properties are challenging because of its strong anharmonicity. Experimental measurements at relevant pressures and temperatures are equally challenging. Here we present ab initio results for CaPv's κ obtained using the phonon quasiparticle approach to address its strong anharmonicity. We also offer experimental measurements of κ up to 67 GPa and 1950 K. Predictions and measurements are in good agreement and reveal a surprisingly large κ for cubic CaPv that can be explained on the basis of its high crystal structure symmetry. Despite its relatively low abundance, CaPv's κ increases the lower mantle κ by ∼10%, if accounted for. κ of mantle regions enriched in subducted crustal materials will be more strongly impacted.

关键词： Anharmonic lattice dynamics Phonons Pressure effects Thermal conductivity Perovskites First-principles calculations Molecular dynamics Thermoreflectance

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Novel Valence Transition in Elemental Metal Europium around 80 GPa

arXiv

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arXiv 2022年

作者： Chen, Bijuan Tian, Mingfeng Zhang, Jurong Li, Bing Xiao, Yuming Chow, Paul Kenney-Benson, Curtis Deng, Hongshan Zhang, Jianbo Sereika, Raimundas Yin, Xia Wang, Dong Hong, Xinguo Jin, Changqing Bi, Yan Liu, Hanyu Liu, Haifeng Li, Jun Jin, Ke Wu, Qiang Chang, Jun Ding, Yang Mao, Ho-Kwang Center for High-Pressure Science and Technology Advanced Research Beijing100094 China Institute of Applied Physics and Computational Mathematics Beijing100088 China Shandong Provincial Engineering and Technical Center of Light Manipulations Shandong Provincial Key Laboratory of Optics and Photonic Device School of Physics and Electronics Shandong Normal University Jinan250358 China HPCAT x-ray Science Division Argonne National Laboratory ArgonneIL60439 United States Institute of Physics Chinese Academy of Sciences Beijing100190 China International Center for Computational Method and Software College of Physics Jilin University Changchun130012 China National Key Laboratory of Shock Wave and Detonation Physics Institute of Fluid Physics CAEP Mianyang621900 China College of Physics and Information Technology Shaanxi Normal University Xi'An710119 China

Valence transition could induce structural, insulator-metal, nonmagnetic-magnetic and superconducting transitions in rare-earth metals and compounds, while the underlying physics remains unclear due to the complex interaction of localized 4f electrons as well as their coupling with itinerant electrons. The valence transition in the elemental metal europium (Eu) still has remained as a matter of debate. Using resonant x-ray emission scattering and x-ray diffraction, we pressurize the states of 4f electrons in Eu and study its valence and structure transitions up to 160 GPa. We provide compelling evidence for a valence transition around 80 GPa, which coincides with a structural transition from a monoclinic (C2/c) to an orthorhombic phase (Pnma). We show that the valence transition occurs when the pressure-dependent energy gap between 4f and 5d electrons approaches the Coulomb interaction. Our discovery is critical for understanding the electrodynamics of Eu, including magnetism and high-pressure superconductivity. © 2022, CC BY.

关键词： Europium

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Understanding viscoelastic flow instabilities: Oldroyd-B and beyond

arXiv

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arXiv 2022年

作者： Sánchez, Hugo A. Castillo Jovanović, Mihailo R. Kumar, Satish Morozov, Alexander Shankar, V. Subramanian, Ganesh Wilson, Helen J. Department Of Applied Mathematics And Statistics Institute Of Mathematics And Computational Sciences University Of Sao Paulo Brazil Ming Hsieh Department Of Electrical And Computer Engineering University Of Southern California Los AngelesCA90089 United States Department Of Chemical Engineering And Materials Science University Of Minnesota MinneapolisMN55455 United States SUPA School Of Physics And Astronomy The University Of Edinburgh EdinburghEH9 3FD United Kingdom Department Of Chemical Engineering Indian Institute Of Technology Kanpur208016 India Engineering Mechanics Unit Jawaharlal Nehru Center For Advanced Scientific Research Bangalore560064 India Mathematics Department University College London Gower Street LondonWC1E 6BT United Kingdom

The Oldroyd-B model has been used extensively to predict a host of instabilities in shearing flows of viscoelastic fluids, often realized experimentally using polymer solutions. The present review, written on the occasion of the birth centenary of James Oldroyd, provides an overview of instabilities found across major classes of shearing flows. These comprise (i) the canonical rectilinear shearing flows including plane Couette, plane and pipe Poiseuille flows;(ii) viscometric shearing flows with curved streamlines such as those in the TaylorCouette, cone-and-plate and parallel-plate geometries;(iii) non-viscometric shearing flows with an underlying extensional flow topology such as the flow in a cross-slot device;and (iv) multilayer shearing flows. While the underlying focus in all these cases is on results obtained using the Oldroyd-B model, we also discuss their relation to the actual instability, and as to how the shortcomings of the Oldroyd-B model may be overcome by the use of more realistic constitutive models. All the three commonly used tools of stability analysis, viz., modal linear stability, nonmodal stability, and weakly nonlinear stability analyses are discussed, with supporting evidence from experiments and numerical simulations as appropriate. Despite only accounting for a shear-rate-independent viscosity and first normal stress coefficient, the Oldroyd-B model is able to qualitatively predict the majority of instabilities in the aforementioned shearing flows. The review also highlights, where appropriate, open questions in the area of viscoelastic stability. © 2022, CC BY.

关键词： Stability

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Modeling the evolution of COVID-19 via compartmental and particle-based approaches: Application to the Cyprus case

arXiv

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arXiv 2020年

作者： Alexandrou, Constantia Harmandaris, Vangelis Irakleous, Anastasios Koutsou, Giannis Savva, Nikos Department of Physics University of Cyprus P/O/ Box 20537 Nicosia1678 Cyprus Computation-based Science and Technology Research Center The Cyprus Institute 20 Constantinou Kavafi Str. Nicosia2121 Cyprus Department of Mathematics and Applied Mathematics University of Crete Institute of Applied and Computational Mathematics FORTH HeraklionGR-71110 Greece

We present two different approaches for modeling the spread of the COVID-19 pandemic. Both approaches are based on the population classes susceptible, exposed, infectious, quarantined, and recovered and allow for an arbitrary number of subgroups with different infection rates and different levels of testing. The first model is derived from a set of ordinary differential equations that incorporates the rates at which population transitions take place among classes. The other is a particle model, which is a specific case of crowd simulation model, in which the disease is transmitted through particle collisions and infection rates are varied by adjusting the particle velocities. The parameters of these two models are tuned using information on COVID-19 from the literature and country-specific data, including the effect of restrictions as they were imposed and lifted. We demonstrate the applicability of both models using data from Cyprus, for which we find that both models yield very similar results, giving confidence in the predictions. Copyright © 2020, The Authors. All rights reserved.

关键词： Ordinary differential equations

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