Crystal Harvesting Research Articles

Tunable topological edge states and energy harvesting of piezoelectric-inductance phononic crystals based on Su-Schrieffer-Heeger model

Based on Su-Schrieffer-Heeger (SSH) model, a one-dimensional tunable topological phononic crystal (PnC) was designed. Piezoelectric column with an inductance was designed as a scatterer embedded in the epoxy resin matrix. And the introduce of an inductance into each piezoelectric column resulted in a new Dirac point in band structure. Subsequently, the new Dirac point was operated to open/close by altering the intracell distance, and the trivial and non-trivial phase transition occurred simultaneously, which demonstrated the topological properties of PnC. The results showed that the obvious edge state was observed at the frequencies of 16.334–27.226 kHz by varying the inductance from 2.5mH to 9.5mH. And the immune of the edge state to the local defects was also verified. Furthermore, the energy harvesting of the wave propagation was performed, and the energy harvesting efficiency of the edge state case was about 40 times larger than that of bulk state case.

Impact of air and vacuum calcination on the properties of lead-free piezoelectric Ba0.85Ca0.15Zr0.1Ti0.9O3 ceramics for mechanical energy harvesting

Piezoelectric materials play a crucial role in energy harvesting applications, efficiently capturing renewable energy from sources like human activities and vibrations. Oxygen vacancies, common imperfections in these materials, significantly influence their overall effectiveness. In our study, Ba0.85Ca0.15Zr0.1Ti0.9O3 (BCZT) powder was calcined under different conditions (air and vacuum) to investigate their impact on crystal structure, microstructure, electrical properties, and energy harvesting performance. X-ray diffraction (XRD) and Rietveld analysis confirmed varied phases in vacuum calcined BCZT with a smaller particle size. X-ray photoelectron spectroscopy (XPS) revealed lower oxygen vacancy concentration for vacuum-calcined samples. The vacuum calcined BCZT ceramics demonstrated a remarkable 580% enhancement in the figure of merit (FOM) when contrasted with traditional ceramics, highlighting superior dielectric and piezoelectric characteristics. In mechanical energy harvesting, BCZT ceramics, protected by polyimide with Cu/Ag electrodes, outperformed conventional ceramics, generating a higher open-circuit voltage (10.61 V) and peak-to-peak power (1.510 mW/cm3). This energy harvester maintained stable output through 7000 cycles, suggesting its potential for powering miniature electronics.

Stress and electric field induced phase transitions for ultra high energy conversion in ferroelectrics

This work focuses on energy harvesting of ferroelectric relaxors PMN-25PT and PZN-8PT single crystals with high uniaxial stress and electric field. Ericsson cycle, which consists of applying and releasing electric field and stress at different steps of the cycle, has been used. A large energy density for PZN-8PT high as 410 mJ/cm3 was obtained. Different working temperatures were tested by experiment and modeled via Landau–Devonshire theory. Optimal working temperatures were identified for high level energy conversion and were successfully predicted by simulation. It appeared that the optimum working temperature was different from that optimizing the d33. Polarization mechanisms induced by these extreme conditions for energy harvesting are explained in the frame of experimental and modeling results. The results obtained at high stress levels tend to indicate that operating along the polarization direction yields the best results, which contradicts conclusions drawn in the case of domain engineered crystals.

Microfluidic rotating-target device capable of three-degrees-of-freedom motion for efficient in situ serial synchrotron crystallography.

There is an increasing demand for simple and efficient sample delivery technology to match the rapid development of serial crystallography and its wide application in analyzing the structural dynamics of biological macromolecules. Here, a microfluidic rotating-target device is presented, capable of three-degrees-of-freedom motion, including two rotational degrees of freedom and one translational degree of freedom, for sample delivery. Lysozyme crystals were used as a test model with this device to collect serial synchrotron crystallography data and the device was found to be convenient and useful. This device enables in situ diffraction from crystals in a microfluidic channel without the need for crystal harvesting. The circular motion ensures that the delivery speed can be adjusted over a wide range, showing its good compatibility with different light sources. Moreover, the three-degrees-of-freedom motion guarantees the full utilization of crystals. Hence, sample consumption is greatly reduced, and only 0.1 mg of protein is consumed in collecting a complete dataset.

Crystal structure of the phospholipase A and acyltransferase 4 (PLAAT4) catalytic domain

Phospholipase A and Acyltransferase 4 (PLAAT4) is a class II tumor suppressor, that also plays a role as a restrictor of intracellular Toxoplasma gondii infection through restriction of parasitic vacuole size. The catalytic N-terminal domain (NTD) interacts with the C-terminal domain (CTD), which is important for sub-cellular targeting and enzymatic function. The dynamics of the NTD main (L1) loop and the L2(B6) loop adjacent to the active site, have been shown to be important regulators of enzymatic activity. Here, we present the crystal structure of PLAAT4 NTD, determined from severely intergrown crystals using automated, laser-based crystal harvesting and data reduction technologies. The structure showed the L1 loop in two distinct conformations, highlighting a complex network of interactions likely influencing its conformational flexibility. Ensemble refinement of the crystal structure recapitulates the major correlated motions observed in solution by NMR. Our analysis offers useful insights on millisecond dynamics based on the crystal structure, complementing NMR studies which preclude structural information at this time scale.

PENENTUAN POSISI TIGA DIMENSI BUAH JAMBU KRISTAL MATANG MENGGUNAKAN PENGINDERAAN STEREO

Crystal Guava is one type of seedless guava that has high economic value and is favored by the people of Indonesia. Crystal guava fruit has a dark green color when it is still unripe and turns light green when it is ripe. With the decreasing workforce in agriculture, it is necessary to think about developing an automatic crystal guava harvesting process, where the three-dimensional positioning of suitable guava fruit is a very important process. The purpose of this study was to determine the three-dimensional position of ripe Crystal Guava fruit using stereo sensing. Crystal guava plants in pots that have been fruitful are imaged using a stereo camera and then the image of the plants obtained is processed to separate the image of the fruit from other components. The fruit image resulting from image processing is then calculated for its three-dimensional position using the triangulation principle. Stereo cameras were placed at a distance of 30 cm to 70 cm from plants with four treatments, the distances between cameras were 8 cm, 10 cm, 12 cm, and 14 cm. The test results with different camera distances show that the average accuracy of three-dimensional positioning is 99.3%, 99.3%, 98.8%, 98.7%, respectively. The average three-timed Root Mean Square Error values ​​for the four camera distance treatments were 0.34 cm, 0.37 cm, 0.61 cm, 0.57 cm, respectively.

On-chip Crystallization and Large-Scale Serial Diffraction at Room Temperature.

Biochemical reactions and biological processes can be best understood by demonstrating how proteins transition among their functional states. Since cryogenic temperatures are non-physiological and may prevent, deter, or even alter protein structural dynamics, a robust method for routine X-ray diffraction experiments at room temperature is highly desirable. The crystal-on-crystal device and its accompanying hardware and software used in this protocol are designed to enable in situ X-ray diffraction at room temperature for protein crystals of different sizes without any sample manipulation. Here we present the protocols for the key steps from device assembly, on-chip crystallization, optical scanning, crystal recognition to X-ray shot planning and automated data collection. Since this platform requires no crystal harvesting nor any other sample manipulation, hundreds to thousands of protein crystals grown on chip can be introduced into an X-ray beam in a programmable and high-throughput manner.

On-Chip Crystallization and Large-Scale Serial Diffraction at Room Temperature

Biochemical reactions and biological processes can be best understood by demonstrating how proteins transition among their functional states. Since cryogenic temperatures are non-physiological and may prevent, deter, or even alter protein structural dynamics, a robust method for routine X-ray diffraction experiments at room temperature is highly desirable. The crystal-on-crystal device and its accompanying hardware and software used in this protocol are designed to enable in situ X-ray diffraction at room temperature for protein crystals of different sizes without any sample manipulation. Here we present the protocols for the key steps from device assembly, on-chip crystallization, optical scanning, crystal recognition to X-ray shot planning and automated data collection. Since this platform requires no crystal harvesting nor any other sample manipulation, hundreds to thousands of protein crystals grown on chip can be introduced into an X-ray beam in a programmable and high-throughput manner.

Using sound pulses to solve the crystal harvesting bottleneck

Using sound pulses to solve the crystal harvesting bottleneck

The effects of pyridine molecules structure on the defects passivation of perovskite solar cells

Pyridine molecules have been widely used to improve the performances of perovskite solar cells (PSCs). However, the effects of pyridine molecular structure, especially the functional group, on the defects passivation of perovskite solar cell have a lack of investigation. In this work, we introduced three pyridine molecules as additives into perovskite layer, including pyridine (PY), 4-methyl-pyridine (MP) and 4-tertbutyl pyridine (TBP), to investigate the influences of the molecular structure on the surface-defect passivation and long-term stability of perovskite solar cells. In fact, the pyridine molecules play two roles in the perovskite films. On the one hand, due to the different molecular structure, these pyridine molecules present differences in electron-pair-donor abilities (TBP > MP > PY), and then affect the interaction of pyridine molecule with Pb2+ in perovskite. Importantly, with the increase of interaction between different functional groups and Pb2+, the defect passivation effect was enhanced. What’s more, the crystal quality and light harvesting ability of the corresponding perovskite layer are improved by large crystal size and slow growth process. Consequently, PSCs with TBP, MP and PY respectively obtained a power conversion efficiency of 17.03%, 15.49% and 14.34%, which are higher than that of without additive (13.34%). On the other hand, owing to the hydrophobicity of groups, the pyridine molecules can enhance the moisture stability of devices. Significantly, the device based on the TBP-modified perovskite film exhibited improved moisture stability among the four type devices, owing to the best characteristic of the tertiary-butyl group with hydrophobicity in TBP.

A day in the life of a biopharmaceutical senior scientist

Dr Jana Broecker is a senior scientist in the Biochemistry Department at Sosei Heptares in the UK, where she is part of a team that develops small-molecule therapeutics using protein structural information. Jana graduated as a Diploma Engineer from the Technical University Berlin (Germany) and did her PhD with the University of Kaiserslautern on the biophysical quantification of membrane-protein stability. She also completed post-doctoral research at the University of Toronto (Canada), where she spearheaded the optimization of membrane-protein crystallization using polymer-bound lipid nanodiscs and where she also developed a method that avoids crystal harvesting.

Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates.

In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low-cost device is presented that functions as a cover for 96-well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi-crystal screening campaigns.

The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting.

Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100-240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.

Microplates for Crystal Growth and in situ Data Collection at a Synchrotron Beamline

An efficient data collection method is important for microcrystals, because microcrystals are sensitive to radiation damage. Moreover, microcrystals are difficult to harvest and locate owing to refraction effects from the surface of the liquid drop or optically invisible, owing to their small size. Collecting X-ray diffraction data directly from the crystallization devices to completely eliminate the crystal harvesting step is of particular interest. To address these needs, novel microplates combining crystal growth and data collection have been designed for efficient in situ data collection and fully tested at Shanghai Synchrotron Radiation Facility (SSRF) crystallography beamlines. The design of the novel microplates fully adapts the advantage of in situ technology. Thin Kapton membranes were selected to seal the microplate for crystal growth, the crystallization plates can support hanging drop and setting drop vapor diffusion crystallization experiments. Then, the microplate was fixed on a magnetic base and mounted on the goniometer head for in situ data collection. Automatic grid scanning was applied for crystal location with a Blu-Ice data collection system and then in situ data collection was performed. The microcrystals of lysozyme were selected as the testing samples for diffraction data collection using the novel microplates. The results show that this method can achieve comparable data quality to that of the traditional method using the nylon loop. In addition, our method can efficiently and diversely perform data acquisition experiments, and be especially suitable for solving structures of multiple crystals at room temperature or cryogenic temperature.

3D-printed holders for in meso in situ fixed-target serial X-ray crystallography.

The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.

In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source.

The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.

BioStruct-Africa: empowering Africa-based scientists through structural biology knowledge transfer and mentoring - recent advances and future perspectives.

Being able to visualize biology at the molecular level is essential for our understanding of the world. A structural biology approach reveals the molecular basis of disease processes and can guide the design of new drugs as well as aid in the optimization of existing medicines. However, due to the lack of a synchrotron light source, adequate infrastructure, skilled persons and incentives for scientists in addition to limited financial support, the majority of countries across the African continent do not conduct structural biology research. Nevertheless, with technological advances such as robotic protein crystallization and remote data collection capabilities offered by many synchrotron light sources, X-ray crystallography is now potentially accessible to Africa-based scientists. This leap in technology led to the establishment in 2017 of BioStruct-Africa, a non-profit organization (Swedish corporate ID: 802509-6689) whose core aim is capacity building for African students and researchers in the field of structural biology with a focus on prevalent diseases in the African continent. The team is mainly composed of, but not limited to, a group of structural biologists from the African diaspora. The members of BioStruct-Africa have taken up the mantle to serve as a catalyst in order to facilitate the information and technology transfer to those with the greatest desire and need within Africa. BioStruct-Africa achieves this by organizing workshops onsite at our partner universities and institutions based in Africa, followed by post-hoc online mentoring of participants to ensure sustainable capacity building. The workshops provide a theoretical background on protein crystallography, hands-on practical experience in protein crystallization, crystal harvesting and cryo-cooling, live remote data collection on a synchrotron beamline, but most importantly the links to drive further collaboration through research. Capacity building for Africa-based researchers in structural biology is crucial to win the fight against the neglected tropical diseases, e.g. ascariasis, hookworm, trichuriasis, lymphatic filariasis, active trachoma, loiasis, yellow fever, leprosy, rabies, sleeping sickness, onchocerciasis, schistosomiasis, etc., that constitute significant health, social and economic burdens to the continent. BioStruct-Africa aims to build local and national expertise that will have direct benefits for healthcare within the continent.

Miniaturization of the Whole Process of Protein Crystallographic Analysis by a Microfluidic Droplet Robot: From Nanoliter-Scale Purified Proteins to Diffraction-Quality Crystals.

To obtain diffraction-quality crystals is one of the largest barriers to analyze the protein structure using X-ray crystallography. Here we describe a microfluidic droplet robot that enables successful miniaturization of the whole process of crystallization experiments including large-scale initial crystallization screening, crystallization optimization, and crystal harvesting. The combination of the state-of-the-art droplet-based microfluidic technique with the microbatch crystallization mode dramatically reduces the volumes of droplet crystallization reactors to tens nanoliter range, allowing large-scale initial screening of 1536 crystallization conditions and multifactor crystallization condition optimization with extremely low protein consumption, and on-chip harvesting of diffraction-quality crystals directly from the droplet reactors. We applied the droplet robot in miniaturized crystallization experiments of seven soluble proteins and two membrane proteins, and on-chip crystal harvesting of six proteins. The X-ray diffraction data sets of these crystals were collected using synchrotron radiation for analyzing the structures with similar diffraction qualities as conventional crystallization methods.

Using sound pulses to solve the crystal-harvesting bottleneck.

Crystal harvesting has proven to be difficult to automate and remains the rate-limiting step for many structure-determination and high-throughput screening projects. This has resulted in crystals being prepared more rapidly than they can be harvested for X-ray data collection. Fourth-generation synchrotrons will support extraordinarily rapid rates of data acquisition, putting further pressure on the crystal-harvesting bottleneck. Here, a simple solution is reported in which crystals can be acoustically harvested from slightly modified MiTeGen In Situ-1 crystallization plates. This technique uses an acoustic pulse to eject each crystal out of its crystallization well, through a short air column and onto a micro-mesh (improving on previous work, which required separately grown crystals to be transferred before harvesting). Crystals can be individually harvested or can be serially combined with a chemical library such as a fragment library.

In situ serial crystallography for rapid de novo membrane protein structure determination

De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.