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Article ; Online: Author Correction: TeV/m catapult acceleration of electrons in graphene layers.

Bonţoiu, Cristian / Apsimon, Öznur / Kukstas, Egidijus / Rodin, Volodymyr / Yadav, Monika / Welsch, Carsten / Resta-López, Javier / Bonatto, Alexandre / Xia, Guoxing

Scientific reports

2023 Volume 13, Issue 1, Page(s) 2845

Language	English
Publishing date	2023-02-17
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-29761-z
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Article ; Online: TeV/m catapult acceleration of electrons in graphene layers.

Bonţoiu, Cristian / Apsimon, Öznur / Kukstas, Egidijus / Rodin, Volodymyr / Yadav, Monika / Welsch, Carsten / Resta-López, Javier / Bonatto, Alexandre / Xia, Guoxing

Scientific reports

2023 Volume 13, Issue 1, Page(s) 1330

Abstract: Recent nanotechnology advances enable fabrication of layered structures with controllable inter-layer gap, giving the ultra-violet (UV) lasers access to solid-state plasmas which can be used as medium for electron acceleration. By using a linearly ... ...

Abstract	Recent nanotechnology advances enable fabrication of layered structures with controllable inter-layer gap, giving the ultra-violet (UV) lasers access to solid-state plasmas which can be used as medium for electron acceleration. By using a linearly polarized 3 fs-long laser pulse of 100 nm wavelength and 10[Formula: see text] W/cm[Formula: see text] peak intensity, we show numerically that electron bunches can be accelerated along a stack of ionized graphene layers. Particle-In-Cell (PIC) simulations reveal a new self-injection mechanism based on edge plasma oscillations, whose amplitude depends on the distance between the graphene layers. Nanometre-size electron ribbons are electrostatically catapulted into buckets of longitudinal electric fields in less than 1 fs, as opposed to the slow electrostatic pull, common to laser wakefield acceleration (LWFA) schemes in gas-plasma. Acceleration then proceeds in the blowout regime at a gradient of 4.79 TeV/m yielding a 0.4 fs-long bunch with a total charge in excess of 2.5 pC and an average energy of 6.94 MeV, after travelling through a graphene target as short as 1.5 [Formula: see text]m. These parameters are unprecedented within the LWFA research area and, if confirmed experimentally, may have an impact on fundamental femtosecond research.
Language	English
Publishing date	2023-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-28617-w
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Article ; Online: Built-In Potentials Induced by Molecular Order in Amorphous Organic Thin Films.

Friederich, Pascal / Rodin, Vadim / von Wrochem, Florian / Wenzel, Wolfgang

ACS applied materials & interfaces

2018 Volume 10, Issue 2, Page(s) 1881–1887

Abstract: Many molecules used to fabricate organic semiconductor devices carry an intrinsic dipole moment. Anisotropic orientation of such molecules in amorphous organic thin films during the deposition process can lead to the spontaneous buildup of an ... ...

Abstract	Many molecules used to fabricate organic semiconductor devices carry an intrinsic dipole moment. Anisotropic orientation of such molecules in amorphous organic thin films during the deposition process can lead to the spontaneous buildup of an electrostatic potential perpendicular to the film. This so-called giant surface potential (GSP) effect can be exploited in organic electronics applications and was extensively studied in experiment. However, presently, an understanding of the molecular mechanism driving the orientation is lacking. Here, we model the physical vapor deposition process of seven small organic molecules employed in organic light-emitting diode applications with atomistic simulations. We are able to reproduce experimental results for a wide range of strength of the GSP effect. We find that the electrostatic interaction between the dipole moments of the molecules limits the GSP strength and identify short-range van der Waals interactions between the molecule and the surface during deposition as the driving force behind the anisotropic orientation. We furthermore show how the GSP effect influences the energy levels responsible for charge transport, which is important for the design of organic semiconductors and devices.
Language	English
Publishing date	2018-01-17
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.7b11762
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Article ; Online: Lensless optical encryption with speckle-noise suppression and QR codes.

Cheremkhin, P A / Evtikhiev, N N / Krasnov, V V / Rodin, V G / Ryabcev, I P / Shifrina, A V / Starikov, R S

Applied optics

2021 Volume 60, Issue 24, Page(s) 7336–7345

Abstract: The majority of contemporary optical encryption techniques use coherent illumination and suffer from speckle-noise pollution, which severely limits their applicability even when information encoded into special "containers" such as a QR code. Spatially ... ...

Abstract	The majority of contemporary optical encryption techniques use coherent illumination and suffer from speckle-noise pollution, which severely limits their applicability even when information encoded into special "containers" such as a QR code. Spatially incoherent encryption does not have this drawback, but it suffers from reduced encryption strength due to formation of an unobscured image right on top of the encrypted one by undiffracted light from the encoding diffraction optical element (DOE) in axial configuration. We present a new lensless encryption scheme, experimentally implemented with two liquid crystal spatial light modulators, that does not have this disadvantage because of a special encoding DOE design, which forms desired light distribution in the photosensor plane under spherically diverging illumination without a converging lens. Results of optical experiments on encryption of QR codes and successful information retrieval from decoded images are presented. Conducted analysis of encryption strength demonstrates sufficiently high key sensitivity and large enough key space to resist any brute force attacks.
Language	English
Publishing date	2021-10-06
Publishing country	United States
Document type	Journal Article
ISSN	1539-4522
ISSN (online)	1539-4522
DOI	10.1364/AO.430968
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Article ; Online: A Viability Approach for Robustness Measurement, Organizational Autopoiesis, and Cell Turnover in a Multicellular System.

Sarr, Abdoulaye / Désilles, Anya / Fronville, Alexandra / Rodin, Vincent

Journal of computational biology : a journal of computational molecular cell biology

2016 Volume 23, Issue 4, Page(s) 256–269

Abstract: In this article, we use the potential of computational biology to highlight the key role of cell apoptosis for studying some tissue's properties through in silico experiments of morphogenesis. Our morphogenesis model is a new approach focusing on the ... ...

Abstract	In this article, we use the potential of computational biology to highlight the key role of cell apoptosis for studying some tissue's properties through in silico experiments of morphogenesis. Our morphogenesis model is a new approach focusing on the deterministic program within cells that controls their placement and their differentiation at the beginning of the embryogenesis. Indeed, when the tissue is made by just a few pair of cells, we consider that cellular mechanisms are related neither to the influence of mechanical forces nor to the spread of chemicals. Dynamics are based on spatial and logical choices, the other factors being involved when the tissue contains a large number of cells. We had established a mathematical formulation of such a model and had enlightened the link between phenotype (cell placement and cell differentiation) and genotype (cell program) at the early embryogenesis. Indeed, that work allowed for generating any early tissue and the associated program that designs it. We propose now to study and assess some properties of these tissues for further selection and classification purposes. More precisely, we present in this article novel methods to measure tissue robustness based on the backward morphogenesis of our model. We also show some implementations of their self-maintenance properties, on the one hand to deal with environment disturbances through autopoiesis and on the other hand to achieve a dynamical steady state which ensures tissue renewal.
MeSH term(s)	Animals ; Apoptosis ; Cell Differentiation ; Cell Survival ; Humans ; Models, Theoretical ; Morphogenesis
Language	English
Publishing date	2016-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2030900-4
ISSN	1557-8666 ; 1066-5277
ISSN (online)	1557-8666
ISSN	1066-5277
DOI	10.1089/cmb.2015.0187
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Article: Hypothermic Preservation of Red Blood Cells in Different Conditions of Inert Gas Xenon: Hyperbaria and Clathrates.

Ponomarev, A / Rodin, V V / Gurevich, L / Melekhin, V / Makeev, O

Cryo letters

2019 Volume 39, Issue 6, Page(s) 391–400

Abstract: Background: Xenon is an inert gas promising for the preservation of biomaterials, which forms clathrate hydrates above 0°C.: Objective: This study addresses the effect of hyperbaric xenon (P = 303 kPa) and water-xenon clathrates (P ≥ 608 kPa) on 30 ... ...

Abstract	Background: Xenon is an inert gas promising for the preservation of biomaterials, which forms clathrate hydrates above 0°C. Objective: This study addresses the effect of hyperbaric xenon (P = 303 kPa) and water-xenon clathrates (P ≥ 608 kPa) on 30 days preservation of red blood cells (RBCs) at +4°C. Materials and methods: RBCs from healthy human donors were preserved under four different conditions: without preservatives (negative control), in CPDA-1, hyperbaric xenon, and xenon clathrate hydrates. Results: The qualitative (mean RBC volume, anisocytosis degree and mean osmotic fragility) and quantitative characteristics (RBC count and hemolysis degree) of preserved RBCs were measured. Conclusion: The positive role of hyperbaric xenon in the preservation of erythrocytes is attributed to the equilibrium extraction and displacement of O
MeSH term(s)	Blood Preservation/methods ; Carbon Dioxide ; Erythrocytes/cytology ; Hemolysis ; Humans ; Oxygen ; Terpenes/analysis ; Xenon
Chemical Substances	Terpenes ; clathric acid ; Carbon Dioxide (142M471B3J) ; Xenon (3H3U766W84) ; Oxygen (S88TT14065)
Language	English
Publishing date	2019-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	756781-9
ISSN	0143-2044
ISSN	0143-2044
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Article: [NMR-relaxation in hydrated collagen from the spotted dogfish]].

Rodin, V V

Biofizika

2005 Volume 50, Issue 2, Page(s) 223–230

Abstract: Collagen samples from dog-fish egg case at different water content were studied by the 1H NMR relaxation method. The dependences of the proton spin-lattice and spin-spin relaxation rates on the concentration of water in hydrated native collagen were ... ...

Abstract	Collagen samples from dog-fish egg case at different water content were studied by the 1H NMR relaxation method. The dependences of the proton spin-lattice and spin-spin relaxation rates on the concentration of water in hydrated native collagen were measured. The fractions of water protons of different mobility and their corresponding spin-spin and spin-lattice relaxation rates were determined in a multi-phase model of water protons in natural biopolymer-water systems. The correlation times were calculated as the characteristics of molecular motion in hydrated collagens with different content of absorbed water. The results obtained were compared with literature data of pulse NMR studies of molecular mobility in other collagen fibers.
MeSH term(s)	Animals ; Collagen/chemistry ; Dogfish ; Magnetic Resonance Spectroscopy ; Water/chemistry
Chemical Substances	Water (059QF0KO0R) ; Collagen (9007-34-5)
Language	Russian
Publishing date	2005-03
Publishing country	Russia (Federation)
Document type	English Abstract ; Journal Article
ZDB-ID	280283-1
ISSN	0006-3029
ISSN	0006-3029
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Article ; Online: Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model.

Jeannin-Girardon, Anne / Ballet, Pascal / Rodin, Vincent

IEEE/ACM transactions on computational biology and bioinformatics

2015 Volume 12, Issue 5, Page(s) 1021–1033

Abstract: The complexity of biological tissue morphogenesis makes in silico simulations of such system very interesting in order to gain a better understanding of the underlying mechanisms ruling the development of multicellular tissues. This complexity is mainly ... ...

Abstract	The complexity of biological tissue morphogenesis makes in silico simulations of such system very interesting in order to gain a better understanding of the underlying mechanisms ruling the development of multicellular tissues. This complexity is mainly due to two elements: firstly, biological tissues comprise a large amount of cells; secondly, these cells exhibit complex interactions and behaviors. To address these two issues, we propose two tools: the first one is a virtual cell model that comprise two main elements: firstly, a mechanical structure (membrane, cytoskeleton, and cortex) and secondly, the main behaviors exhibited by biological cells, i.e., mitosis, growth, differentiation, molecule consumption, and production as well as the consideration of the physical constraints issued from the environment. An artificial chemistry is also included in the model. This virtual cell model is coupled to an agent-based formalism. The second tool is a simulator that relies on the OpenCL framework. It allows efficient parallel simulations on heterogenous devices such as micro-processors or graphics processors. We present two case studies validating the implementation of our model in our simulator: cellular proliferation controlled by cell signalling and limb growth in a virtual organism.
MeSH term(s)	Animals ; Cell Cycle/physiology ; Computer Simulation ; Extremities/anatomy & histology ; Extremities/growth & development ; Humans ; Mechanotransduction, Cellular/physiology ; Models, Biological ; Morphogenesis/physiology
Language	English
Publishing date	2015-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-9964
ISSN (online)	1557-9964
DOI	10.1109/TCBB.2015.2418994
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Article ; Online: Positronium Laser Cooling via the 1^{3}S-2^{3}P Transition with a Broadband Laser Pulse.

Glöggler, L T / Gusakova, N / Rienäcker, B / Camper, A / Caravita, R / Huck, S / Volponi, M / Wolz, T / Penasa, L / Krumins, V / Gustafsson, F P / Comparat, D / Auzins, M / Bergmann, B / Burian, P / Brusa, R S / Castelli, F / Cerchiari, G / Ciuryło, R /

Consolati, G / Doser, M / Graczykowski, Ł / Grosbart, M / Guatieri, F / Haider, S / Janik, M A / Kasprowicz, G / Khatri, G / Kłosowski, Ł / Kornakov, G / Lappo, L / Linek, A / Malamant, J / Mariazzi, S / Petracek, V / Piwiński, M / Pospíšil, S / Povolo, L / Prelz, F / Rangwala, S A / Rauschendorfer, T / Rawat, B S / Rodin, V / Røhne, O M / Sandaker, H / Smolyanskiy, P / Sowiński, T / Tefelski, D / Vafeiadis, T / Welsch, C P / Zawada, M / Zielinski, J / Zurlo, N

Physical review letters

2024 Volume 132, Issue 8, Page(s) 83402

Abstract: We report on laser cooling of a large fraction of positronium (Ps) in free flight by strongly saturating the 1^{3}S-2^{3}P transition with a broadband, long-pulsed 243 nm alexandrite laser. The ground state Ps cloud is produced in a magnetic and electric ...

Abstract	We report on laser cooling of a large fraction of positronium (Ps) in free flight by strongly saturating the 1^{3}S-2^{3}P transition with a broadband, long-pulsed 243 nm alexandrite laser. The ground state Ps cloud is produced in a magnetic and electric field-free environment. We observe two different laser-induced effects. The first effect is an increase in the number of atoms in the ground state after the time Ps has spent in the long-lived 2^{3}P states. The second effect is one-dimensional Doppler cooling of Ps, reducing the cloud's temperature from 380(20) to 170(20) K. We demonstrate a 58(9)% increase in the fraction of Ps atoms with v_{1D}<3.7×10^{4} ms^{-1}.
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.132.083402
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Article ; Online: Multi-Scale Modeling and Oxygen Impact on Tumor Temporal Evolution: Application on Rectal Cancer During Radiotherapy.

Apeke, Sena / Gaubert, Laurent / Boussion, Nicolas / Lambin, Philippe / Visvikis, Dimitris / Rodin, Vincent / Redou, Pascal

IEEE transactions on medical imaging

2018 Volume 37, Issue 4, Page(s) 871–880

Abstract: We present a multi-scale approach of tumor modeling in order to predict its evolution during radiotherapy. Within this context we focus on three different scales of tumor modeling: microscopic (individual cells in a voxel), mesoscopic (population of ... ...

Abstract	We present a multi-scale approach of tumor modeling in order to predict its evolution during radiotherapy. Within this context we focus on three different scales of tumor modeling: microscopic (individual cells in a voxel), mesoscopic (population of cells in a voxel) and macroscopic (whole tumor), with transition interfaces between these three scales. At the cellular level, the description is based on phase transfer probabilities in the cellular cycle. At the mesoscopic scale we represent populations of cells according to different stages in a cell cycle. Finally, at the macroscopic scale, the tumor description is based on the use of FDG PET image voxels. These three scales exist naturally: biological data are collected at the macroscopic scale, but the pathological behavior of the tumor is based on an abnormal cell-cycle at the microscopic scale. On the other hand, the introduction of a mesoscopic scale is essential in order to reduce the gap between the two extreme, in terms of resolution, description levels. It also reduces the computational burden of simulating a large number of individual cells. As an application of the proposed multi-scale model, we simulate the effect of oxygen on tumor evolution during radiotherapy. Two consecutive FDG PET images of 17 rectal cancer patients undergoing radiotherapy are used to simulate the tumor evolution during treatment. The simulated results are compared with those obtained on a third FDG PET image acquired two weeks after the beginning of the treatment.
MeSH term(s)	Cell Cycle/physiology ; Cell Hypoxia/physiology ; Databases, Factual ; Humans ; Models, Biological ; Neoplastic Processes ; Oxygen/metabolism ; Positron-Emission Tomography ; Rectal Neoplasms/diagnostic imaging ; Rectal Neoplasms/metabolism ; Rectal Neoplasms/physiopathology ; Rectal Neoplasms/radiotherapy
Chemical Substances	Oxygen (S88TT14065)
Language	English
Publishing date	2018-04-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	622531-7
ISSN	1558-254X ; 0278-0062
ISSN (online)	1558-254X
ISSN	0278-0062
DOI	10.1109/TMI.2017.2771379
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