Dynamics of intermediate filament assembly followed in micro-flow by small angle X-ray scattering

Micro- and milli-fluidic sample environments for in situ X-ray analysis in the chemical and materials sciences

X-ray-based methods are powerful tools for structural and chemical studies of materials and processes, particularly for performing time-resolved measurements. In this critical review, we highlight progress in the development of X-ray compatible microfluidic and millifluidic platforms that enable high temporal and spatial resolution X-ray analysis across the chemical and materials sciences. With a focus on liquid samples and suspensions, we first present the origins of microfluidic sample environments for X-ray analysis by discussing some alternative liquid sample holder and manipulator technologies. The bulk of the review is then dedicated to micro- and milli-fluidic devices designed for use in the three main areas of X-ray analysis: (1) scattering/diffraction, (2) spectroscopy, and (3) imaging. While most research to date has been performed at synchrotron radiation facilities, the recent progress made using commercial and laboratory-based X-ray instruments is then reviewed here for the first time. This final section presents the exciting possibility of performing in situ and operando X-ray analysis in the 'home' laboratory and transforming microfluidic and millifluidic X-ray analysis into a routine method in physical chemistry and materials research.

Penetration Coefficients of Commercial Nanolimes and a Liquid Mineral Precursor for Pore-Imitating Test Systems-Predictability of Infiltration Behavior

Nanolimes have been commercially available for over a decade as a remineralization agent for natural stone to combat deterioration. While they have been applied successfully and studied extensively, their penetration abilities in different materials have not yet been readily quantifiable in situ and in real time. Using two transparent pore-imitating test systems (acrylic glass (PMMA) and polydimethylsiloxane (PDMS)) and light microscopy, the penetration coefficients (PCs) of two nanolimes (CaLoSiL (CLS) and Nanorestore Plus (NRP)), as well as their solvents, were determined experimentally in square channels of about 100 µm diameter. Their PCs and those for a previously published glass-resin-based test system were also predicted based on measurable material parameters or literature values using the Lucas-Washburn equation. Additionally, a liquid mineral precursor (LMP) of calcium carbonate based on complex coacervation (CC) was investigated as an alternative to the solid particle dispersions of nanolime. In general, the dispersions behaved like their pure solvents. Overall, trends could be reasonably well predicted with both literature and experimentally determined properties using the Lucas-Washburn equation. In absolute terms, the prediction of observed infiltration behavior was satisfactory for alcohols and nanolimes but deviated substantially for water and the aqueous LMP. The commercially available PMMA chips and newly designed PDMS devices were mostly superior to the previously published glass-resin-based test system, except for the long-term monitoring of material deposition. Lastly, the transfer of results from these investigated systems to a different, nontransparent mineral, calcite, yielded similar PC values independently of the original data when used as the basis for the conversion (all PC types and all material/liquid combinations except aqueous solutions in PDMS devices). This knowledge can be used to improve the targeted design of tailor-made remineralization treatments for different application cases by guiding solvent choice, and to reduce destructive sampling by providing a micromodel for pretesting, if transferability to real stone samples proves demonstrable in the future.

Microfluidic Nanomaterial Synthesis and In Situ SAXS, WAXS, or SANS Characterization: Manipulation of Size Characteristics and Online Elucidation of Dynamic Structural Transitions

With the ability to cross biological barriers, encapsulate and efficiently deliver drugs and nucleic acid therapeutics, and protect the loaded cargos from degradation, different soft polymer and lipid nanoparticles (including liposomes, cubosomes, and hexosomes) have received considerable interest in the last three decades as versatile platforms for drug delivery applications and for the design of vaccines. Hard nanocrystals (including gold nanoparticles and quantum dots) are also attractive for use in various biomedical applications. Here, microfluidics provides unique opportunities for the continuous synthesis of these hard and soft nanomaterials with controllable shapes and sizes, and their in situ characterization through manipulation of the flow conditions and coupling to synchrotron small-angle X-ray (SAXS), wide-angle scattering (WAXS), or neutron (SANS) scattering techniques, respectively. Two-dimensional (2D) and three-dimensional (3D) microfluidic devices are attractive not only for the continuous production of monodispersed nanomaterials, but also for improving our understanding of the involved nucleation and growth mechanisms during the formation of hard nanocrystals under confined geometry conditions. They allow further gaining insight into the involved dynamic structural transitions, mechanisms, and kinetics during the generation of self-assembled nanostructures (including drug nanocarriers) at different reaction times (ranging from fractions of seconds to minutes). This review provides an overview of recently developed 2D and 3D microfluidic platforms for the continuous production of nanomaterials, and their simultaneous use in in situ characterization investigations through coupling to nanostructural characterization techniques (e.g., SAXS, WAXS, and SANS).

Development of a sticker sealed microfluidic device for in situ analytical measurements using synchrotron radiation

Shedding synchrotron light on microfluidic systems, exploring several contrasts in situ/operando at the nanoscale, like X-ray fluorescence, diffraction, luminescence, and absorption, has the potential to reveal new properties and functionalities of materials across diverse areas, such as green energy, photonics, and nanomedicine. In this work, we present the micro-fabrication and characterization of a multifunctional polyester/glass sealed microfluidic device well-suited to combine with analytical X-ray techniques. The device consists of smooth microchannels patterned on glass, where three gold electrodes are deposited into the channels to serve in situ electrochemistry analysis or standard electrical measurements. It has been efficiently sealed through an ultraviolet-sensitive sticker-like layer based on a polyester film, and The burst pressure determined by pumping water through the microchannel(up to 0.22 MPa). Overall, the device has demonstrated exquisite chemical resistance to organic solvents, and its efficiency in the presence of biological samples (proteins) is remarkable. The device potentialities, and its high transparency to X-rays, have been demonstrated by taking advantage of the X-ray nanoprobe Carnaúba/Sirius/LNLS, by obtaining 2D X-ray nanofluorescence maps on the microchannel filled with water and after an electrochemical nucleation reaction. To wrap up, the microfluidic device characterized here has the potential to be employed in standard laboratory experiments as well as in in situ and in vivo analytical experiments using a wide electromagnetic window, from infrared to X-rays, which could serve experiments in many branches of science.

An innovative data processing method for studying nanoparticle formation in droplet microfluidics using X-rays scattering

X-ray scattering techniques provide a powerful means of characterizing the formation of nanoparticles in solution. Coupling these techniques to segmented-flow microfluidic devices that offer well-defined environments gives access to in situ time-resolved analysis, excellent reproducibility, and eliminates potential radiation damage. However, analysis of the resulting datasets can be extremely time-consuming, where these comprise frames corresponding to the droplets alone, the continuous phase alone, and to both at their interface. We here describe a robust, low-cost, and versatile droplet microfluidics device and use it to study the formation of magnetite nanoparticles with simultaneous synchrotron SAXS and WAXS. Lateral outlet capillaries facilitate the X-ray analysis and reaction times of between a few seconds and minutes can be accommodated. A two-step data processing method is then described that exploits the unique WAXS signatures of the droplets, continuous phase, and interfacial region to identify the frames corresponding to the droplets. These are then sorted, and the background scattering is subtracted using an automated frame-by-frame approach, allowing the signal from the nanoparticles to be isolated from the raw data. Modeling these data gives quantitative information about the evolution of the sizes and structures of the nanoparticles, in agreement with TEM observations. This versatile platform can be readily employed to study a wide range of dynamic processes in heterogeneous systems.

Millisecond timescale reactions observed via X-ray spectroscopy in a 3D microfabricated fused silica mixer

Determination of electronic structures during chemical reactions remains challenging in studies which involve reactions in the millisecond timescale, toxic chemicals, and/or anaerobic conditions. In this study, a three-dimensionally (3D) microfabricated microfluidic mixer platform that is compatible with time-resolved X-ray absorption and emission spectroscopy (XAS and XES, respectively) is presented. This platform, to initiate reactions and study their progression, mixes a high flow rate (0.50-1.5 ml min^-1) sheath stream with a low-flow-rate (5-90 µl min^-1) sample stream within a monolithic fused silica chip. The chip geometry enables hydrodynamic focusing of the sample stream in 3D and sample widths as small as 5 µm. The chip is also connected to a polyimide capillary downstream to enable sample stream deceleration, expansion, and X-ray detection. In this capillary, sample widths of 50 µm are demonstrated. Further, convection-diffusion-reaction models of the mixer are presented. The models are experimentally validated using confocal epifluorescence microscopy and XAS/XES measurements of a ferricyanide and ascorbic acid reaction. The models additionally enable prediction of the residence time and residence time uncertainty of reactive species as well as mixing times. Residence times (from initiation of mixing to the point of X-ray detection) during sample stream expansion as small as 2.1 ± 0.3 ms are also demonstrated. Importantly, an exploration of the mixer operational space reveals a theoretical minimum mixing time of 0.91 ms. The proposed platform is applicable to the determination of the electronic structure of conventionally inaccessible reaction intermediates.

Exploring early time points of vimentin assembly in flow by fluorescence fluctuation spectroscopy

Despite the importance for cellular processes, the dynamics of molecular assembly, especially on fast time scales, is not yet fully understood. To this end, we present a multi-layer microfluidic device and combine it with fluorescence fluctuation spectroscopy. We apply this innovative combination of methods to investigate the early steps in assembly of vimentin intermediate filaments (IFs). These filaments, together with actin filaments and microtubules, constitute the cytoskeleton of cells of mesenchymal origin and greatly influence their mechanical properties. We are able to directly follow the two-step assembly process of vimentin IFs and quantify the time scale of the first lateral step to tens of ms with a lag time of below 3 ms. Although demonstrated for a specific biomolecular system here, our method may potentially be employed for a wide range of fast molecular reactions in biological or, more generally, soft matter systems, as it allows for a precise quantification of the kinetics underlying the aggregation and assembly.

Vimentin S-glutathionylation at Cys328 inhibits filament elongation and induces severing of mature filaments in vitro

Vimentin intermediate filaments are a significant component of the cytoskeleton in cells of mesenchymal origin. In vivo, filaments assemble and disassemble and thus participate in the dynamic processes of the cell. Post-translational modifications (PTMs) such as protein phosphorylation regulate the multiphasic association of vimentin from soluble complexes to insoluble filaments and the reverse processes. The thiol side chain of the single vimentin cysteine at position 328 (Cys328) is a direct target of oxidative modifications inside cells. Here, we used atomic force microscopy, electron microscopy and a novel hydrogen-deuterium exchange mass spectrometry (HDex-MS) procedure to investigate the structural consequences of S-nitrosylation and S-glutathionylation of Cys328 for in vitro oligomerisation of human vimentin. Neither modification affects the lateral association of tetramers to unit-length filaments (ULF). However, S-glutathionylation of Cys328 blocks the longitudinal assembly of ULF into extended filaments. S-nitrosylation of Cys328 does not hinder but slows down the elongation. Likewise, S-glutathionylation of preformed vimentin filaments causes their extensive fragmentation to smaller oligomeric species. Chemical reduction of the S-glutathionylated Cys328 thiols induces reassembly of the small fragments into extended filaments. In conclusion, our in vitro results suggest S-glutathionylation as a candidate PTM for an efficient molecular switch in the dynamic rearrangements of vimentin intermediate filaments, observed in vivo, in response to changes in cellular redox status. Finally, we demonstrate that HDex-MS is a powerful method for probing the kinetics of vimentin filament formation and filament disassembly induced by PTMs.

OSTE+ for in situ SAXS analysis with droplet microfluidic devices

In recent years, microfluidic-based sample preparation techniques have emerged as a powerful tool for measurements at large scale X-ray facilities. Most often the microfluidic device was a form of hybrid system, i.e. an assembly of different materials, because a simple, versatile and inexpensive microfabrication method, on the one hand, and X-ray compatibility, on the other hand, cannot generally be achieved by the same material. The arrival of a new polymer family based on off-stoichiometric thiol-ene-epoxy (OSTE+) has recently redistributed the cards. In this context, we studied the relevance and the compatibility of OSTE+ for small-angle X-ray scattering (SAXS) studies. The material was characterized regarding its X-ray properties (transmission coefficient, attenuation coefficient, scattering pattern and polymer aging under X-ray light) and their comparison with those of the usual polymers used in microfluidics and/or for synchrotron radiation experiments. We show that OSTE+ has a better SAXS signal than polyimide, the polymer of reference in the SAXS community. Then a detailed protocol to manufacture a suitably thin full OSTE+ chip (total thickness <500 μm) is described and the potency of full OSTE+ devices for in situ SAXS studies is highlighted in two case-studies: the characterization of gold nanoparticles and the precipitation of cerium oxalate particles, both in moving droplets. Additionally, a method to analyze the scattering signals from droplet and carrier phase in a segmented flow is proposed.

3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow

Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX.

3D Micromachined Polyimide Mixing Devices for in Situ X-ray Imaging of Solution-Based Block Copolymer Phase Transitions

Advances in modern interface- and material sciences often rely on the understanding of a system's structure-function relationship. Designing reproducible experiments that yield in situ time-resolved structural information at fast time scales is therefore of great interest, e.g., for better understanding the early stages of self-assembly or other phase transitions. However, it can be challenging to accurately control experimental conditions, especially when samples are only available in small amounts, prone to agglomeration, or if X-ray compatibility is required. We address these challenges by presenting a microfluidic chip for triggering dynamics via rapid diffusive mixing for in situ time-resolved X-ray investigations. This polyimide/Kapton-only-based device can be used to study the structural dynamics and phase transitions of a wide range of colloidal and soft matter samples down to millisecond time scales. The novel multiangle laser ablation three-dimensional (3D) microstructuring approach combines, for the first time, the highly desirable characteristics of Kapton (high X-ray stability with low background, organic solvent compatibility) with a 3D flow-focusing geometry that minimizes mixing dispersion and wall agglomeration. As a model system, to demonstrate the performance of these 3D Kapton microfluidic devices, we selected the non-solvent-induced self-assembly of biocompatible and amphiphilic diblock copolymers. We then followed their structural evolution in situ at millisecond time scales using on-the-chip time-resolved small-angle X-ray scattering under continuous-flow conditions. Combined with complementary results from 3D finite-element method computational fluid dynamics simulations, we find that the nonsolvent mixing is mostly complete within a few tens of milliseconds, which triggers initial spherical micelle formation, while structural transitions into micelle lattices and their deswelling only occur on the hundreds of milliseconds to second time scale. These results could have an important implication for the design and formulation of amphiphilic polymer nanoparticles for industrial applications and their use as drug-delivery systems in medicine.

Mutation-induced alterations of intra-filament subunit organization in vimentin filaments revealed by SAXS

Vimentin intermediate filaments constitute a distinct filament system in mesenchymal cells that is instrumental for cellular mechanics and migration. In vitro, the rod-like monomers assemble in a multi-step, salt-dependent manner into micrometer long biopolymers. To disclose the underlying mechanisms further, we employed small angle X-ray scattering on two recombinant vimentin variants, whose assembly departs at strategic points from the normal assembly route: (i) vimentin with a tyrosine to leucine change at position 117; (ii) vimentin missing the non-α-helical carboxyl-terminal domain. Y117L vimentin assembles into unit-length filaments (ULFs) only, whereas ΔT vimentin assembles into filaments containing a higher number of tetramers per cross section than normal vimentin filaments. We show that the shape and inner structure of these mutant filaments is significantly altered. ULFs assembled from Y117L vimentin contain more, less tightly bundled vimentin tetramers, and ΔT vimentin filaments preserve the number density despite the higher number of tetramers per filament cross-section.

Effect of ionic strength on the structure and elongational kinetics of vimentin filaments

Intermediate filaments are a major structural element in the cytoskeleton of animal cells that mechanically integrate other cytoskeletal components and absorb externally applied stress. Their role is likely to be linked to their complex molecular architecture which is the product of a multi-step assembly pathway. Intermediate filaments form tetrameric subunits which assemble in the presence of monovalent salts to form unit length filaments that subsequently elongate by end-to-end annealing. The present work characterizes this complex assembly process using reconstituted vimentin intermediate filaments with monovalent salts as an assembly trigger. A multi-scale approach is used, comprising static light scattering, dynamic light scattering and quantitative scanning transmission electron microscopy (STEM) mass measurements. Light scattering reveals the radius of gyration (Rg), molecular weight (Mw) and diffusion coefficient (D) of the assembling filaments as a function of time and salt concentration (cS) for the given protein concentration of 0.07 g L-1. At low cS (10 mM KCl) no lateral or elongational growth is observed, whereas at cS = 50-200 mM, the hydrodynamic cross-sectional radius and the elongation rate increases with cS. Rgversus Mw plots suggest that the mass per unit length increases with increasing salt content, which is confirmed by STEM mass measurements. A kinetic model based on rate equations for a two step process is able to accurately describe the variation of mass, length and diffusion coefficient of the filaments with time and provides a consistent description of the elongation accelerated by increasing cS.

Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions

Radiation damage by intense X-ray beams at modern synchrotron facilities is one of the major complications for biological small-angle X-ray scattering (SAXS) investigations of macromolecules in solution. To limit the damage, samples are typically measured under a laminar flow through a cell (typically a capillary) such that fresh solution is continuously exposed to the beam during measurement. The diameter of the capillary that optimizes the scattering-to-absorption ratio at a given X-ray wavelength can be calculated a priori based on fundamental physical properties. However, these well established scattering and absorption principles do not take into account the radiation susceptibility of the sample or the often very limited amounts of precious biological material available for an experiment. Here it is shown that, for biological solution SAXS, capillaries with smaller diameters than those calculated from simple scattering/absorption criteria allow for a better utilization of the available volumes of radiation-sensitive samples. This is demonstrated by comparing two capillary diameters di (di = 1.7 mm, close to optimal for 10 keV; and di = 0.9 mm, which is nominally sub-optimal) applied to study different protein solutions at various flow rates. The use of the smaller capillaries ultimately allows one to collect higher-quality SAXS data from the limited amounts of purified biological macromolecules.

Microfluidic devices for small-angle neutron scattering

A comparative examination is presented of materials and approaches for the fabrication of microfluidic devices for small-angle neutron scattering (SANS). Representative inorganic glasses, metals, and polymer materials and devices are evaluated under typical SANS configurations. Performance criteria include neutron absorption, scattering background and activation, as well as spatial resolution, chemical compatibility and pressure resistance, and also cost, durability and manufacturability. Closed-face polymer photolithography between boron-free glass (or quartz) plates emerges as an attractive approach for rapidly prototyped microfluidic SANS devices, with transmissions up to ∼98% and background similar to a standard liquid cell (I ≃ 10-3 cm-1). For applications requiring higher durability and/or chemical, thermal and pressure resistance, sintered or etched boron-free glass and silicon devices offer superior performance, at the expense of various fabrication requirements, and are increasingly available commercially.

Hydrogelation Kinetics Measured in a Microfluidic Device with in Situ X-ray and Fluorescence Detection

Efficient hydrogelators will gel water fast and at low concentrations. Small molecule gelling agents that assemble into fibers and fiber networks are particularly effective hydrogelators. Whereas it is straightforward to determine their critical concentration for hydrogelation, the kinetics of hydrogelation is more difficult to study because it is often very fast, occurring on the subsecond time scale. We used a 3D focusing microfluidic device combined with fluorescence microscopy and in situ small-angle X-ray scattering (SAXS) to study the fast pH-induced gelation of a model small molecule gelling agent at the millisecond time scale. The gelator is a 1,3,5-benzene tricarboxamide which upon acidification assembles into nanofibrils and fibril networks that show a characteristic photoluminescence. By adjusting the flow rates, the regime of early nanofibril formation and gelation could be followed along the microfluidic reaction channel. The measured fluorescence intensity profiles were analyzed in terms of a diffusion-advection-reaction model to determine the association rate constant, which is in a typical range for the small molecule self-assembly. Using in situ SAXS, we could determine the dimensions of the fibers that were formed during the early self-assembly process. The detailed structure of the fibers was subsequently determined by cryotransmission electron microscopy. The study demonstrates that 3D focusing microfluidic devices are a powerful means to study the self-assembly on the millisecond time scale, which is applied to reveal early state of hydrogelation kinetics. In combination with in situ fluorescence and X-ray scattering, these experiments provide detailed insights into the first self-assembly steps and their reaction rates.

Assembly Kinetics of Vimentin Tetramers to Unit-Length Filaments: A Stopped-Flow Study

Intermediate filaments (IFs) are principal components of the cytoskeleton, a dynamic integrated system of structural proteins that provides the functional architecture of metazoan cells. They are major contributors to the elasticity of cells and tissues due to their high mechanical stability and intrinsic flexibility. The basic building block for the assembly of IFs is a rod-like, 60-nm-long tetrameric complex made from two antiparallel, half-staggered coiled coils. In low ionic strength, tetramers form stable complexes that rapidly assemble into filaments upon raising the ionic strength. The first assembly products, "frozen" by instantaneous chemical fixation and viewed by electron microscopy, are 60-nm-long "unit-length" filaments (ULFs) that apparently form by lateral in-register association of tetramers. ULFs are the active elements of IF growth, undergoing longitudinal end-to-end annealing with one another and with growing filaments. Originally, we have employed quantitative time-lapse atomic force and electron microscopy to analyze the kinetics of vimentin-filament assembly starting from a few seconds to several hours. To obtain detailed quantitative insight into the productive reactions that drive ULF formation, we now introduce a "stopped-flow" approach in combination with static light-scattering measurements. Thereby, we determine the basic rate constants for lateral assembly of tetramers to ULFs. Processing of the recorded data by a global fitting procedure enables us to describe the hierarchical steps of IF formation. Specifically, we propose that tetramers are consumed within milliseconds to yield octamers that are obligatory intermediates toward ULF formation. Although the interaction of tetramers is diffusion controlled, it is strongly driven by their geometry to mediate effective subunit targeting. Importantly, our model conclusively reflects the previously described occurrence of polymorphic ULF and mature filaments in terms of their number of tetramers per cross section.

SAXS on a chip: from dynamics of phase transitions to alignment phenomena at interfaces studied with microfluidic devices

The field of microfluidics offers attractive possibilities to perform novel experiments that are difficult (or even impossible) to perform using conventional bulk and surface-based methods. Such attractiveness comes from several important aspects inherent to these miniaturized devices. First, the flow of fluids under submillimeter confinement typically leads to a drop of inertial forces, meaning that turbulence is practically suppressed. This leads to predictable and controllable flow profiles, along with well-defined chemical gradients and stress fields that can be used for controlled mixing and actuation on the micro and nanoscale. Secondly, intricate microfluidic device designs can be fabricated using cleanroom standard procedures. Such intricate geometries can take diverse forms, designed by researchers to perform complex tasks, that require exquisite control of flow of several components and gradients, or to mimic real world examples, facilitating the establishment of more realistic models. Thirdly, microfluidic devices are usually compatible with in situ or integrated characterization methods that allow constant real-time monitoring of the processes occurring inside the microchannels. This is very different from typical bulk-based methods, where usually one can only observe the final result, or otherwise, take quick snapshots of the evolving process or take aliquots to be analyzed separately. Altogether, these characteristics inherent to microfluidic devices provide researchers with a set of tools that allow not only exquisite control and manipulation of materials at the micro and nanoscale, but also observation of these effects. In this review, we will focus on the use and prospects of combining microfluidic devices with in situ small-angle X-ray scattering (and related techniques such as small-angle neutron scattering and X-ray photon correlation spectroscopy), and their enormous potential for physical-chemical research, mainly in self-assembly and phase-transitions, and surface characterization.

Cyclic olefin copolymer as an X-ray compatible material for microfluidic devices

The combination of microfluidics and X-ray methods attracts a lot of attention from researchers as it brings together the high controllability of microfluidic sample environments and the small length scales probed by X-rays. In particular, the fields of biophysics and biology have benefited enormously from such approaches. We introduce a straightforward fabrication method for X-ray compatible microfluidic devices made solely from cyclic olefin copolymers. We benchmark the performance of the devices against other devices including more commonly used Kapton windows and obtain data of equal quality using small angle X-ray scattering. An advantage of the devices presented here is that no gluing between interfaces is necessary, rendering the production very reliable. As a biophysical application, we investigate the early time points of the assembly of vimentin intermediate filament proteins into higher-order structures. This weakly scattering protein system leads to high quality data in the new devices, thus opening up the way for numerous future applications.

Soft electrostatic trapping in nanofluidics

Trapping and manipulation of nano-objects in solution are of great interest and have emerged in a plethora of fields spanning from soft condensed matter to biophysics and medical diagnostics. We report on establishing a nanofluidic system for reliable and contact-free trapping as well as manipulation of charged nano-objects using elastic polydimethylsiloxane (PDMS)-based materials. This trapping principle is based on electrostatic repulsion between charged nanofluidic walls and confined charged objects, called geometry-induced electrostatic (GIE) trapping. With gold nanoparticles as probes, we study the performance of the devices by measuring the stiffness and potential depths of the implemented traps, and compare the results with numerical simulations. When trapping 100 nm particles, we observe potential depths of up to Q≅24 k B T that provide stable trapping for many days. Taking advantage of the soft material properties of PDMS, we actively tune the trapping strength and potential depth by elastically reducing the device channel height, which boosts the potential depth up to Q~200 k B T, providing practically permanent contact-free trapping. Due to a high-throughput and low-cost fabrication process, ease of use, and excellent trapping performance, our method provides a reliable platform for research and applications in study and manipulation of single nano-objects in fluids.

Innovative High-Throughput SAXS Methodologies Based on Photonic Lab-on-a-Chip Sensors: Application to Macromolecular Studies

The relevance of coupling droplet-based Photonic Lab-on-a-Chip (PhLoC) platforms and Small-Angle X-Ray Scattering (SAXS) technique is here highlighted for the performance of high throughput investigations, related to the study of protein macromolecular interactions. With this configuration, minute amounts of sample are required to obtain reliable statistical data. The PhLoC platforms presented in this work are designed to allow and control an effective mixing of precise amounts of proteins, crystallization reagents and buffer in nanoliter volumes, and the subsequent generation of nanodroplets by means of a two-phase flow. Spectrophotometric sensing permits a fine control on droplet generation frequency and stability as well as on concentration conditions, and finally the droplet flow is synchronized to perform synchrotron radiation SAXS measurements in individual droplets (each one acting as an isolated microreactor) to probe protein interactions. With this configuration, droplet physic-chemical conditions can be reproducibly and finely tuned, and monitored without cross-contamination, allowing for the screening of a substantial number of saturation conditions with a small amount of biological material. The setup was tested and validated using lysozyme as a model of study. By means of SAXS experiments, the proteins gyration radius and structure envelope were calculated as a function of protein concentration. The obtained values were found to be in good agreement with previously reported data, but with a dramatic reduction of sample volume requirements compared to studies reported in the literature.

Rapid contrast matching by microfluidic SANS

We report a microfluidic approach to perform small angle neutron scattering (SANS) measurements of contrast variation and matching, extensively employed in soft and biological matter research. We integrate a low scattering background microfluidic mixer and serpentine channel in a SANS beamline to yield a single phase, continuous flow, reconfigurable liquid cell. By contrast with conventional, sequential measurements of discrete (typically 4-6) solutions of varying isotopic solvent composition, our approach continually varies solution composition during SANS acquisition. We experimentally and computationally determine the effects of flow dispersion and neutron beam overillumination of microchannels in terms of the composition resolution and precision. The approach is demonstrated with model systems: H₂O/D₂O mixtures, a surfactant (sodium dodecyl sulfate, SDS), a triblock copolymer (pluronic F127), and silica nanoparticles (Ludox) in isotopic aqueous mixtures. The system is able to zoom into a composition window to refine contrast matching conditions, and robustly resolve solute structure and form factors by simultaneous fitting of scattering data with continuously varying contrast. We conclude by benchmarking our microflow-SANS with the discrete approach, in terms of volume required, composition resolution and (preparation and measurement) time required, proposing a leap forward in equilibrium, liquid solution phase mapping and contrast variation by SANS.

Brownian and advective dynamics in microflow studied by coherent X-ray scattering experiments

Combining microfluidics with coherent X-ray illumination offers the possibility to not only measure the structure but also the dynamics of flowing samples in a single-scattering experiment. Here, the power of this combination is demonstrated by studying the advective and Brownian dynamics of colloidal suspensions in microflow of different geometries. Using an experimental setup with a fast two-dimensional detector and performing X-ray correlation spectroscopy by calculating two-dimensional maps of the intensity auto-correlation functions, it was possible to evaluate the sample structure and furthermore to characterize the detailed flow behavior, including flow geometry, main flow directions, advective flow velocities and diffusive dynamics. By scanning a microfocused X-ray beam over a microfluidic device, the anisotropic auto-correlation functions of driven colloidal suspensions in straight, curved and constricted microchannels were mapped with the spatial resolution of the X-ray beam. This method has not only a huge potential for studying flow patterns in complex fluids but also to generally characterize anisotropic dynamics in materials.

Recent advances in X-ray compatible microfluidics for applications in soft materials and life sciences

The increasingly narrow and brilliant beams at X-ray facilities reduce the requirements for both sample volume and data acquisition time. This creates new possibilities for the types and number of sample conditions that can be examined but simultaneously increases the demands in terms of sample preparation. Microfluidic-based sample preparation techniques have emerged as elegant alternatives that can be integrated directly into the experimental X-ray setup remedying several shortcomings of more traditional methods. We review the use of microfluidic devices in conjunction with X-ray measurements at synchrotron facilities in the context of 1) mapping large parameter spaces, 2) performing time resolved studies of mixing-induced kinetics, and 3) manipulating/processing samples in ways which are more demanding or not accessible on the macroscale. The review covers the past 15 years and focuses on applications where synchrotron data collection is performed in situ, i.e. directly on the microfluidic platform or on a sample jet from the microfluidic device. Considerations such as the choice of materials and microfluidic designs are addressed. The combination of microfluidic devices and measurements at large scale X-ray facilities is still emerging and far from mature, but it definitely offers an exciting array of new possibilities.

Direct monitoring of calcium-triggered phase transitions in cubosomes using small-angle X-ray scattering combined with microfluidics

This article introduces a simple microfluidic device that can be combined with synchrotron small-angle X-ray scattering (SAXS) for monitoring dynamic structural transitions. The microfluidic device is a thiol–ene-based system equipped with 125 µm-thick polystyrene windows, which are suitable for X-ray experiments. The device was prepared by soft lithography using elastomeric molds followed by a simple UV-initiated curing step to polymerize the chip material and simultaneously seal the device with the polystyrene windows. The microfluidic device was successfully used to explore the dynamics of the structural transitions of phytantriol/dioleoylphosphatidylglycerol-based cubosomes on exposure to a buffer containing calcium ions. The resulting SAXS data were resolved in the time frame between 0.5 and 5.5 s, and a calcium-triggered structural transition from an internal inverted-type cubic phase of symmetryIm3mto an internal inverted-type cubic phase of symmetryPn3mwas detected. The combination of microfluidics with X-ray techniques opens the door to the investigation of early dynamic structural transitions, which is not possible with conventional techniques such as glass flow cells. The combination of microfluidics with X-ray techniques can be used for investigating protein unfolding, for monitoring the formation of nanoparticles in real time, and for other biomedical and pharmaceutical investigations.

Scanning-SAXS of microfluidic flows: nanostructural mapping of soft matter

The determination of in situ structural information of soft matter under flow is challenging, as it depends on many factors, such as temperature, concentration, confinement, channel geometry, and type of imposed flow. Here, we combine microfluidics and scanning small-angle X-ray scattering (scanning-SAXS) to create a two-dimensional spatially resolved map, which represents quantitatively the variation of molecular properties under flow. As application examples, mappings of confined amyloid fibrils and wormlike micelles under flow into various channel geometries are compared. A simple process to fabricate X-rays resistant chips, based on polyimide and UV-curing resin, is discussed. During experiments, these chips remained in high-energy synchrotron radiation for more than 24 hours, causing constant low background scattering. Thus, sufficient statistics were obtained from sample scattering at exposure times as low as 0.1 s, even with the small scattering volumes in microfluidic channels. Scanning-SAXS of microfluidic flows has many potential applications from biology to fundamental soft matter physics. In general, any fluid which has enough contrast for X-ray scattering can be measured to obtain the dependence of molecular shape, conformation, alignment and size on the flow field. Besides, dynamic processes of soft matter caused by flow, temperature, concentration gradient, and confinement, for example self-assembling, aggregation, mixing, diffusion, and disintegration of macromolecules, can be quantified and visualized on a single image by this mapping technique.

Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study

Vimentin intermediate filaments (IFs) are part of a family of proteins that constitute one of the three filament systems in the cytoskeleton, a major contributor to cell mechanics. One property that distinguishes IFs from the other cytoskeletal filament types, actin filaments and microtubules, is their highly hierarchical assembly pathway, where a lateral association step is followed by elongation. Here we present an innovative technique to follow the elongation reaction in solution and in situ by time-resolved static and dynamic light scattering, thereby precisely capturing the relevant time and length scales of seconds to minutes and 60-600 nm, respectively. We apply a quantitative model to our data and succeed in consistently describing the entire set of data, including particle mass, radius of gyration, and hydrodynamic radius during longitudinal association.

In Vitro Assembly Kinetics of Cytoplasmic Intermediate Filaments: A Correlative Monte Carlo Simulation Study

Intermediate filament (IF) elongation proceeds via full-width "mini-filaments", referred to as "unit-length" filaments (ULFs), which instantaneously form by lateral association of extended coiled-coil complexes after assembly is initiated. In a comparatively much slower process, ULFs longitudinally interact end-to-end with other ULFs to form short filaments, which further anneal with ULFs and with each other to increasingly longer filaments. This assembly concept was derived from time-lapse electron and atomic force microscopy data. We previously have quantitatively verified this concept through the generation of time-dependent filament length-profiles and an analytical model that describes assembly kinetics well for about the first ten minutes. In this time frame, filaments are shorter than one persistence length, i.e. ~1 μm, and thus filaments were treated as stiff rods associating via their ends. However, when filaments grow several μm in length over hours, their flexibility becomes a significant factor for the kinetics of the longitudinal annealing process. Incorporating now additional filament length distributions that we have recorded after extended assembly times by total internal reflection fluorescence microscopy (TIRFM), we developed a Monte Carlo simulation procedure that accurately describes the underlying assembly kinetics for large time scales.

The filament forming reactions of vimentin tetramers studied in a serial-inlet microflow device by small angle x-ray scattering

The structural organization of metazoan cells and their shape are established through the coordinated interaction of a composite network consisting of three individual filament systems, collectively termed the cytoskeleton. Specifically, microtubules and actin filaments, which assemble from monomeric globular proteins, provide polar structures that serve motor proteins as tracks. In contrast, intermediate filaments (IFs) assemble from highly charged, extended coiled coils in a hierarchical assembly mechanism of lateral and longitudinal interaction steps into non-polar structures. IF proteins are expressed in a distinctly tissue-specific way and thereby serve to generate the precise plasticity of the respective cells and tissues. Accordingly, in the cell, numerous parameters such as pH and salt concentration are adjusted such that the generation of functional networks is ensured. Here, we transfer the problem for the mesenchymal IF protein vimentin to an in vitro setting and combine small angle x-ray scattering with microfluidics and finite element method simulations. Our approach is adapted to resolve the early assembly steps, which take place in the sub-second to second range. In particular, we reveal the influence of ion species and concentrations on the assembly. By tuning the flow rates and thus concentration profiles, we find a minimal critical salt concentration for the initiation of the assembly. Furthermore, our analysis of the surface sensitive Porod regime in the x-ray data reveals that the formation of first assembly intermediates, so-called unit length filaments, is not a one-step reaction but consists of distinct consecutive lateral association steps followed by radial compaction as well as smoothening of the surface of the full-width filament.

Physical properties of cytoplasmic intermediate filaments

Intermediate filaments (IFs) constitute a sophisticated filament system in the cytoplasm of eukaryotes. They form bundles and networks with adapted viscoelastic properties and are strongly interconnected with the other filament types, microfilaments and microtubules. IFs are cell type specific and apart from biochemical functions, they act as mechanical entities to provide stability and resilience to cells and tissues. We review the physical properties of these abundant structural proteins including both in vitro studies and cell experiments. IFs are hierarchical structures and their physical properties seem to a large part be encoded in the very specific architecture of the biopolymers. Thus, we begin our review by presenting the assembly mechanism, followed by the mechanical properties of individual filaments, network and structure formation due to electrostatic interactions, and eventually the mechanics of in vitro and cellular networks. This article is part of a Special Issue entitled: Mechanobiology.

Implementation of in situ SAXS/WAXS characterization into silicon/glass microreactors

A successful implementation of in situ X-ray scattering analysis of synthetized particle materials in silicon/glass microreactors is reported. Calcium carbonate (CaCO3) as a model material was precipitated inside the microchannels through the counter-injection of two aqueous solutions, containing carbonate ions and calcium ions, respectively. The synthesized calcite particles were analyzed in situ in aqueous media by combining Small Angle X-ray Scattering (SAXS) and Wide Angle X-ray Scattering (WAXS) techniques at the ESRF ID02 beam line. At high wavevector transfer, WAXS patterns clearly exhibit different scattering features: broad scattering signals originating from the solvent and the glass lid of the chip, and narrow diffraction peaks coming from CaCO3 particles precipitated rapidly inside the microchannel. At low wavevector transfer, SAXS reveals the rhombohedral morphology of the calcite particles together with their micrometer size without any strong background, neither from the chip nor from the water. This study demonstrates that silicon/glass chips are potentially powerful tools for in situ SAXS/WAXS analysis and are promising for studying the structure and morphology of materials in non-conventional conditions like geological materials under high pressure and high temperature.

Intermediate filament mechanics in vitro and in the cell: from coiled coils to filaments, fibers and networks

Intermediate filament proteins form filaments, fibers and networks both in the cytoplasm and the nucleus of metazoan cells. Their general structural building plan accommodates highly varying amino acid sequences to yield extended dimeric α-helical coiled coils of highly conserved design. These 'rod' particles are the basic building blocks of intrinsically flexible, filamentous structures that are able to resist high mechanical stresses, that is, bending and stretching to a considerable degree, both in vitro and in the cell. Biophysical and computer modeling studies are beginning to unfold detailed structural and mechanical insights into these major supramolecular assemblies of cell architecture, not only in the 'test tube' but also in the cellular and tissue context.

Formation of lipid and polymer based gold nanohybrids using a nanoreactor approach

Nanocarriers encapsulating gold nanoparticles hold tremendous promise for biomedical applications. The nanoreactor approach offers a versatile, efficient, and highly reproducible preparation technology.

Online determination of anisotropy during cellulose nanofibril assembly in a flow focusing device

In order to utilize the high strength and stiffness of cellulose nanofibrils in a macroscopic material or composite, the structure of the elongated fibrils in the material must be controlled.

Direct observation of subunit exchange along mature vimentin intermediate filaments

Actin filaments, microtubules, and intermediate filaments (IFs) are central elements of the metazoan cytoskeleton. At the molecular level, the assembly mechanism for actin filaments and microtubules is fundamentally different from that of IFs. The former two types of filaments assemble from globular proteins. By contrast, IFs assemble from tetrameric complexes of extended, half-staggered, and antiparallel oriented coiled-coils. These tetramers laterally associate into unit-length filaments; subsequent longitudinal annealing of unit-length filaments yields mature IFs. In vitro, IFs form open structures without a fixed number of tetramers per cross-section along the filament. Therefore, a central question for the structural biology of IFs is whether individual subunits can dissociate from assembled filaments and rebind at other sites. Using the fluorescently labeled IF-protein vimentin for assembly, we directly observe and quantitatively determine subunit exchange events between filaments as well as with soluble vimentin pools. Thereby we demonstrate that the cross-sectional polymorphism of donor and acceptor filaments plays an important role. We propose that in segments of donor filaments with more than the standard 32 molecules per cross-section, subunits are not as tightly bound and are predisposed to be released from the filament.

Investigating increasingly complex macromolecular systems with small-angle X-ray scattering

The biological solution small-angle X-ray scattering (BioSAXS) field has undergone tremendous development over recent decades. This means that increasingly complex biological questions can be addressed by the method. An intricate synergy between advances in hardware and software development, data collection and evaluation strategies and implementations that readily allow integration with complementary techniques result in significant results and a rapidly growing user community with ever increasing ambitions. Here, a review of these developments, by including a selection of novel BioSAXS method-ologies and recent results, is given.

Fast diffusion-limited lyotropic phase transitions studied in situ using continuous flow microfluidics/microfocus-SAXS

Fast concentration-induced diffusion-limited lyotropic phase transitions can be studied in situ with millisecond time resolution using continuous flow microfluidics in combination with microfocus small-angle X-ray scattering. The method was applied to follow a classical self-assembly sequence where amphiphiles assemble into micelles, which subsequently assemble into an ordered lattice via a disorder/order transition. As a model system we selected the self-assembly of an amphiphilic block copolymer induced by the addition of a nonsolvent. Using microchannel hydrodynamic flow-focusing, large concentration gradients can be generated, leading to a deep quench from the miscible to the microphase-separated state. Within milliseconds the block copolymers assembly via a spinodal microphase separation into micelles, followed by a disorder/order transition into an FCC liquid-crystalline phase with late-stage domain growth and shear-induced domain orientation into a mesocrystal. A comparison with a slow macroscopic near-equilibrium kinetic experiment shows that the fast structural transitions follow a direct pathway to the equilibrium structure without the trapping of metastable states.

Room-temperature macromolecular serial crystallography using synchrotron radiation

A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.

Impact of ion valency on the assembly of vimentin studied by quantitative small angle X-ray scattering

The assembly kinetics of intermediate filament (IF) proteins from tetrameric complexes to single filaments and networks depends on the protein concentration, temperature and the ionic composition of their environment. We systematically investigate how changes in the concentration of monovalent potassium and divalent magnesium ions affect the internal organization of the resulting filaments. Small angle X-ray scattering (SAXS) is very sensitive to changes in the filament cross-section such as diameter or compactness. Our measurements reveal that filaments formed in the presence of magnesium chloride differ distinctly from filaments formed in the presence of potassium chloride. The principle multi-step assembly mechanism from tetramers via unit-length filaments (ULF) to elongated filaments is not changed by the valency of ions. However, the observed differences indicate that the magnesium ions free the head domains of tetramers from unproductive interactions to allow assembly but at the same time mediate strong inter-tetrameric interactions that impede longitudinal annealing of unit-length filaments considerably, thus slowing down filament growth.

Coaxial flow focusing in poly(dimethylsiloxane) microfluidic devices

We have developed a coaxial flow focusing geometry that can be fabricated using soft lithography in poly(dimethylsiloxane) (PDMS). Like coaxial flow focusing in glass capillary microfluidics, our geometry can form double emulsions in channels with uniform wettability and of a size much smaller than the channel dimensions. However, In contrast to glass capillary coaxial flow focusing, our geometry can be fabricated using lithographic techniques, allowing it to be integrated as the drop making unit in parallel drop maker arrays. Our geometry enables scalable formation of emulsions down 7 μm in diameter, in large channels that are robust against fouling and clogging.