| 1. |
- Aquila, Andrew, et al.
(författare)
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Time-resolved protein nanocrystallography using an X-ray free-electron laser
- 2012
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Ingår i: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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| 2. |
- Bujack, Roxana, et al.
(författare)
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State of the Art in Time-Dependent Flow Topology: Interpreting Physical Meaningfulness Through Mathematical Properties
- 2020
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Ingår i: Computer graphics forum (Print). - : WILEY. - 0167-7055 .- 1467-8659. ; 39:3, s. 811-835
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Tidskriftsartikel (refereegranskat)abstract
- We present a state-of-the-art report on time-dependent flow topology. We survey representative papers in visualization and provide a taxonomy of existing approaches that generalize flow topology from time-independent to time-dependent settings. The approaches are classified based upon four categories: tracking of steady topology, reference frame adaption, pathline classification or clustering, and generalization of critical points. Our unique contributions include introducing a set of desirable mathematical properties to interpret physical meaningfulness for time-dependent flow visualization, inferring mathematical properties associated with selective research papers, and utilizing such properties for classification. The five most important properties identified in the existing literature include coincidence with the steady case, induction of a partition within the domain, Lagrangian invariance, objectivity, and Galilean invariance.
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| 3. |
- Chapman, Henry N, et al.
(författare)
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Femtosecond X-ray protein nanocrystallography.
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
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Tidskriftsartikel (refereegranskat)abstract
- X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200nm to 2μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
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| 4. |
- Gorkhover, Tais, et al.
(författare)
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Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
- 2018
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Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 12:3, s. 150-153
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast X-ray imaging on individual fragile specimens such as aerosols 1 , metastable particles 2 , superfluid quantum systems 3 and live biospecimens 4 provides high-resolution information that is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely defined 4,5 . Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lateral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond timescale.
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| 5. |
- Koopmann, Rudolf, et al.
(författare)
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In vivo protein crystallization opens new routes in structural biology
- 2012
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 9:3, s. 259-262
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Tidskriftsartikel (refereegranskat)abstract
- Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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| 6. |
- Lukasczyk, Jonas, et al.
(författare)
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Cinema Darkroom : A Deferred Rendering Framework for Large-Scale Datasets
- 2020
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Ingår i: 2020 IEEE 10TH SYMPOSIUM ON LARGE DATA ANALYSIS AND VISUALIZATION (LDAV). - : IEEE. - 9781728184685 ; , s. 37-41
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Konferensbidrag (refereegranskat)abstract
- This paper presents a framework that fully leverages the advantages of a deferred rendering approach for the interactive visualization of large-scale datasets. Geometry buffers (G-Buffers) are generated and stored in situ, and shading is performed post hoc in an interactive image-based rendering front end. This decoupled framework has two major advantages. First, the G-Buffers only need to be computed and stored once-which corresponds to the most expensive part of the rendering pipeline. Second, the stored G-Buffers can later be consumed in an image-based rendering front end that enables users to interactively adjust various visualization parameters-such as the applied color map or the strength of ambient occlusion-where suitable choices are often not known a priori. This paper demonstrates the use of Cinema Darkroom on several real-world datasets, highlighting CDs ability to effectively decouple the complexity and size of the dataset from its visualization.
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| 7. |
- Lundholm, Ida V., et al.
(författare)
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Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
- 2018
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Ingår i: IUCrJ. - : International Union of Crystallography. - 2052-2525. ; 5, s. 531-541
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Tidskriftsartikel (refereegranskat)abstract
- Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
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| 8. |
- Masood, Talha Bin, et al.
(författare)
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An Overview of the Topology ToolKit
- 2021
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Ingår i: Topological Methods in Data Analysis and Visualization VI. - Cham : Springer. - 9783030835002 - 9783030834999 ; , s. 327-342
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Bokkapitel (refereegranskat)abstract
- This software paper gives an overview of the features supported by the Topology ToolKitTopology ToolKit (TTK), which is an  Open-sourceopen-source library for  Topological data analysistopological data analysis (TDA). TTK implements, in a generic and efficient way, a substantial collection of reference algorithms in TDA. Since its initial public release in 2017, both its user and developer bases have grown, resulting in a significant increase in the number of supported features. In contrast to the original paper introducing TTK [40] (which detailed the core algorithms and data structures of TTK), the purpose of this Softwaresoftware paper is to describe the list of features currently supported by TTK, ranging from image segmentation tools to advanced topological analysis of high-dimensional data, with concrete usage examples available on the TTK website [42].
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| 9. |
- Nilsson, Emma, et al.
(författare)
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Exploring Cyclone Evolution with Hierarchical Features
- 2022
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Ingår i: 2022 IEEE WORKSHOP ON TOPOLOGICAL DATA ANALYSIS AND VISUALIZATION (TOPOINVIS 2022). - : IEEE. - 9781665493543 - 9781665493550 ; , s. 92-102
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Konferensbidrag (refereegranskat)abstract
- The problem of tracking and visualizing cyclones is still an active area of climate research, since the nature of cyclones varies depending on geospatial location and temporal season, resulting in no clear mathematical definition. Thus, many cyclone tracking methods are tailored to specific datasets and therefore do not support general cyclone extraction across the globe. To address this challenge, we present a conceptual application for exploring cyclone evolution by organizing the extracted cyclone tracks into hierarchical groups. Our approach is based on extrema tracking, and the resulting tracks can be defined in a multi-scale structure by grouping the points based on a novel feature descriptor defined on the merge tree, so-called crown features. Consequently, multiple parameter settings can be visualized and explored in a level-of-detail approach, supporting experts to quickly gain insights on cyclonic formation and evolution. We describe a general cyclone exploration pipeline that consists of four modular building blocks: (1) an extrema tracking method, (2) multiple definitions of cyclones as groups of extrema, including crown features, (3) the correlation of cyclones based on the underlying tracking information, and (4) a hierarchical visualization of the resulting feature tracks and their spatial embedding, allowing exploration on a global and local scale. In order to be as flexible as possible, our pipeline allows for exchanging every module with different techniques, such as other tracking methods and cyclone definitions.
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| 10. |
- Nilsson, Emma, et al.
(författare)
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Towards Benchmark Data Generation for Feature Tracking in Scalar Fields
- 2022
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Ingår i: 2022 IEEE WORKSHOP ON TOPOLOGICAL DATA ANALYSIS AND VISUALIZATION (TOPOINVIS 2022). - : IEEE. - 9781665493543 - 9781665493550 ; , s. 103-112
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Konferensbidrag (refereegranskat)abstract
- We describe a benchmark data generator for tracking methods for two- and three-dimensional time-dependent scalar fields. More and more topology-based tracking methods are presented in the visualization community, but the validation and evaluation of the tracking results are currently limited to qualitative visual approaches. We present a pipeline for creating different ground truth features that support evaluating tracking methods based on quantitative measures. In short, our approach randomly simulates a temporal point cloud with birth, death, split, merge, and continuation events, where the points are then used to derive a scalar field whose topological features correspond to the points. These scalar fields can be used as the input for different tracking methods, where the computed tracks can be compared against the ground truth feature evolution. This approach facilitates directly comparing the results of different tracking methods, independent of the initial feature characterization.
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