The HARE chip for efficient time-resolved serial synchrotron crystallography

Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.

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The use of time resolved aerosol assisted chemical vapour deposition in mapping metal oxide thin film growth and fine tuning functional properties

Journal of Materials Chemistry A ◽

10.1039/c4ta05922k ◽

2015 ◽

Vol 3 (9) ◽

pp. 4811-4819 ◽

Cited By ~ 5

Author(s):

Nicholas P. Chadwick ◽

Sanjayan Sathasivam ◽

Salem M. Bawaked ◽

Mohamed Mokhtar ◽

Shaeel A. Althabaiti ◽

...

Keyword(s):

Thin Film ◽

Film Growth ◽

Chemical Vapour ◽

Thin Film Growth ◽

Fine Tuning ◽

Oxide Thin Film ◽

Time Resolved ◽

Use Of Time ◽

Metal Oxide Thin Film ◽

Changes Over Time

Time resolved analysis of a thin film has allowed, for the first time, analysis of how thin film growth occurs and changes over time by aerosol assisted CVD.

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Precise Cache Profiling for Studying Radiation Effects

ACM Transactions on Embedded Computing Systems ◽

10.1145/3442339 ◽

2021 ◽

Vol 20 (3) ◽

pp. 1-25

Author(s):

James Marshall ◽

Robert Gifford ◽

Gedare Bloom ◽

Gabriel Parmer ◽

Rahul Simha

Keyword(s):

Radiation Effects ◽

Fault Injection ◽

Error Correcting Codes ◽

Direct Access ◽

Transient Faults ◽

Large Area ◽

Common Multiple ◽

Single Event Upsets ◽

On Chip ◽

Future Work

Increased access to space has led to an increase in the usage of commodity processors in radiation environments. These processors are vulnerable to transient faults such as single event upsets that may cause bit-flips in processor components. Caches in particular are vulnerable due to their relatively large area, yet are often omitted from fault injection testing because many processors do not provide direct access to cache contents and they are often not fully modeled by simulators. The performance benefits of caches make disabling them undesirable, and the presence of error correcting codes is insufficient to correct for increasingly common multiple bit upsets. This work explores building a program’s cache profile by collecting cache usage information at an instruction granularity via commonly available on-chip debugging interfaces. The profile provides a tighter bound than cache utilization for cache vulnerability estimates (50% for several benchmarks). This can be applied to reduce the number of fault injections required to characterize behavior by at least two-thirds for the benchmarks we examine. The profile enables future work in hardware fault injection for caches that avoids the biases of existing techniques.

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Determination of Carbon Content in Steel Using Laser-Induced Breakdown Spectroscopy

Applied Spectroscopy ◽

10.1366/0003702924123692 ◽

1992 ◽

Vol 46 (9) ◽

pp. 1382-1387 ◽

Cited By ~ 73

Author(s):

J. A. Aguilera ◽

C. Aragón ◽

J. Campos

Keyword(s):

Carbon Content ◽

Matrix Effects ◽

Sample Surface ◽

Nitrogen Atmosphere ◽

Laser Induced Breakdown Spectroscopy ◽

Time Resolved ◽

Breakdown Spectroscopy ◽

Use Of Time ◽

Laser Induced Breakdown

Laser-induced breakdown spectroscopy has been used to determine carbon content in steel. The plasma was formed by focusing a Nd:YAG laser on the sample surface. With the use of time-resolved spectroscopy and generation of the plasma in nitrogen atmosphere, a precision of 1.6% and a detection limit of 65 ppm have been obtained. These values are similar to those of other accurate conventional techniques. Matrix effects for the studied steels are reduced to a small slope difference between the calibration curves for stainless and nonstainless steels.

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The biochemical resolving power of fluorescence lifetime imaging

10.1101/2021.02.03.429635 ◽

2021 ◽

Author(s):

Andrew L. Trinh ◽

Alessandro Esposito

Keyword(s):

Fluorescence Lifetime ◽

Resolving Power ◽

Fluorescence Lifetime Imaging ◽

Time Resolved ◽

Instrument Response Function ◽

Lifetime Imaging ◽

Use Of Time ◽

Single Living Cells ◽

Microscopy Techniques

AbstractA deeper understanding of spatial resolution in microscopy fostered a technological revolution that is now permitting us to investigate the structure of the cell with nanometer resolution. Although fluorescence microscopy techniques enable scientists to investigate both the structure and biochemistry of the cell, the biochemical resolving power of a microscope is a physical quantity that is not well-defined or studied. To overcome this limitation, we carried out a theoretical investigation of the biochemical resolving power in fluorescence lifetime imaging microscopy, one of the most effective tools to investigate biochemistry in single living cells. With the theoretical analysis of information theory and Monte Carlo simulations, we describe how the ‘biochemical resolving power’ in time-resolved sensing depends on instrument specifications. We unravel common misunderstandings on the role of the instrument response function and provide theoretical insights that have significant practical implications in the design and use of time-resolved instrumentation.

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The use of time-resolved fluorescence for diagnosis of atherosclerotic plaque and malignant tumours

Spectrochimica Acta Part A Molecular Spectroscopy ◽

10.1016/0584-8539(90)80196-6 ◽

1990 ◽

Vol 46 (8) ◽

pp. 1203-1210 ◽

Cited By ~ 31

Author(s):

S. Andersson-Engels ◽

J. Johansson ◽

S. Svanberg

Keyword(s):

Atherosclerotic Plaque ◽

Malignant Tumours ◽

Time Resolved Fluorescence ◽

Time Resolved ◽

Use Of Time

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Learning the non-equilibrium dynamics of Brownian movies

Nature Communications ◽

10.1038/s41467-020-18796-9 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Federico S. Gnesotto ◽

Grzegorz Gradziuk ◽

Pierre Ronceray ◽

Chase P. Broedersz

Keyword(s):

Degrees Of Freedom ◽

Time Lapse ◽

Direct Access ◽

Dynamical Analysis ◽

Entropy Production Rate ◽

Microscopy Imaging ◽

Time Resolved ◽

Equilibrium Dynamics ◽

Many Body Systems ◽

Non Equilibrium

Abstract Time-lapse microscopy imaging provides direct access to the dynamics of soft and living systems. At mesoscopic scales, such microscopy experiments reveal intrinsic thermal and non-equilibrium fluctuations. These fluctuations, together with measurement noise, pose a challenge for the dynamical analysis of these Brownian movies. Traditionally, methods to analyze such experimental data rely on tracking embedded or endogenous probes. However, it is in general unclear, especially in complex many-body systems, which degrees of freedom are the most informative about their non-equilibrium nature. Here, we introduce an alternative, tracking-free approach that overcomes these difficulties via an unsupervised analysis of the Brownian movie. We develop a dimensional reduction scheme selecting a basis of modes based on dissipation. Subsequently, we learn the non-equilibrium dynamics, thereby estimating the entropy production rate and time-resolved force maps. After benchmarking our method against a minimal model, we illustrate its broader applicability with an example inspired by active biopolymer gels.

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