2017-02-21Application

Draft Nikitin, Viktor

Information about applicant

Name: Viktor Niki tin

Birthdate: 19900517

Gender: Male

Doctorial degree: 2016-08-19

Academic title: Doktor

Employer: Lunds univers i tet

Administrating organisation: Lunds univers i tet

Project site: Max IV Lab

Information about application

Call name: International Postdoc 1 2017 (Vetenskapsrådet)

Type of grant: International Postdoc Grant

Focus: Undirected

Call for proposals subject area: HS, AR, ES, MH, NE

Project title (english): Streaming Images of Geomateria ls

Project start: 2017-07-01

Review panel applied for: IPD-NT1

Project end: 2020-06-30

Classification code: 10105. Computational Mathematics , 20306. Fluid Mechanics and Acoustics , 10205.Software Engineering

Keywords: 4D X-ray tomography, synchrotron measurements , geomateria ls , gas hydrates

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Project title (Swedish)*

Streaming Bilder av Geomaterial

Project title (English)*

Streaming Images of Geomaterials

Abstract (English)*

Main topic of my research will be to develop techniques for real-time data analysis of synchrotrontomographic data measurements for future use at MAX IV laboratory in Lund. The intended results will opena new dimension for in-situ dynamic characterization of changing micro-structure of materials. The techniquehas a wide range of applications in geology, materials science, and medical research. Geoscienceapplications are attractive because of wide spectrum of heterogeneity scales as well as great variety ofprocesses involved. In this project we are focused on studying gas hydrates, namely their formation ingeomaterials, gas/liquid filtration, thawing-freezing weathering of matrix.

The project consists of 3 phases. The first-phase research (October 1,2017-September 31,2019) iscoordinated by the imaging group at the Argonne National Laboratory in Chicago, where methods fordynamic data reconstruction will be developed. The second phase (4x2-weeks during 2018-2020) impliesvisits to the Institute of Petroleum Geology and Geophysics in Novosibirsk. During these visits I will take partin the design of a high-pressure chamber for gas-hydrate formation with acoustic and simultaneous X-raymeasurements. Main idea is to develop imaging algorithms that suppress specific artifacts. The third phase(October 1,2019-September 31,2020) takes place at MAX IV laboratory where the real-time tomographyplatform will be established at the HPC cluster and tested for studying geomaterials.

Descriptive data

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Popular scientific description (Swedish)*

Datortomografi med röntgenstrålar är en metod för att återskapa en tredimensionell modell av ett objekt, utan att föremålet förstörs. Röntgenkällans intensitet påverkar upplösningen och apparaturens prestanda. En typ av röntgenkälla är en synkrotron, en särskild sorts partikelaccelerator där högenergetiska elektroner används för att producera mycket intensivt ljus såsom röntgenstrålning. Ljuset leds genom strålrör till ett antal experimentstationer, där det används för vetenskapliga experiment. I datortomografi leds strålarna genom objektet, där de delvis absorberas. Bakom objektet placeras en detektor som därför avbildar objektet i två dimensioner. Genom att rotera provet och upprepa mätningen kan objektet avbildas tredimensionellt.Högenergetisk röntgenstrålning skapar nya möjligheter för att tillämpa datortomografi. Synkrotronmätningar är relativt vanliga i många forskningsfält såsom materialvetenskap, geologi, biologi och medicin. Nyligen byggdes nästa generations synkrotron, MAX IV, i Lund.Numera görs många avbildningsexperiment med röntgen dynamiskt, vilket betyder att objektets inre struktur förändras under experimentets gång. I materialvetenskap avbildar man till exempel prover medan de utsätts för förändrade yttre omständigheter såsom tryck och temperatur. I medicinsk forskning tittar man till exempel på rörliga processer såsom andning. I geologi är man ofta intresserad av flöden eller gashydratbildning i porösa material. Beroende på hur tidsskalan för sådana processer förhåller sig till tiden det tar att göra en avbildning, orsakar detta mätfel i de slutliga tredimensionella modellerna.Detta projekt syftar till att utveckla metoder för att analysera sådana dynamiska data (streaming bilder) med tillämpning på geologiska system. Geologiska tillämpningar är attraktiva på grund av att struktura kan finnas på många längdskalor, och eftersom en stor mängd processer kan studeras.Detta projekt fokuserar på gashydratbildning i geologiska material. Gashydraternas egenskaper i små geologiska prover under olika förhållanden (tryck, temperatur, etc.) kan utökas till större prover med hjälp av matematiska modeller. Det är viktigt att förstå gashydrater, eftersom de kan utgöra en kolvätekälla. Vidare kan anrikning av gashydrater i marina sediment orsaka miljöpåverkan såsom ökade utsläpp av växthusgaser och undervattenserosion.Detta projekt planeras i tre faser. Den första fasen (1 oktober 2017 till 31 september 2019) koordineras av avbildningsgruppen vid Argonne National Laboratory i Chicago, USA, där nya metoder för dynamisk datortomografi kommer att utvecklas. Den andra fasen (4 x 2 veckor under 2018 till 2020) innebär fyra resor till Institution of Petroleum Geology and Geophysics SB RAS, Novosibirsk, Ryssland. De utvecklade metoderna för analys av dynamiska tomografidata kommer att användas tillsammans med akustiska data, med tillämpning på geofysikaliska material. Den tredje fasen (1 oktober 2019 till 31 september 2020) förläggs till avbildningsgruppen på MAX IV-laboratoriet i Lund. Med stöd från IT-avdelningen kommer en plattform för realtidstomografi att etableras på MAX IV:s beräkningskluster och testas för tillämpning på geologiska material.

Host country abroad*

USA, Russia

Host university abroad*

Argonne National Laboratory, Institute of Petroleum Geology and Geophysics SB RAS

Department at host university abroad*

Advanced Photon Source, Division of geophysics

Subject area*

Natural and engineering sciences NE

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Calculated project time*

2017-07-01 - 2020-06-30

Deductible time

CauseCause MonthsMonths

Career age is a description of the time from your first doctoral degree until the last day of the call. Yourcareer age changes if you indicate deductible time due to a reason approved by the funder. For some callsthere are restrictions in the allowed career age.

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Reporting of ethical considerations*

The research does not raise any ethical issues.

The project includes handling of personal data

No

The project includes animal experiments

No

The project includes experiments involving human subjects

No

Research description

Research plan (a maximum of 8 A4-pages)*

See following page for attachment

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VIKTOR NIKITIN RESEARCH PLAN 1(8)

Streaming Images of Geomaterials1 Purpose and aims

The goal of this project is to enable scientific exploration of the micro-structural dynamics of matter throughreal-time analysis and visualization of experiments.

In biomedical sciences there are well established protocols for acquiring simultaneously two or more sig-nals (e.g. X-ray computed tomography and positron emission tomography) where one provides the structuraland the other the functional information on the sample. In material science the properties of a system arestrongly linked to its micro-structure. At the resolution level of 1 µm for parallel X-ray geometry [15, 26],and of 20 nm for transmission X-ray microscope geometry [3], synchrotron based tomography is outper-forming all other three-dimensional (3D) imaging methods for fast dynamic processes in bulky samples [16].This is now further enhanced by the onset of a new generation of synchrotron light sources such as the MAXIV Laboratory in Lund and the of Advanced Photon Source Upgrade in Chicago.

The development of high-speed time-resolved tomographic microscopy is of great interest for variousthree-dimensional in-situ studies. Perhaps the fastest growing community is geologists who use synchrotronimaging in their applications. Imaging techniques are combined with acoustic techniques to provide a pow-erful experimental tool that can capture propagation of the oil or gas hydrates inside a geological sample.Synchrotron based tomography gives a big impact in probing geological matter because of the penetrationdepth of the X-rays and at the same time the high spatio-temporal resolution.

One of the main difficulties of in-situ studies of dynamic samples is the determination of the optimalacquisition system control parameters. Without real-time feedback during the tomographic acquisition thereis little hope to make synchrotron imaging a modality that can be successfully and reliably used by industryand academia to shed light on rapidly evolving processes in matter. The specific research objectives are:

• Gaining experience in handling of large data streams in tomography

• Develop an open-source streaming platform for real-time tomography at the light sources

• Develop methodology to study dynamic processes in matter and apply them to geomaterials

2 Survey of the field

Different variants of X-ray tomography are widely used for non-destructive 3D imaging and analysis of theinternal structure of materials in various applications. With the growing demand for these techniques a lotof research is done in order to improve imaging algorithms and solve technical problems for broadening thenumber of applications.

There exist many methods for reconstruction of 3D tomography data sets. One of the most popular meth-ods is by means of the filtered back-projection (FBP) formula [25] which involves procedures of filteringand computing the back-projection operator. In some situations it is preferable to use an iterative methodsuch as algebraic reconstruction techniques (ART) [6, 17] for doing reconstruction from tomographic data.This could, for instance, be because of missing data, e.g., that data for some angles are missing; suppressionof artifacts; or that additional information about the noise contamination can be used to improve the recon-struction results. Most algorithms for 3D tomography data reconstruction and processing were implementedin software packages, e.g, TomoPy [18], Astra toolbox [27], Savu reconstruction pipeline [4]. Methods forreal-time 4D (3D+time) tomography data reconstruction are more challenging. Recent research activities byKazantsev and Eyndhoven [19, 28] still do not solve all the coming problems of 4D imaging.

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VIKTOR NIKITIN RESEARCH PLAN 2(8)

Studying the structure of geomaterials was an important topic during the last decades [8]. X-ray and otherimaging methods played an important role in recovering complicated structure of rocks used for developingrealistic numerical models of geomaterials behavior [2]. Recently the research focus is developing towards4D imaging of processes taking place in the geomaterials. Important applications include multi-phase fluidflow in porous rocks [31, 7, 14], deformation and geomechanical testing of samples [5, 22, 30]. Interestingnew applications that can greatly benefit from 4D X-ray imaging include laboratory experiments on forma-tion/dissociation of gas hydrates [32], and hydraulic fracturing [20]. Thus 4D X-ray imaging will become anindispensable technique in the field of geosciences.

2.1 Following dynamic processes in matter

In material engineering one principal challenge is to understand the response of various new materials tomechanical stress. A recent study [23] demonstrates that it is now principally possible to follow the crackpropagation in 3D at a 20 Hz rate. However, the success rate for this case is 5 %, because the insufficient real-time feedback that could be gained if real-time data visualization would be possible. A number of studieswith geology background pointed to similar conclusions.

Physical properties of hydrate-containing rocks are studied under laboratory conditions in order to inves-tigate their dependence on the rock structure, quantity and hydrate formations in samples. Acoustic, electricaland mechanical properties are measured in real time, however they still do not answer all the questions beingposed. Kinetics of the gas-hydrate formation may result in different structure of its filling the pores [29]including cementing, filling pores etc. These different hydrate structures strongly affect macro-properties ofsamples, especially acoustic wave speeds. Dissociation of gas hydrates produces gas which causes filtrationin the sample as well as acoustic emission. Also porous matrix is changed (grains and matrix are brokenbecause of ice expansion during freezing) during freezing-thawing cycles used for efficient gas-hydrate for-mation [9]. Finally, hydraulic fracturing experiments are interesting for methane-hydrate-bearing sand [21],because this technology can be used for methane production from gas hydrates.

Dynamic processes in geomaterials are studied in various applications. IPGG SB RAS has a long historyof laboratory experiments on forming gas hydrates in porous samples and measuring their physical properties.These studies include the development of the laboratory setup for measuring thermo-physical properties ofhydrate bearing samples, i.e. thermal conductivity and diffusivity [12, 13]. Another laboratory research wasdone on measuring electric properties of the hydrate bearing sediments [10, 11]. Finally, laboratory setup atIPGG SB RAS for forming methane gas hydrates in rock samples and measuring their acoustic properties.Acoustic properties depend on the structure of gas hydrates in pores: cementing or filling. Present activityis a development of a new laboratory setup compatible with X-ray tomography in collaboration with thecompany Geologika (http://www.geologika.ru/english).

There is an important question of combining these experiments with real-time imaging of gas-hydrateformation (longer process) and dissociation (faster process). The texture of gas hydrates and its distributionin the pore space is important for understanding kinetics of the hydrate formation in geomaterials and itsinfluence on the acoustic properties of samples.

2.2 Data streaming at large scale synchrotron facilities

A number of software tools for higher level analysis and visualization of X-ray tomographic data have beendeveloped. The majority of the tools used by the diverse scientific communities to exploit X-ray tomographicdata lack support of high-performance data intensive computing. This is the first reasons that in the contextof high speed imaging the data is reconstructed off-line. The second reason is that there is no commercially

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VIKTOR NIKITIN RESEARCH PLAN 3(8)

available solution for high frame-rate (multi-GB/s) streaming of tomographic data and therefore no access tothem is possible during the acquisition process. The development of fast detector systems in the last yearswas driven by the wish to match the great advances in X-ray probes brilliance and the desire to capture thedynamics of life at high resolution. Somewhat forgotten was the aspect of smart classification of the streameddata in order to make informed decisions during the experiment to reduce unnecessary data or to modifythe acquisition based on specific events occurring in the studied sample. All commercially available fastdetectors (pixel detectors and CMOS cameras) share a common feature that they do not offer the possibilityto stream high frame rates over an extended period directly to a computing infrastructure. This hampersthe possibility to use online data monitoring and processing schemes resulting in a significant amount ofunnecessary data stored.

As of today there is only one successful synchrotron imaging data streaming system in operation at theSwiss Light Source (SLS) [24]. In this system the camera streams 8 GB/s to the RAM of the server wherethe data may be processed before writing them to the disks. Yet the performance of the image reconstructionand analysis algorithms is far inferior to what would be required to exploit the information in the data streamand provide real-time feedback to the acquisition. What remains to be realized is to turn this flow into a smartdata stream with the help of classifiers.

The first instruments at the MAX IV synchrotron laboratory started operation in 2016. In 2019 the firsttomographic imaging beamline will come online and will produce many Terabytes of data per day. Datacapture, management and real-time analysis will be essential for an efficient use of the facility. As of todaythere is no solution to achieve these goals. The same problem has been undertaken by the APS, and a newprogram is currently launched with the aim to develop and implement method streaming data processing.

3 Project description

The project will be realized in three phases:

1. Training in ’How to access data streams?’ at the Advances Photon Source. Research on time-resolvedand real-time tomographic reconstruction algorithms. Demonstration of real-time tomography at APS.

2. Development of simultaneous acoustic and X-ray reconstruction algorithms in Novosibirsk. Integra-tion of the implementation of these algorithms in the to-be developed streaming platform.

3. Dissemination of know-how through research publications, conferences, and software documentation.Demonstration of the real-time tomographic platform integration at MAX IV imaging beamlines.

In the first phase I will join the imaging group at APS led by Dr. Francesco De Carlo. The group ispreparing the generic framework of data streaming at the synchrotron facility. I will contribute mainly bydesigning classifiers for the imaging data streams. Once the streams from the detectors are accessible the nextchallenge is to process these data on-the-fly and produce simple quantifiers which can be used as feedbackinformation. At this level the interpretation of the data may differ depending on the acquisition technique.Taking the recently introduced fast reconstruction implementations will serve as the base for the developmentof new algorithms which are optimized for time-resolved imaging and are compatible with large data streams.

In the second phase I will have multiple research visits to of the Institute of Petroleum Geology andGeophysics SB RAS. There I will visit the research group of Anton Duchkov which is studying acousticproperties of gas-hydrate bearing rock samples. During these visits I will have access to the laboratoryequipment and will get involved in the laboratory experiments on gas-hydrate formation in geomaterials andstudying their acoustic properties. I will take part in designing a new gas-hydrate chamber so that it can be

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VIKTOR NIKITIN RESEARCH PLAN 4(8)

installed and operated at the MAX IV laboratory for simultaneous 4D imaging and an improved acousticsystem (minimize imaging artifacts by hardware design and develop new imaging algorithms for eliminatingremaining artifacts). The modification of the existing gas-hydrate formation chamber will be driven by theadvances in the algorithms development in fast tomographic microscopy. The production of the chamber forcombined microstructure kinetics and acoustic properties of gas hydrate formation and acoustic emission ofgas-hydrate bearing samples will be formulated as a separate research project between MAX IV Laboratoryand the host institution in Novosibirsk.

For the third phase I will return to the imaging group at MAX IV led by Rajmund Mokso. With thesupport of IT team we will first establish the real-time tomography platform at the HPC cluster. Second, wewill establish a platform for simultaneous reconstruction from acoustic and tomography measurements. Myexperience obtained at the APS and IPGG SB RAS will substantially contribute to design these platforms.

The work consists of research and implementation oriented tasks. The major research tasks are:

1. Building visualization tools for data streams

2. Development of fast tomographic reconstruction algorithms

3. Exploration of simultaneous acoustic and X-ray tomography

Each research task is followed by an implementation step. The major implementation tasks are:

1. Formating imaging data streams

2. Optimization of the log-polar tomographic reconstruction concept for best performance on multi Gi-gabyte rate data streams

3. Installation of the real-time tomography platform at MAX IV Laboratory

4. Setting up the simultaneous acoustic-X-ray measurement on geological samples

The project is designed for three years. The first phase, training and research at the APS in Chicago,will take two years. The last year and the third project phase will take place at MAX IV laboratory in Lundwhere we will establish the real-time tomographic platform. During the whole period I am going to have fourtwo-week visits to the Institute of Petroleum Geology and Geophysics, Novosibirsk where the developmentof simultaneous acoustic and X-ray reconstruction algorithms (phase 2) will be performed. Table 3 showsconcrete time periods of the work at different places.

Time period PlaceOctober 1, 2017 – September 31, 2019 Argonne National Laboratory, Chicago, USAOctober 1, 2019 – September 31, 2020 MAX IV Laboratory, Lund, Sweden

4×2-weeks during 2018-2020 IPGG SB RAS, Novosibirsk, Russia

4 Significance

By the realization of real-time X-ray tomographic microscopy a new dimension will open for in-situ dynamiccharacterization of the micro-structure of matter. The technique could have a wide range of applications notonly in geosciences but also in materials science, environmental science and medical research. The developed

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VIKTOR NIKITIN RESEARCH PLAN 5(8)

imaging methods will allow to image objects in a non-invasive manner to reveal their physical and chemicalnano-properties and relate them to their distribution in three-dimensional space at the micron scale. Suchrelationships are key to understanding the properties of materials and so could be used to identify mineralsand oil-bearing rocks, look at in-situ chemical reactions, distinguish between healthy and diseased tissue orprobe stress-strain gradients in manufactured components.

Geosciences applications are attractive because of wide spectrum of heterogeneity scales as well as greatvariety of processes involved. Main application fields for 4D tomography would be multi-phase fluid flowin porous rocks, deformation and geomechanics, hydraulic fracturing, formation of gas hydrates etc. Notethat understanding evolution of gas-hydrate natural accumulations is important not only because they areviewed as a perspective source of hydrocarbons. Gas hydrates accumulations in marine sediments may causeeven stronger impact on the humanity being a potential source of a greenhouse gas (methane), and othertypes of ecological disasters, such as underwater landslides. Thus establishing a new effort for laboratorystudies of methane gas-hydrate formation/dissociation seems to be an important application of the 4D X-ray tomography. This result will have an impact on planning the development of facilities and researchinfrastructure at MAX IV Laboratory.

5 Preliminary results

We developed a fast method for computing forward and inverse Radon transform operators [1] that constitutethe main mathematical tool for computed tomography data reconstruction. The method is based on switch-ing to log-polar coordinates where the operator can be represented as a convolution which can be rapidlyevaluated in terms of Fast Fourier Transforms. The proposed implementation on Graphical Processor Unitsoutperforms all known analogues and demonstrates favorable accuracy.

The Tomographic reconstruction platform was established at MAX IV and the new log-polar based algo-rithm is part of it. The basic functionality allows to work with tomography data files (HDF5 formats), applydark and flat field corrections, and compute the inverse Radon transform. A simple Graphical User Interfacewas documented and published in open access (https://github.com/math-vrn/lprec). The platform was testedfor processing real tomography measurements.

We also plugged the developed software module in the package Savu [4] developed at Diamond LightSource for pipeline tomography data processing. The package is under active development and currentlycontains more than 50 plugins for working with tomography measurements. The package exploits dataparallelism by running across a cluster to process big data sets. We have recently adapted it for HPC clusterfacilities available at MAX IV.

6 Results

There are two main results expected from this project. First, we will have a framework for real-time tomogra-phy at MAX IV Laboratory. The framework installation on the MAX IV cluster will be available for the staffand for all users of synchrotron facilities. In more general terms the concept of simultaneous tomographicacquisition and reconstruction of multiple signals will find its applications in numerous areas of materialscience. Moreover only small modifications of the proposed framework will be required to realize in vivoimaging of small animals which is planned for 2020 at the MAX IV Laboratory.

The second result is related to a specific application of studying dynamic processes in geomaterials. Four-dimensional tomographic algorithms for studying high-resolution structure of the gas-hydrate formation and

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VIKTOR NIKITIN RESEARCH PLAN 6(8)

dissociation processes simultaneously with acoustic measurements. A re-design of existing sample environ-ments used today at the Novosibirsk host institution and in Lund will be based on the advanced know-howon the specific reconstruction routines developed during this PostDoc application. This is a new approach, inwhich the development of the processing tools will drive the acquisition protocols. This will avoid the majorsource of failure in similar studies today, when most of the acquired data is never used because of the lack ofsuitable reconstruction tools.

7 Independent line of research

The research conducted during the doctoral studies with the former research advisor is related to the mathe-matical part of the current project. It involves the development of fast methods for solving inverse problemsin computed tomography and geophysics by using particular structure of the involved mathematical opera-tors. Spatial and time-frequency analysis of the operators allows constructing fast algorithms by decreasingtheir computational complexity. Several algorithms have been implemented with using HPC facilities such asmulti-core CPUs and GPUs and tested with real applications in computed tomography and geophysics. Theproposed mathematical methods for reconstruction and data processing will be considered for high-speedtime-resolved imaging procedures.

8 Equipment

Laboratory setup for studying acoustic properties of gas-hydrate bearing sediments, Novosibirsk:IPGG SB RAS have developed and operates the laboratory setup enables formation of synthetic gas hydratesin porous samples and measure variations of acoustic properties caused by gas hydrates.

Independent Scientific and Laboratory Centre (ISLC) of core and proppant analysis, Novosibirsk:Upon request we have access to petrophysical laboratory equipment owned by JSC Geologika and usedfor rock samples and formation fluids tests with applications to studying conventional and unconventionalreservoirs. Methods include geomechanical core testing, multi-phase liquid and gas relative permeabilitytesting, hydraulic fracturing materials testing.

9 Need for infrastructure

Advanced Photon Source (APS), Argonne: U.S. Department of Energys Argonne provides the westernhemispheres brightest storage ring-generated multi-keV x-ray beams for research in almost all scientificdisciplines. The APS is a 7 GeV storage ring with 64 separate end stations where experiments are carriedout simultaneously, and a $500M upgrade of the facility has begun with support from the U.S. Departmentof Energy. Access to the APS is through no-cost competitive proposals, and APS beamline staff is able toallocate up to 20% of beamtime for their own research programs.

Argonne Leadership Computing Facility (ALCF), Argonne: We have access to a discretionary allo-cation and is also able to write user proposals for access to machines at ALCF, including Mira with 786,432compute cores and 768 Terabytes of RAM with a theoretical peak performance of 10,000 Teraflops. ALCFalso has smaller machines with the same architecture as Mira for program development and testing (Cetusand Vesta), and the Tukey visualization system with 1536 cores and 6 TB of RAM coupled with 192 TeslaM2070 GPUs with 1.1 TB of GPU RAM. Also ALCF has a cloud-computing system, Magellan, for on-

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VIKTOR NIKITIN RESEARCH PLAN 7(8)

demand computing with multiple 10s of teraflops and multiple petabytes of storage, as well as appropriatecloud software.

MAX IV laboratory, Lund: MAX IV is the next-generation synchrotron radiation facility which isunder construction now. The new laboratories, including two storage rings and a full-energy linac, havebeen built. The larger of the two storage rings operates at 3 GeV energy, and has been optimized for high-brightness X-rays. The smaller storage ring is operated at 1.5 GeV energy and has been optimized forultraviolet. The users have access to an HPC cluster located in the laboratory. The cluster has a 1 petabytesmemory storage and contains 8 nodes Intel Xeon E5-2650 with 64Gb RAM on each and 1 GPU node with 4Tesla K80.

10 Other grants

The current one-year postdoctoral position (October, 2016 - September, 2017) is funded by the CrafoordFoundation.

References

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[2] H. Andra, N. Combaret, J. Dvorkin, E. Glatt, J. Han, M. Kabel, Y. Keehm, F. Krzikalla, M. Lee, C. Madonna,et al. Digital rock physics benchmarkspart i: Imaging and segmentation. Computers & Geosciences, 50:25–32,2013.

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[7] M. J. Blunt, B. Bijeljic, H. Dong, O. Gharbi, S. Iglauer, P. Mostaghimi, A. Paluszny, and C. Pentland. Pore-scaleimaging and modelling. Advances in Water Resources, 51:197–216, 2013.

[8] V. Cnudde and M. N. Boone. High-resolution x-ray computed tomography in geosciences: A review of the currenttechnology and applications. Earth-Science Reviews, 123:1–17, 2013.

[9] T. De Kock, M. Boone, T. De Schryver, H. Derluyn, J. Van Stappen, D. Van Loo, B. Masschaele, and V. Cnudde.Freeze-thaw decay in sedimentary rocks: a laboratory study with ct under controlled ambient conditions. In 2ndInternational conference on Tomography of Materials and Structures (ICTMS 2015), pages 578–582, 2015.

[10] A. D. Duchkov, A. A. Duchkov, M. E. Permyakov, A. Y. Manakov, N. A. Golikov, and A. N. Drobchik. Labora-tory measurements of acoustic properties of gas-hydrate bearing sand samples (equipment, methods and results).Russian Geology and Geophysics, 58(1), 2017, in press.

[11] A. D. Duchkov, N. A. Golikov, A. A. Duchkov, A. Y. Manakov, M. E. Permyakov, and A. N. Drobchik. Equip-ment for the studies of the acoustic properties of hydrate-containing samples in laboratory conditions. SeismicInstruments, 52(1):70–78, 2015.

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[12] A. D. Duchkov, A. Y. Manakov, S. A. Kazantsev, M. E. Permyakov, and A. G. Ogienko. Thermal conductivitymeasurement of the synthetic samples of bottom sediments containing methane hydrates. Izvestiya, Physics ofthe Solid Earth, 45(8):661–669, 2009.

[13] I. I. Fadeeva, A. A. Duchkov, and M. E. Permyakov. Thermophysical method for quantitative estimation ofhydrate content in samples imitating bottom sediments. Russian Geology and Geophysics, 57(6):984–992, 2016.

[14] F. Fusseis, H. Steeb, X. Xiao, W.-l. Zhu, I. B. Butler, S. Elphick, and U. Mader. A low-cost x-ray-transparentexperimental cell for synchrotron-based x-ray microtomography studies under geological reservoir conditions.Journal of synchrotron radiation, 21(1):251–253, 2014.

[15] F. Fusseis, X. Xiao, C. Schrank, and F. D. Carlo. A brief guide to synchrotron radiation-based microtomographyin (structural) geology and rock mechanics. Journal of Structural Geology, 65:1 – 16, 2014.

[16] J. W. Gibbs, K. A. Mohan, E. B. Gulsoy, A. J. Shahani, X. Xiao, C. A. Bouman, M. De Graef, and P. W. Voorhees.The three-dimensional morphology of growing dendrites. Scientific Reports, 5:11824 EP –, Jul 2015. Article.

[17] N. Gubareni. Algebraic algorithms for image tomographic reconstruction from incomplete projection data. IN-TECH Open Access Publisher, 2009.

[18] D. Gursoy, F. De Carlo, X. Xiao, and C. Jacobsen. Tomopy: a framework for the analysis of synchrotron tomo-graphic data. Journal of synchrotron radiation, 21(5):1188–1193, 2014.

[19] D. Kazantsev, W. M. Thompson, W. R. Lionheart, G. Van Eyndhoven, A. P. Kaestner, K. J. Dobson, P. J. Withers,and P. D. Lee. 4d-ct reconstruction with unified spatial-temporal patch-based regularization. Inverse problemsand imaging., 9(2):447–467, 2015.

[20] A. M. Kiss, A. D. Jew, C. Joe-Wong, K. M. Maher, Y. Liu, G. E. Brown, and J. Bargar. Synchrotron-basedtransmission x-ray microscopy for improved extraction in shale during hydraulic fracturing. In SPIE OpticalEngineering+ Applications, pages 95920O–95920O. International Society for Optics and Photonics, 2015.

[21] Y. Konno, Y. Jin, J. Yoneda, T. Uchiumi, K. Shinjou, and J. Nagao. Hydraulic fracturing in methane-hydrate-bearing sand. RSC Advances, 6(77):73148–73155, 2016.

[22] T. Li, D. Fan, L. Lu, J. Huang, F. Zhao, M. Qi, T. Sun, K. Fezzaa, X. Xiao, X. Zhou, et al. Dynamic fracture ofc/sic composites under high strain-rate loading: microstructures and mechanisms. Carbon, 91:468–478, 2015.

[23] E. Maire, C. Le Bourlot, J. Adrien, A. Mortensen, and R. Mokso. 20 hz x-ray tomography during an in situ tensiletest. International Journal of Fracture, 200(1-2):3–12, 2016.

[24] R. Mokso, C. Schleputz, and M. Stampanoni. Gigafrost: High frame rate camera for data streaming. J. Syn-chrotron radiation, 1, 2017.

[25] F. Natterer. Computerized tomography. In The Mathematics of Computerized Tomography, pages 1–8. Springer,1986.

[26] T. Saif, Q. Lin, K. Singh, B. Bijeljic, and M. J. Blunt. Dynamic imaging of oil shale pyrolysis using synchrotronx-ray microtomography. Geophysical Research Letters, 43(13):6799–6807, 2016. 2016GL069279.

[27] W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers. The astratoolbox: A platform for advanced algorithm development in electron tomography. Ultramicroscopy, 157:35–47,2015.

[28] G. Van Eyndhoven, K. J. Batenburg, D. Kazantsev, V. Van Nieuwenhove, P. D. Lee, K. J. Dobson, and J. Sijbers.An iterative ct reconstruction algorithm for fast fluid flow imaging. IEEE Transactions on Image Processing,24(11):4446–4458, 2015.

[29] W. F. Waite, J. C. Santamarina, D. D. Cortes, B. Dugan, D. Espinoza, J. Germaine, J. Jang, J. Jung, T. J. Kneafsey,H. Shin, et al. Physical properties of hydrate-bearing sediments. Reviews of geophysics, 47(4), 2009.

[30] M. Wang, L. Lu, C. Li, X. Xiao, X. Zhou, J. Zhu, and S. Luo. Deformation and spallation of a magnesium alloyunder high strain rate loading. Materials Science and Engineering: A, 661:126–131, 2016.

[31] S. Youssef, H. Deschamps, J. Dautriat, E. Rosenberg, R. Oughanem, E. Maire, and Mokso R. 4D imaging of fluidflow dynamics in natural porous media by ultrafast x-ray microtomography . SCA Proceedings, 12, 2013.

[32] J. Zhao, L. Yang, Y. Liu, and Y. Song. Microstructural characteristics of natural gas hydrates hosted in varioussand sediments. Physical Chemistry Chemical Physics, 17(35):22632–22641, 2015.

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Budget and research resources

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Publications (PDF)Publications (pdf)*

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VIKTOR NIKITIN PUBLICATIONS 1(2)

Peer-reviewed articles[1] Viktor V. Nikitin, Anton A. Duchkov, and Fredrik Andersson. “Parallel algorithm of 3D wave-packet

decomposition of seismic data: implementation and optimization for GPU”. Journal of ComputationalScience 3.6 (2012), pp. 469–473.

[2] Viktor V. Nikitin, Alexey A. Romanenko, Anton A. Duchkov, and Fredrik Andersson. “Parallel im-plementation of 3D-wave package decomposition on GPU and its application in geophysics”. Vestnikof NSU. IT series 11.1 (2013), pp. 93–104.

[3] * Fredrik Andersson, Marcus Carlsson, and Viktor V. Nikitin. “Fast algorithms and efficient GPUimplementation for the Radon transform and the back-projection operator represented as convolutionoperators”. SIAM Journal on Imaging Sciences. 9.2 (2016), pp. 637–664.

[4] Sergey V. Nikitin, Viktor V. Nikitin, Ivan I. Oleynik, Irina V. Oleynik, and Elena G. Bagryanskaya.“Activity of phenoxy-imine titanium catalysts in ethylene polymerization: A quantum chemical ap-proach”. Journal of Molecular Catalysis A: Chemical 423 (2016), pp. 285–292.

[5] * Fredrik Andersson, Marcus Carlsson, and Viktor V. Nikitin. “Fast Laplace transforms for the expo-nential Radon transform”. Accepted. Journal of Fourier Analysis and Applications (2017).

[6] Fredrik Andersson, Adriana Citlali Ramırez Perez, Torgeir Wiik, and Viktor V. Nikitin. “Directionalinterpolation of multicomponent data”. Geophysical Prospecting (2017).

[7] * Viktor V. Nikitin, Fredrik Andersson, Marcus Carlsson, and Anton A. Duchkov. “Fast hyperbolicRadon transform represented as convolutions in log-polar coordinates”. Accepted. Computers & Geo-sciences journal (2017).

Peer-reviewed conference contributions[1] Viktor V. Nikitin, Alexey A. Romanenko, Anton A. Duchkov, and Fredrik Andersson. “3D Wave-

packet decomposition implemented on GPUs”. Expanded abstracts of SEG Annual Meeting. San An-tonio, 2011, pp. 3409–3413.

[2] Fredrik Andersson and Viktor V. Nikitin. “Fast inversion of the exponential Radon transform byusing fast Laplace transforms”. Proceedings of the Project Review, Geo-Mathematical Imaging Group.Vol. 1. West Lafayette IN, Purdue University, 2013, pp. 65–73.

[3] * Viktor V. Nikitin, Fredrik Andersson, Marcus Carlsson, and Anton A. Duchkov. “Fast hyperbolicradon transform by log-polar convolutions”. SEG Technical Program Expanded Abstracts 2016. Soci-ety of Exploration Geophysicists, 2016, pp. 4534–4539.

Popular science publications including books/presentations[1] Viktor V. Nikitin. “Using GPUs for wave-packet decomposition”. Vol. 1. Belgorod: BSU, 2011,

pp. 544–554.

[2] Viktor V. Nikitin, Alexey A. Romanenko, Anton A. Duchkov, and Fredrik Andersson. “De-noisingand compression seismic data using wave-packet decomposition”. Proceedings of the Conference forYoung Scientists: Trofimuk Readings. Novosibirsk: IPGG SB RAS, 2011.

[3] Viktor V. Nikitin, Alexey A. Romanenko, Anton A. Duchkov, and Fredrik Andersson. “Seismic datadecomposition into wave packets - implementation on GPU”. Proceedings of the Geophysical Confer-ence in Memory of S.V. Goldin (75th anniversary). Novosibirsk: IPGG SB RAS, 2011, p. 57.

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VIKTOR NIKITIN PUBLICATIONS 2(2)

[4] Viktor V. Nikitin. “Parallel algorithm of 3D wave-packet decomposition of seismic data: implemen-tation and optimization for GPU”. Abstracts of Internatioanl Young Scientific Conference: High Per-formance Computing and Simulation. Amsterdam: Science Park, 2012, p. 72.

[5] Viktor V. Nikitin. “Using GPUs for wave-packet decomposition”. Abstracts of the XLIX InternationalScientific Student Conference: IT section. Novosibirsk: NSU, 2012, p. 112.

[6] Viktor V. Nikitin. “Using hybrid systems for seismic data processing with wave-packet decomposi-tion”. Abstracts of the L International Scientific Student Conference: IT section. Novosibirsk: NSU,2012, p. 115.

[7] Viktor V. Nikitin, Anton A. Duchkov, and Fredrik Andersson. “Regularization of seismic data usingdecomposition with Gaussian wave packets”. Abstracts of IV International Young Scientific Confer-ence - Theory and numerical methods for solving inverse problems. Novosibirsk: IPGG SB RAS,2012, p. 89.

[8] Viktor V. Nikitin, Alexey A. Romanenko, and Anton A. Duchkov. “Parallel algorithm of seismicdata decomposition: implementation and optimization for GPU”. Proceedings of the InternationalScientific Conference - Parallel Computing Technologies. Novosibirsk: ICM and MG SB RAS, 2012,p. 734.

[9] Viktor V. Nikitin. “Fast algorithm of 3D function representation (on GPU and CPU) and its applica-tion in seismic data processing”. Proceedings of the IV International Conference - High performancecomputing technologies in the oil and gas industry. Moscow: MSU, 2013.

[10] Viktor V. Nikitin, Marcus Carlsson, and Fredrik Andersson. “The exponential Radon transform by us-ing unequally spaced fast Laplace transforms”. Abstracts of the VII International conference - Inverseproblems: modeling and simulation. Fethiye, Turkey, 2014, p. 149.

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AttachmentsLetter of invitation from the administrating organisation*

See following page for attachment

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Letter of invitation from the host institution abroad*

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A U.S. Department of Energy laboratory managed by UChicago Argonne, LLC

Stephen Streiffer, Ph.D. Associate Laboratory Director Director, Advanced Photon Source Photon Sciences Argonne National Laboratory 9700 South Cass Avenue, Bldg. 401 Argonne, IL 60439 1-630-252-7990 phone aps-director@aps.anl.gov

February 19, 2017

SUBJECT: Endorsement letter for Dr. Viktor Nikitin for VR International Postdoc Program To whom it may concern, The research proposal of Dr. Nikitin on “enabling scientific exploration of the dynamics of matter through real time visualization of the changes in the microstructure”, fits perfectly within the scope of Department of Energy’s Office of Science funded programs at the Argonne National Laboratory. Argonne National Laboratory offers a unique place that combines a world leading 7 GeV synchrotron facility located next to a leadership-scale computer. Dr. Nikitin’s proposal leverages these strengths of Argonne in synchrotron-based imaging and scientific computing to build the essential computational capabilities and their integration with x-ray instruments, to digest and interpret the massive data volumes collected at the Advanced Photon Source (APS) such that experiments can be autonomously steered in real-time based on evolving experimental outcomes. This would greatly enhance the ability of the APS to support users in efficiently obtaining scientific results, rather than obtaining data that must be analyzed post-facto and that may have been collected in sub-optimal conditions. The APS is currently developing an upgrade project that will establish the first high-energy ultrabright synchrotron facility in the United States, based on multiband achromat technology as pioneered at MAX IV. Dr. Nikitin, as a member of the imaging group at the newly build Swedish synchrotron facility MAX IV, will also contribute to strengthening and extending the existing collaboration between the APS and MAX IV to address the many new scientific challenges ahead. Therefore I strongly endorse his proposed activity, and welcome him to conduct the proposed research at APS. Sincerely,

Stephen Streiffer

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Description and motivation*

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VIKTOR NIKITIN DESCRIPTION AND JUSTIFICATION 1(1)

Streaming Images of Geomaterials

The choice of the X-ray Imaging Group at the APS led by Prof. Francesco De Carlo is justified by severalfactors. First, I would like to extend my knowledge of mathematical methods in tomography by becominga member of this group. The group has a great experience in these methods since it has been working onimaging and reconstruction techniques more than 10 years with regular publishing of research results.

Second, I am interested in extending my knowledge of the package tomoPy developed in this group byDoga Gursoy. TomoPy is a collaborative Python/C++ based framework for the analysis of synchrotron to-mographic data. It includes direct Fourier and nonlinear reconstruction methods for incomplete tomographicdataset. With clear understanding functionality and features of tomoPy we could improve the Tomographicreconstruction platform at Max IV laboratory.

Finally, I would like to obtain an experience in the process of synchrotron data measuring. The groupcurrently operates two beamlines, 2-BM and 32-ID, at the APS. Beamline 2-BM is optimized for fast micro-tomography and radiography. Beamline 32-ID provides various full field imaging techniques, includingHigh-Speed Imaging, Real Time Radiography, Transmission X-ray Microscopy. The case of high-speedtime-resolved measurements is directly related to my research goals.

The geophysical laboratory at IPGG SB RAS led by Prof. Anton Duchkov was chosen because of itsvast experience in the techniques for laboratory measurements of gas-hydrate bearing sediments. At themoment the group is working on a development a new laboratory setup with improved acoustic system forstudying acoustic properties and acoustic emission of gas-hydrate bearing sediments and rock samples. Thisis of particular interest in my research to consider the application of the real-time synchrotron imaging inthe dynamic process of gas-hydrate formation and dissociation in geomaterials. Becoming a member ofthis group I would like to learn mathematical and geophysical description of acoustic methods for analysisof geological samples. It is important to get a deeper understanding of technical and algorithmical aspectsacoustic measurements and 4D tomography.

Another reason for choosing this geophysical group is that it produces real geological samples and hasaccess to professional petrophysical equipment. Moreover, the group actively collaborates with the companyGeologika which produces geological equipment of different type. In this sense, I would like to obtain anexperience in the measuring process by getting involved into the laboratory experiments for better under-standing methodology of gas-hydrate formation in geomaterials and their acoustic properties. I will alsoparticipate in the planning and a new design of the gas-hydrate chamber so that it can be installed and oper-ated at MAX IV facilities. For that case, my experience in data processing methods such as artifact reduction,interpolation and denoising will help to improve the new acoustic system suited for time-resolved imaging.

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Name: Viktor Niki tinBirthdate: 19900517Gender: MaleCountry:Sweden

Doctorial degree: 2016-08-19Academic title: DoktorEmployer: Lunds univers i tet

CVCV - Viktor Nikitin

Doctors degree

Examination Organisation Dissertation title (original language) Supervisor

10105. ComputationalMathematics, 2016-08-19

Lund University,Matematikcentrum107150

Fast Radon transforms andreconstruction techniques inseismology

Fredrik Andersson

Educational history

Research education

Examination Organisation Dissertation title (en)

PhD degree, 10105. ComputationalMathematics, 2016-08-19

Lund University,Matematikcentrum 107150

Fast Radon transforms and reconstruction techniques inseismology

Basic education

Year Examination

2012 10205. Software Engineering, Degree of Master, Novosibirsk State University

2011 10205. Software Engineering, Degree of Bachelor, Novosibirsk State University

Professional history

Employments

Period Position Part of research in

employment

Employer Other information

oktober 2016 - september2017 (Present)

Postdoctoral fellow,Temporary position

100 Lund University, Max IVLab

a member of the Imaging groupled by Dr. Rajmund Mokso

Post doctoral assignments

Period Organisation Subject

oktober 2016 - september 2017 Lund University, Max IV Lab 10205. Software Engineering

Research exchange assignments

Period Type Organisation Subject

juni 2017 - juli 2017 Guest researcher Argonne National Laboratory 10105. Computational Mathematics

november 2016 - november 2016 Guest researcher Paul Scherrer Institute 20205. Signal Processing

oktober 2016 - oktober 2016 Guest researcher Technical University ofDenmark

10105. Computational Mathematics

Merits and awards

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Name: Viktor Niki tinBirthdate: 19900517Gender: MaleCountry:Sweden

Doctorial degree: 2016-08-19Academic title: DoktorEmployer: Lunds univers i tet

Awards and distinctions

Year Name of award/distinction Issuer

2012 Finalist of the selection competitionfor the Young Scientists Conference”High-Performance Computing andSimulation”

University of Amsterdam

2011 Winner of the research projectcompetition ”Effective use of GPUs forsolving computationally intensiveproblems”

T-platforms and Moscow State University

PublicationsPublications - Viktor Nikitin

Publications are disabled for Nikitin, Viktor on this application.

RegisterTerms and conditions

The application must be signed by the applicant as well as the official representative of the administratingorganisation. This representative is normally the head of the department where the research will beconducted, but that will depend on the organisational structure of the administrating organisation.

The signature of the applicant confirms that:

The information contained in the appl ication is correct and in l ine with the instructions from the SwedishResearch Counci l .Any s ide-l ine occupation and/or commercial ties have been reported to the administrating organisation,and that no confl ict with the principles of good research practice has been establ ished.

The necessary permits and approvals are in place at the start of the project, e.g. concerning the ethicalreview.

The signature of the administrating organisation confirms that:

The organisation wi l l accommodate the research and the equipment, and employ the appl icant during thetime period and to the extent presented in the appl ication.The organisation approves the cost estimate presented in the appl ication.

The project wi l l be conducted in accordance with Swedish law.

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The parties must have discussed the above-mentioned points before the representative of the administratingorganisation approves and signs the application.

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