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Recent developments in computational modelling of nucleation in phase transformations

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npj Computational Materials 2016年第1期2卷 180-188页

作者： Lei Zhang Weiqing Ren amit samanta Qiang Du Beijing International Center for Mathematical Research Center for Quantitative BiologyPeking UniversityBeijingChina Department of Mathematics National University of SingaporeSingapore Institute of High Performance Computing Agency for ScienceTechnology and ResearchSingapore Physics Division Lawrence Livermore National LaboratoryLivermoreCAUSA Department of Applied Physics and Applied Mathematics Columbia UniversityNew YorkNYUSA

Nucleation is one of the most common physical phenomena in physical,chemical,biological and materials *** to the complex multiscale nature of various nucleation events and the difficulties in their direct experimental observation,development of effective computational methods and modeling approaches has become very important and is bringing new light to the study of this challenging *** discussions in this manuscript provide a sampler of some newly developed numerical algorithms that are widely applicable to many nucleation and phase transformation *** first describe some recent progress on the design of efficient numerical methods for computing saddle points and minimum energy paths,and then illustrate their applications to the study of nucleation events associated with several different physical systems.

关键词： transformation phase bringing

Observation of a single protein by ultrafast X-ray diffraction

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Light(Science & Applications) 2024年第1期13卷 80-90页

作者： Tomas Ekeberg Dameli Assalauova Johan Bielecki Rebecca Boll Benedikt J.Daurer Lutz A.Eichacker Linda E.Franken Davide E.Galli Luca Gelisio Lars Gumprecht Laura H.Gunn Janos Hajdu Robert Hartmann Dirk Hasse Alexandr Ignatenko Jayanath Koliyadu Olena Kulyk Ruslan Kurta Markus Kuster Wolfgang Lugmayr Jannik Lübke Adrian P.Mancuso Tommaso Mazza Carl Nettelblad Yevheniy Ovcharenko Daniel E.Rivas Max Rose amit K.samanta Philipp Schmidt Egor Sobolev Nicusor Timneanu Sergey Usenko Daniel Westphal Tamme Wollweber Lena Worbs Paul Lourdu Xavier Hazem Yousef Kartik Ayyer Henry N.Chapman Jonas A.Sellberg Carolin Seuring Ivan A.Vartanyants Jochen Küpper Michael Meyer Filipe R.N.C.Maia Laboratory of Molecular Biophysics Department of Cell and Molecular BiologyUppsala UniversityHusargatan 3(Box 596)SE-75124 UppsalaSweden Deutsches Electronen-Synchrotron DESY Notkestrasse 8522607 HamburgGermany European XFEL Holzkoppel 422869 SchenefeldGermany Diamond Light Source Harwell Science&Innovation CampusDidcot OX110DEUK University of Stavanger Centre Organelle ResearchRichard-Johnsensgate 44021 StavangerNorway Leibniz Institute for Experimental Virology(HPI) Centre for Structural Systems BiologyNotkestraße 8522607 HamburgGermany Dipartimento di Fisica“Aldo Pontremoli” Universitàdegli Studi di Milanovia Celoria 1620133 MilanoItaly Center for Free-Electron Laser Science DESY22607 HamburgGermany Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA PNSensor GmbH Otto-Hahn-Ring 6D-81739 MünchenGermany Biomedical and X-Ray Physics Department of Applied PhysicsAlbaNova University CenterKTH Royal Institute of TechnologySE-10691 StockholmSweden ELI Beamlines/IoP Institute of Physics AS CR v.v.i.Na Slovance 218221 Prague 8Czech Republic Multi-User CryoEM Facility Centre for Structural Systems BiologyNotkestr.8522607 HamburgGermany University Medical Center Hamburg-Eppendorf(UKE) Martinistrasse 5220246 HamburgGermany The Hamburg Center for Ultrafast Imaging Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Physics Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Chemistry and Physics La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVIC 3086Australia Division of Scientific Computing Science for Life LaboratoryDepartment of Information TechnologyUppsala UniversityBox 337SE-75105 UppsalaSweden European Molecular Biology Laboratory c/o DESYNotkestrasse 8522607 HamburgGermany Department of Physics and Astronomy Uppsala UniversityBox 516SE-75120 UppsalaSweden Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 14922761 HamburgGe

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired *** was one of the arguments for building X-ray free-electron *** to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably *** was first demonstrated on biological samples a decade ago on the giant *** then,a large collaboration has been pushing the limit of the smallest sample that can be *** ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of *** we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single *** the pattern,it is possible to determine the approximate orientation of the *** experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词： smallest intense ultrafast

Switching effect on a two prey-one predator system with strong Allee effect incorporating prey refuge

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International Journal of Biomathematics 2024年第2期17卷 1-50页

作者： Sangeeta Saha Guruprasad samanta Department of Mathematics Indian Institute of Engineering Science and Technology Shibpur Howrah 711103India

In an environment,the food chains are balanced by the prey-predator *** a predator species is provided with more than one prey population,it avails the option of prey switching between prey species according to their ***,prey switching of predators mainly helps to increase the overall growth rate of a predator *** this work,we have proposed a two prey-one predator system where the predator population adopts switching behavior between two prey species at the time of *** the prey population exhibit a strong Allee effect and the predator population is considered to be a generalist *** proposed system is biologically well-defined as the system variables are positive and do not increase abruptly with *** local stability analysis reveals that all the predator-free equilibria are saddle points whereas the prey-free equilibrium is always *** intrinsic growth rates of prey,the strong Allee parameters,and the prey refuge parameters are chosen to be the controlling parameters *** numerical simulation reveals that in absence of one prey,the other prey refuge parameter can change the system dynamics by forming a stable or unstable limit ***,a situation of bi-stability,tri-stability,or even multi-stability of equilibrium points occurs in this *** in presence of the switching effect,the predator chooses prey according to their abundance,so,increasing refuge in one prey population decreases the count of the second prey *** is also observed that the count of predator population reaches a comparatively higher value even if they get one prey population at its fullest quantity and only a portion of other prey ***,in the scarcity of one prey species,switching to the other prey is beneficial for the growth of the predator population.

关键词： Prey-predator model switching effect strong Allee effect prey refuge

Constructing a biofunctionalized 3D-printed gelatin/sodium alginate/chitosan tri-polymer complex scaffold with improvised biological andmechanical properties for bone-tissue engineering

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Bio-Design and Manufacturing 2024年第1期7卷 57-73页

作者： amit Kumar Singh Krishna Pramanik amit Biswas Centre of Excellence in Tissue Engineering Department of Biotechnology and Medical EngineeringNational Institute of TechnologyRourkela 769008India

Sodium alginate(SA)/chitosan(CH)polyelectrolyte scaffold is a suitable substrate for tissue-engineering *** present study deals with further improvement in the tensile strength and biological properties of this type of scaffold to make it a potential template for bone-tissue *** experimented with adding 0%–15%(volume fraction)gelatin(GE),a protein-based biopolymer known to promote cell adhesion,proliferation,and *** resulting tri-polymer complex was used as bioink to fabricate SA/CH/GEmatrices by three-dimensional(3D)*** studies using scanning electron microscopy revealed the microfibrous porous architecture of all the structures,which had a pore size range of 383–419μm.X-ray diffraction and Fourier-transform infrared spectroscopy analyses revealed the amorphous nature of the scaffold and the strong electrostatic interactions among the functional groups of the polymers,thereby forming polyelectrolyte complexes which were found to improve mechanical properties and structural *** scaffolds exhibited a desirable degradation rate,controlled swelling,and hydrophilic characteristics which are favorable for bone-tissue *** tensile strength improved from(386±15)to(693±15)kPa due to the increased stiffness of SA/CH scaffolds upon addition of *** enhanced protein adsorption and in vitro bioactivity(forming an apatite layer)confirmed the ability of the SA/CH/GE scaffold to offer higher cellular adhesion and a bone-like environment to cells during the process of tissue *** vitro biological evaluation including the MTT assay,confocal microscopy analysis,and alizarin red S assay showed a significant increase in cell attachment,cell viability,and cell proliferation,which further improved biomineralization over the scaffold *** addition,SA/CH containing 15%gelatin designated as SA/CH/GE15 showed superior performance to the other fabricated 3D structures,demonstrating its pote

关键词： Scaffold Biomaterial Sodium alginate Chitosan Gelatin 3D printing Tissue engineering

Protected simultaneous quantum remote state preparation scheme by weak and reversal measurements in noisy environments

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Chinese Physics B 2024年第2期33卷 169-177页

作者： Mandal Manoj Kumar Choudhury Binayak S. samanta Soumen Department of Mathematics Indian Institute of Engineering Science and TechnologyShibpur B.GardenHowrah 711103West BengalIndia

We discuss a quantum remote state preparation protocol by which two parties, Alice and Candy, prepare a single-qubit and a two-qubit state, respectively, at the site of the receiver Bob. The single-qubit state is known to Alice while the two-qubit state which is a non-maximally entangled Bell state is known to Candy. The three parties are connected through a single entangled state which acts as a quantum channel. We first describe the protocol in the ideal case when the entangled channel under use is in a pure state. After that, we consider the effect of amplitude damping(AD) noise on the quantum channel and describe the protocol executed through the noisy channel. The decrement of the fidelity is shown to occur with the increment in the noise parameter. This is shown by numerical computation in specific examples of the states to be created. Finally, we show that it is possible to maintain the label of fidelity to some extent and hence to decrease the effect of noise by the application of weak and reversal measurements. We also present a scheme for the generation of the five-qubit entangled resource which we require as a quantum channel. The generation scheme is run on the IBMQ platform.

关键词： multi-qubit entangled channel quantum remote state preparation noisy environments weak and reversal measurements

Quantification of grain boundary effects on the geometrically necessary dislocation density evolution and strain hardening of polycrystalline Mg-4Al using in situ tensile testing in scanning electron microscope and HR-EBSD

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Journal of Magnesium and Alloys 2024年第5期12卷 1815-1829页

作者： Eunji Song Mohsen Taheri Andani amit Misra Department of Materials Science and Engineering University of MichiganAnn ArborMI 48109USA Department of Mechanical Engineering University of MichiganAnn ArborMI 48109USA Department of Mechanical Engineering Texas A&M UniversityCollege StationTX 77843USA

In situ tensile testing in a scanning electron microscope(SEM)in conjunction with high-resolution electron backscatter diffraction(HR-EBSD)under load was used to characterize the evolution of geometrically necessary dislocation(GND)densities at individual grain boundaries as a function of applied strain in a polycrystalline Mg-4Al *** increase in GND density was investigated at plastic strains of 0%,0.6%,2.2%,3.3% from the area including 76 grains and correlated with(i)geometric compatibility between slip systems across grain boundaries,and(ii)plastic *** develop expressions for the grain boundary GND density evolution as a function of plastic strain and plastic incompatibility,from which uniaxial tensile stress-strain response of polycrystalline Mg-4Al are computed and compared with experimental *** findings in this study contribute to understanding the mechanisms governing the strain hardening response of single-phase polycrystalline alloys and more reliable prediction of mechanical behaviors in diverse microstructures.

关键词： Mg-Al alloys Grain boundaries Geometrically necessary dislocations Strain gradient plasticity HR-EBSD

Unveiling childhood asthma:Exploring biomarkers,zinc,and beyond

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World Journal of Clinical Pediatrics 2024年第2期13卷 7-10页

作者： amit Agrawal Department of Pediatrics Gandhi Medical CollegeHamidia Hospital CampusBhopal 462022India

This editorial discusses a case-control study by Ibrahim et al,published in the recent issue of the World Journal of Clinical *** bronchial asthma is a chronic inflammatory respiratory *** was found that an increase in oxidative stress leads to a decrease in antioxidants causing oxidative damage to mitochondrial respiratory chain complexes resulting in the inflammation of the airway,hypersecretion of mucus causing a cascade of clinical manifestations ranging from recurrent episodes of coughing,wheezing,and breathlessness to shortness of *** oxidative stress mediates the inflammatory response in asthma,the supplementation of anti-oxidants can be one strategy to manage this *** is one such antioxidant that has attracted much attention about asthma and airway *** is a crucial trace element for human metabolism that helps to regulate gene expression,enzyme activity,and protein *** from zinc,free serum ferritin levels are also elevated in case of *** previous studies found that ferritin levels may also help determine the pathology of disease and predict prognosis in addition to tracking disease ***,this study's results were different from the findings of the previous studies and the zinc levels did not show a significant difference between asthmatic children and non-asthmatic children but ferritin levels were significantly high in asthmatic children as compared to the ***,the possible role of the biochemical nutritional assessment including zinc and ferritin as biomarkers for asthma severity should be assessed in the future.

关键词： Asthma Biomarker Children Zinc Ferritin Immunoglobulin E

Evaluation of slope stability through rock mass classification and kinematic analysis of some major slopes along NH-1A from Ramban to Banihal, North Western Himalayas

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第1期16卷 167-182页

作者： amit Jaiswal A.K.Verma T.N.Singh Department of Civil and Environmental Engineering Indian Institute of Technology PatnaPatna801106India

The network of Himalayan roadways and highways connects some remote regions of valleys or hill slopes,which is vital for India’s socio-economic *** to natural and artificial factors,frequency of slope instabilities along the networks has been increasing over last few *** of stability of natural and artificial slopes due to construction of these connecting road networks is significant in safely executing these roads throughout the *** rock mass classification methods are generally used to assess the strength and deformability of rock *** study assesses slope stability along the NH-1A of Ramban district of North Western *** structurally and non-structurally controlled rock mass classification systems have been applied to assess the stability conditions of 14 *** evaluating the stability of these slopes,kinematic analysis was performed along with geological strength index(GSI),rock mass rating(RMR),continuous slope mass rating(CoSMR),slope mass rating(SMR),and Q-slope in the present *** SMR gives three slopes as completely unstable while CoSMR suggests four slopes as completely *** stability of all slopes was also analyzed using a design chart under dynamic and static conditions by slope stability rating(SSR)for the factor of safety(FoS)of 1.2 and 1 respectively.Q-slope with probability of failure(PoF)1%gives two slopes as stable *** slope angle has been determined based on the Q-slope safe angle equation and SSR design chart based on the *** value ranges given by different empirical classifications were RMR(37-74),GSI(27.3-58.5),SMR(11-59),and CoSMR(3.39-74.56).Good relationship was found among RMR&SSR and RMR&GSI with correlation coefficient(R 2)value of 0.815 and 0.6866,***,a comparative stability of all these slopes based on the above classification has been performed to identify the most critical slope along this road.

关键词： Rock mass classification Kinematic analysis Slope stability Himalayan road Static and dynamic conditions

Dual-wavelength all-fiber Q-switched fiber laser using bismuth-doped fiber as saturable absorber

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Optoelectronics Letters 2024年第3期20卷 147-151页

作者： Aruna Ghosh Abdulkadir Mukhtar Diblawe Uttam Kumar samanta Moh Yasin Sulaiman Wadi Harun Mukul Chandra Paul Fiber Optics and Photonics Division CSIR-Central Glass and Ceramic Research InstituteKolkata 700032India Physics Department Jadavpur UniversityKolkata 700032India Photonics Engineering Laboratory Department of Electrical EngineeringUniversity of MalayaKuala Lumpur 50603Malaysia Department of Physics Faculty of Science and TechnologyAirlangga UniversitySurabayaIndonesia

A passively Q-switched all-fiber laser is demonstrated using a 10-cm-long bismuth-doped fiber(BDF) as a saturable absorber(SA). The dual-wavelength operation was obtained due to the nonlinear effect inside the fabricated BDF, which has a high germanium content. Stable Q-switched pulses were obtained at the dual synchronous wavelengths of 1 530.1 nm and 1 531.1 nm. When the pump power is tuned from 105.3 mW to 191.0 mW, the repetition rate can be varied from 82.6 kMz to 117.6 kHz. The maximum pulse energy and average output power were 83.4 nJ and 9.8 mW, respectively while the minimum pulse width was 8.5 μs at the maximum pump power of 191.0 mW. Our results indicate that BDF could be a promising alternative optical modulator for pulsed fiber laser application.

关键词： fiber switched pump