News Article | April 25, 2017
Rust usually indicates neglect; it undermines the structures and tools we rely on every day, from cars to bridges and buildings. But if carefully controlled, the same process that creates rust – metal oxidation – could offer scientists ways to advance state-of-the-art battery or drug delivery technologies. To achieve such control, scientists must first understand exactly how the oxidation process works. With the help of supercomputers and synchrotrons, researchers at the U.S. Department of Energy’s (DOE) Argonne National Laboratory and Temple University are illustrating the process on a finer scale than ever before. In a paper published today in Science, Argonne and Temple University researchers describe the behavior of metal nanoparticles by watching them in real time as they oxidized. By using a combination of X-ray scattering and computational simulation, the researchers were able to observe and model the changes in nanoparticle geometry as they occurred. This knowledge adds to our understanding of fundamental everyday reactions like corrosion, and builds a foundation for developing new techniques to image, manipulate and control such reactions at the atomic scale. “During oxidation of metals, there is a directional flow of material across a solid/gas or solid/liquid interface which can sometimes lead to the formation of holes in the atomic lattice. This process is known as the Kirkendall effect. If well understood, it can be used to design exotic materials at the nanoscale,” said computational scientist Subramanian Sankaranarayanan, one of the principal investigators of the study and a researcher at Argonne’s Center for Nanoscale Materials. In their study, researchers sought to understand the Kirkendall effect in small particles of iron during oxidation at the nanoscale level, specifically in the 10-nanometer range. At this scale, roughly 10,000 times thinner than a sheet of paper, iron nanoparticles exposed to an oxygen environment exhibit a unique property – they form exotic structures, such as hollowed-out nanoparticles or nanoshells, which already have been used as electrodes in battery applications and as vehicles for drug delivery in medicine. The shape, structure and distribution of the holes in these nanoshells depend on how oxidation progresses in time. “What we’ve done, through experimental and theoretical approaches, is build an understanding of the process itself — how these holes form and coalesce,” said co-author Badri Narayanan, an Argonne staff scientist who was a postdoctoral appointee at the time of study. “Without understanding these processes as they naturally occur, you can never hope to control them to produce new materials with exceptional functionality.” The Argonne study was the first time-resolved analysis to use two X-ray scattering techniques to monitor structural evolution during nanoparticle oxidation in 3-D. Small-angle X-ray scattering at the Advanced Photon Source helped characterize the void structures, while wide-angle X-ray scattering provided information on the crystalline structure of the nanoparticles; the combination of the two enabled researchers to experimentally investigate both the metal lattice and pore structure. With these experimental techniques, researchers could see how voids formed at a relatively high spatial resolution, but not one that reached the level of individual atoms. For this insight, researchers turned to the supercomputing resources at the Argonne Leadership Computing Facility. Computer simulations complemented the experimental observations and enabled the researchers to simulate the oxidation of iron nanoparticles atom-by-atom – meaning researchers could visualize the formation and breakage of bonds and track the movement of individual atoms. X-ray experiments and multimillion-atom reactive simulations were performed on exactly the same particle size to facilitate direct comparison of the evolving structure. “We needed the immense computing power of the Argonne Leadership Computing Facility’s 10-petaflop supercomputer, Mira, to perform these large-scale reactive simulations,” said Narayanan. “The simulations provided more detailed insight into the transformation of nanoparticles into nanoshells and the atomic-scale processes that govern their evolution.” The ability to integrate synthesis and experimental methods (X-ray imaging and nanoparticle synthesis and transmission electron microscopy performed at the Center for Nanoscale Materials) with computer modeling and simulation to build new knowledge is among the most valuable aspects of the study, the authors said. “A full 3-D evolution of morphologies of nanoparticles under real reaction conditions with sub-nanometer to atomistic resolution had not been realized until this study,” said Sankaranarayanan. “This truly exemplifies how the sum can be greater than the parts – how theory and imaging together give us information that is better than what can be obtained when these methods are used independently.” The study, titled “Quantitative 3D Evolution of Colloidal Nanoparticle Oxidation in Solution,” is published in Science. Other authors of this study include Yugang Sun, Xiaobing Zuo, Sheng Peng and Ganesh Kamath. The research was supported by Temple University. The work was completed using resources at the Advanced Photon Source, the Center for Nanoscale Materials and the Argonne Leadership Computing Facility, as well as the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory – all DOE Office of Science User Facilities. Computing time at the Argonne Leadership Computing Facility was awarded through the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program and the ASCR Leadership Computing Challenge.
News Article | April 25, 2017
CHICAGO --- An international team of scientists, led by Northwestern University Feinberg School of Medicine, has determined the 3-D atomic structure of more than 1,000 proteins that are potential drug and vaccine targets, to combat some of the world's most dangerous emerging and re-emerging infectious diseases. These experimentally determined structures have been deposited into the World-Wide Protein Data Bank, an archive supported by the National Institutes of Health (NIH), and are freely available to the scientific community. The 3-D structures help expedite drug and vaccine research and advance the understanding of pathogens and organisms causing infectious disease. "Almost 50 percent of the structures that we have deposited in the Protein Data Bank are proteins that were requested by scientific investigators from around the world," said Feinberg's Wayne Anderson, PhD, director of the project. "The NIH has also requested us to work on proteins for potential drug targets or vaccine candidates for many diseases, such as the Ebola virus, the Zika virus and antibiotic-resistant bacteria. We have determined several key structures from these priority organisms and published the results in high-impact journals such as Nature and Cell." This milestone effort, funded by two five-year contracts from the National Institute of Allergy and Infectious Diseases (NIAID), totaling a budget of $57.7 million, represents a decade of work by the Center for Structural Genomics of Infectious Diseases (CSGID) at Feinberg, led by Anderson in partnership with these institutions: Before work begins on a targeted protein, a board appointed by the NIH examines each request. Once approved, the protein must be cloned, expressed and crystallized, and then X-ray diffraction data is collected at the Advanced Photon Source at Argonne National Laboratory. This data defines the location of each of the hundreds or even thousands of atoms to generate 3-D models of the structures that can be analyzed with graphics software. Each institution in the Center has an area of expertise it contributes to the project, working in parallel on many requests at once. Until recently the process of determining the 3-D structure of a protein took many months or even years to complete, but advances in technology, such as the Advanced Photon Source, and upgrades to computational hardware and software has dramatically accelerated the process. The Seattle Structural Genomics Center for Infectious Disease, a similar center funded by NIAID, is also on track to complete 1,000 3-D protein structures soon. Browse all of the structures deposited by the CSGID. Anyone in the scientific community interested in requesting the determination of structures of proteins from pathogens in the NIAID Category A-C priority lists or organisms causing emerging and re-emerging infectious diseases, can submit requests to the Center's web portal. As part of the services offered to the scientific community, the CSGID can also provide expression clones and purified proteins, free of charge. This project has been supported by federal funds from the NIAID, NIH, Department of Health and Human Services, under contract numbers HHSN272200700058C and HHSN272201200026C
News Article | April 17, 2017
We deleted residues from the C termini of the TmoA and TmoE polypeptides, which were disordered in previous crystal structures, by introducing stop codons at codons 492 and 307, respectively. This yielded an enzyme variant that could be rapidly and reproducibly crystallized. We also found that the crystals prepared from this variant could be immersed in neat toluene without the loss of crystal quality and toluene could be trapped in the active site. Q228A T4moH was produced by standard site-specific mutation. All procedures for cloning, protein expression, purification, and catalytic studies have been reported elsewhere12, 13. T4moH was crystallized using the hanging drop method by mixing 1.5 μl of 10 mg ml−1 protein with 1.5 μl of crystallization solution containing 100 mM MOPS/HEPES, pH 7.5, (10× stock obtained by mixing 49% 1 M MOPS with 51% 1 M HEPES), 12% polyethylene glycol (PEG) 4K and 100 mM MgCl . Crystals appeared within two days, and grew to a maximum size of 200 × 100 × 200 μm. Crystals of T4moH were submerged in neat toluene for several seconds to obtain the substrate bound enzyme. The crystals were cryo-protected with Fomblin 2500 and frozen in liquid nitrogen. This preparation yielded the structure PDB 5TDS. Q228A T4moHD was crystallized as reported for PDB 3DHH9 with substitution of 200 mM NH C H O with 200 mM NH Cl. Crystals were transferred to an anaerobic chamber and reduced by incubation in an anaerobic crystallization solution containing 100 mM Bis-Tris, pH 6.0, 16–22% PEG 3350, 200 mM NH Cl, 10 mM sodium dithionite and 1 mM methyl viologen. To obtain the structure of the T4moHD Q228A μ-1,1 superoxo complex (PDB 5TDV), the reduced crystals prepared as above were passed through the anaerobic crystallization solution that lacked sodium dithionite and methyl viologen several times. The washed crystals were removed from the anaerobic chamber and 100% O was slowly bubbled through the crystallization solution. To obtain the T4moHD oxygenated toluene intermediate (PDB 5TDT), T4moH was incubated with saturating toluene before addition of T4moD, and then crystals were obtained as reported above for Q228A T4moHD with the exception of adding 5 μl toluene to the crystallization solution, which is assumed to create a saturated solution. The T4moHD oxygenated toluene intermediate crystals were reduced as described above and were then left under reducing conditions when they were removed from the anaerobic chamber. Then 100% O was slowly bubbled through the crystallization solution until the colour changed from dark blue (indicative of reduced methyl viologen) to colourless, which indicated that the solution had become aerobic. The aerobic crystals were incubated for 5 min, cryo-protected with Fomblin 2500, and frozen in liquid nitrogen. To obtain the structure of the enzyme–product complex (PDB 5TDU), T4moHD was crystallized in an anaerobic chamber. Before crystallization, all solutions including protein and toluene were stored overnight in the anaerobic chamber to remove O . The crystallization buffer was the same as above with the inclusion of 10 mM sodium dithionite, 1 mM methyl viologen, and 5 μl toluene. Prior to mixing the protein and crystallization buffer, the T4moH preparation was incubated with saturating toluene for 10 min, and then T4moD was added to give 140 μM T4moH and 280 μM T4moD. Hanging drops were formed by mixing 1.5 μl of protein solution and 1.5 μl of crystallization buffer. Thick glass cover slips were used to overcome cracking during manipulation in the anaerobic chamber. Crystals reached maximum size after 3–5 days. The reduced crystals were passed through the anaerobic crystallization solution that lacked sodium dithionite and methyl viologen several times. The washed crystals were removed from the anaerobic chamber and 100% O was slowly bubbled through the crystallization solution. The aerobic crystals were incubated for 10 min, cryo-protected with Fomblin 2500, and frozen in liquid nitrogen. Diffraction data were collected at the Life Sciences-Collaborative Access Team (LS-CAT) beamline 21-ID-G at the Advanced Photon Source (Argonne National Laboratory). The data were indexed, integrated and scaled using HKL200037. The structure of the enzyme–substrate complex (PDB 5TDS) was solved by molecular replacement with the CCP4 suite program MolRep38 using one protomer of T4moH 3DHG as the starting model. The structures of the oxygenated toluene intermediate (PDB 5TDT) and the enzyme product complex (PDB 5TDU) were solved by molecular replacement using Phenix.phaser39 and T4moH 3DHH as the starting model. The electron density was fitted and refined in multiple iterations using Phenix.refine and Coot39, 40. Ramachandran and rotamer analyses were performed using MolProbity41. Ramachandran analyses of residues in favoured, allowed, and outlier regions for the enzyme–substrate complex, enzyme–product complex, μ-1,1 O-O Q228A T4moHD and the oxygenated toluene intermediate were as follows: 98/1.8/0.2%; 98/2/0%; 98/2/0%; and 98/2/0%, respectively. Omit maps were created using Phenix.refine with simulated annealing. Figures were prepared using Pymol42. DFT was used to elucidate the electronic structures of several substrate–T4moH complexes; namely, the T4moHD Q228A μ-1,1 O-O adduct, the oxygenated toluene intermediate and the post O–O bond homolysis intermediate. All DFT calculations were performed with ORCA software package version 3.0343 using the B3LYP44, 45 hybrid functional and the polarized split valence (SV(P)) basis46 in conjunction with the SV/C auxiliary basis for all atoms except Fe, for which Ahlrichs’ valence triple-ξ with a polarization function basis set47 was used. Each computational model consisted of the two iron centres, all coordinating amino acid residues, the substrate(s) toluene and O if present, and key solvent molecules identified in the corresponding X-ray crystal structures (PDB 5TDV for the μ-1,1 O–O adduct and 5TDT for the others). All models were subjected to constrained geometry optimizations in which the positions of the Fe atoms and terminal C atoms of truncated amino acid residues were kept fixed so as to account for steric constraints imposed by portions of the protein matrix not explicitly included in our models. Geometry optimizations were performed for the ferromagnetically coupled total spin (S = 5) spin state to impose the desired high-spin electron configurations on the two Fe centres. The ORCA keyword “FlipSpin” was used in subsequent single-point calculations to achieve convergence on the antiferromagnetically coupled spin state (microstate M = 1 for the μ-1,1 O–O adduct and oxygenated toluene intermediate and M = 0 for the post O–O bond homolysis intermediate). The Fe and substrate oxidation states were identified on the basis of the computed spin density distributions and the compositions of the O -, toluene-, and Fe-based frontier molecular orbitals. Plots of the geometry-optimized models, molecular orbitals, and spin density distributions were generated using PyMOL42. Atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession codes 5TDS, 5TDT, 5TDU and 5TDV.
News Article | May 4, 2017
Focused Ion Beam Milling (FIB), a widely used technique that enables scientists to manipulate and study materials at the nano-scale may have dramatic unintended consequences, according to researchers at Oxford University. FIB uses a tiny beam of highly energetic particles to cut and analyse materials smaller than one thousandth of a strand of human hair and has become an essential tool for a number of applications including microscopy, researching high performance alloys for aerospace engineering, nuclear and automotive applications and for prototyping in micro-electronics and micro-fluidics. Whilst the technique was previously understood to cause structural damage within a thin surface layer of the material being cut it was assumed that its effects would not extend beyond this thin damaged layer. However, the Oxford University research, published in Scientific Reports, reveals that FIB can in fact dramatically alter a material’s structural identity. The team studied the damage caused by FIB using a technique called coherent synchrotron X-ray diffraction. This relies on ultra-bright high energy X-rays, available only at central facilities such as the Advanced Photon Source at Argonne National Lab, USA, with whom the Oxford team collaborated. These X-rays were used to probe the 3D structure of materials at the nano-scale and revealed that even very low FIB doses, previously thought negligible, have a dramatic effect. Felix Hofmann, Associate Professor in Oxford’s Department of Engineering Science and lead author on the study, said: “Our research shows that FIB beams have much further-reaching consequences than first thought, and that the structural damage caused is considerable. “It affects the entire sample, fundamentally changing the material. Given the role FIB has come to play in science and technology, there is an urgent need to develop new strategies to properly understand the effects of FIB damage and how it might be controlled.” The team is now looking to build on its work to gain a better understanding of the damage formed and how it might be removed. “We have gone from using the technique blindly, to working out how we can actually see the distortions caused by FIB. Next we can consider approaches to mitigate FIB damage,” said Hofmann. “Importantly the new X-ray techniques that we have developed will allow us to assess how effective these approaches are. From this information we can then start to formulate strategies for actively managing FIB damage.”
News Article | May 3, 2017
No statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. CNT was expressed from a modified pET26 vector containing a pelB leader sequence and an N-terminal PreScission protease cleavable His -maltose-binding-protein tag, as described previously for vcCNT26. Protein was expressed in Escherichia coli C41(DE3) cells for 4 h at 37 °C. SeMet-labelled protein was expressed in E. coli C41(DE3) cells grown in M9 medium supplemented with 100 mg ml−1 lysine, phenylalanine, and threonine; 50 mg ml−1 isoleucine, leucine, and valine; and 60 mg ml−1 SeMet at time of induction31. After expression, SeMet-labelled protein was purified in the same way as non-labelled protein. Cells were lysed by sonication and membrane proteins were extracted from the lysate in 30 mM dodecyl maltoside. The insoluble fraction was removed by centrifugation and CNT was purified from the supernatant by Co2+-affinity chromatography. Protein was digested overnight with PreScission protease. The protein was exchanged to decyl maltoside neopentyl glycol (DMNG) for crystallization and isothermal titration calorimetry experiments or decyl maltoside (DM) for proteoliposome preparation by concentration and subsequent dilution in the new detergent. The sample was applied to a Superdex 200 size-exclusion column pre-equilibrated with 20 mM Tris pH 8, 150 mM NaCl, 2 mM DTT, and 4 mM DM or 0.5 mM DMNG. For crystallization and ITC experiments in the absence of sodium, sodium was removed from the purification in the wash step of affinity chromatography and subsequent buffers contained 150 mM KCl instead of NaCl. For cross-linking experiments, protein was purified in the absence of DTT. The protein was concentrated to ~10 mg ml−1 and mixed with the crystallization solution at a 1:1 ratio in 24-well sitting drop trays. Crystals grew in a wide range of conditions, but crystals grown in the following conditions were used in structure determination. The structure of wild-type CNT was solved from crystals grown in 1 M NaCl, 35% PEG400, pH 9.5; CNT N149L-1 grew in 50 mM Mg(OAc) , 30% PEG400, 100 mM KCl, pH 7.5; CNT N149L-2 grew in 50 mM Mg(OAc) , 30% PEG400, pH 7.5; CNT N149S,F366A crystallized in 50 mM Mg(OAc) , 30% PEG400, pH 7.5; and CNT N149S,E332A crystallized in 200 mM choline chloride, 14% poly(ethylene glycol) monomethyl ether 2000 (PEG MME 2000), pH 6.5. Crystals of SeMet-labelled protein were grown in the following conditions: CNT N149L-3 (purified in presence of 5 mM TCEP and 10 mM DTT in the size-exclusion chromatography buffer) grew in 10 mM Mg(OAc) , 25% PEG400, pH 7.0 (crystals were grown in a wide range of pHs but the best diffracting data were obtained from the crystal grown in pH 7.0); CNT N149L-1 crystallized in 10 mM Mg(OAc) , 25% PEG400, pH 7.5, 3% DMSO; Se marker mutant CNT N149L,L159M in the intermediate 1 conformation crystallized in 75 mM Mg(OAc) , 25% PEG400, pH 7.0, 3% DMSO; Se marker mutant CNT N149L,V328M in the intermediate 1 conformation crystallized in 25 mM Mg(OAc) , 30% PEG400, pH 7.0, 100 mM KCl; and Se marker mutant CNT N149L,V328M in the intermediate 3 conformation crystallized in 25 mM Mg(OAc) , 25% PEG400, pH 7.5, 3% DMSO. Crystals were transferred to a cryo solution containing 35% PEG400 and flash-frozen in liquid nitrogen. Data were collected at the Advanced Photon Source, beamlines 22-ID and 24ID-C. The native data were processed with iMosfilm32, SeMet data of CNT N149L-3 were processed with HKL200033, and the remaining SeMet data were processed with XDS34. Data for CNT N149L-1 were anisotropically truncated to 4.2 Å × 4.2 Å × 4.1 Å using the UCLA Anisotropy Server ( http://services.mbi.ucla.edu/anisoscale/)35. For wild-type CNT , molecular replacement was performed using the vcCNT monomer (PDB ID: 3TIJ) using PHASER36. For molecular replacement of CNT N149L, CNT N149S,F366A, and CNT N149S,E332A, solutions for protomers A and B were found using wild-type CNT as a search model. As for protomer C, transport and scaffold domains were used as separate search models after observing a substantial domain movement. The connecting regions between the domains such as interfacial helices were built manually during refinement. Coot37 and PHENIX38 were used to refine the structures. Refinement of protomers A and B was restrained by non-crystallographic symmetry (NCS) and reference model (wild-type CNT ) until near convergence. Protomer C was refined using secondary structure restraints generated from wild-type CNT . Manual refinement of protomer C was performed initially only by rigid-body fitting of whole domains. The sizes of the rigid bodies were gradually decreased to individual helices as the electron density map improved. Only when the main chain location was accurately determined were the side chain positions refined. To determine the conformation of HP1 in each structure, omit maps were generated and HP1 was rebuilt manually into positive density. Near convergence the NCS and reference model restraints were released. Each structure was analysed using MolProbity39 and further refined to minimize clashes and optimize geometry. The structures were aligned on protomers A and B to visualize and quantify the movement of protomer C. The side chains of certain residues in the interface between the transport and scaffold domain and binding site cavity were not supported by electron density. Therefore, these residues were truncated to the Cβ position in the deposited coordinates. However, to provide a more reliable representation of the interactions, the side chains of these residues, built as the most likely rotamer, were included for the analysis of the interface and binding site. The buried surface area was calculated in PyMOL with a high sampling density (dot_density 3) using the following equation: ((solvent accessible surface area of the transport domain alone) + (solvent accessible surface area of TM3 and TM6)) − (solvent-accessible surface area of the transport domain, TM3, and TM6 together). The binding site cavity was created by selection of cavity-lining residues shown in surface cavity mode in PyMOL40 and clipped for clarity. Anomalous difference Fourier maps of the SeMet-substituted and Se marker mutants were calculated using MR phases of two protomers (A and B), excluding protomer C. Single wavelength anomalous dispersion phases of CNT N149L-3 were calculated using these Se sites from anomalous difference Fourier maps followed by solvent flattening using AutoSol38. DMNG-solubilized CNT protein, purified in the absence or presence of sodium, was concentrated to 25 μM. Uridine (3 mM) was titrated into the protein solution 4 μl at a time using a MicroCal VP-ITC system. For ITC experiments with CNT N149L, 12 mM uridine was titrated 2 μl at a time into an 80-μM protein solution using a MicroCal ITC200 system. The data were fit to a single-site binding isotherm. Protein purified in DM was reconstituted into lipid vesicles as described previously41. Briefly, lipid vesicles were prepared consisting of 10 mg ml−1 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) in a 3:1 POPE:POPG ratio. Protein was reconstituted in the lipid vesicles at a 1:500 protein to lipid mass ratio. The vesicles contained 20 mM HEPES pH 7.4, 200 mM KCl, and 100 mM choline chloride (ChCl). Vesicles were flash-frozen in liquid nitrogen and stored at −80 °C until further use. For flux experiments, vesicles were thawed and frozen three times before extrusion through a 1-μm filter. For flux assay experiments with the cysteine cross-linking mutants, the vesicles were incubated with or without 10 mM DTT at 37 °C for 10 min before extrusion. The vesicles were diluted 20 times into flux assay buffer (20 mM HEPES pH 7.4, 100 mM KCl, and 200 mM ChCl or NaCl). The flux assay was performed with 2 μM radioactively labelled uridine and 1 μM valinomycin at 30 °C for 5 min. Vesicles were harvested on GF/B glass microfibre filters and counted by scintillation. Cross-linking mutants of CNT were prepared in a Cys-less background. The following mutants were cloned by QuikChange mutagenesis: Cys-less mutant CNT C364S, negative control CNT S109C,C364S,A373C, inward-facing cross-linking mutant CNT T243C,C364S,A373C, intermediate cross-linking mutant CNT E240C,C364S,R387C, and outward-facing cross-linking mutant CNT T243C,C364S,K388C. For membrane cross-linking experiments, protein was expressed for 1 h at 37 °C and cells were collected by centrifugation. Cells were lysed by sonication and lysate was spun down twice at 6,660g for 15 min at 4 °C, followed by a high-speed spin (120,000g for 1 h) of the supernatant to pellet the membrane fraction. The membrane was resuspended in assay buffer (20 mM Tris pH 8.0, 150 mM NaCl). The crude membrane was sonicated twice for 1 min each in a water bath sonicator and incubated for 20 min at room temperature with 20 μM copper phenantroline or 10 mM DTT. The cross-linking reaction was quenched by addition of 20 μM N-ethylmaleimide and 50 mM EDTA. Loading buffer with 4% sodium dodecyl sulphate and 4 M urea was added to the samples. The samples were incubated at 60 °C for 10 min before loading onto an SDS–PAGE gel for western blot analysis using an anti-histidine tag primary antibody (Sigma-Aldrich catalogue number H1029; antibody-validation information is available at http://www.sigmaaldrich.com/catalog/product/sigma/h1029?lang=en®ion=US) and an anti-mouse secondary antibody (Licor catalogue number 926-32212; antibody-validation information is available at https://www.licor.com/documents/x8h1udxje8ker0tcaf8q7utpleagu4tv). For gel source data, see Supplementary Fig. 1. For proteoliposome reconstitution, cross-linking mutants were prepared in the same way as liposomes with wild-type protein. The sequence of CNT can be found in the National Center for Biotechnology Information protein database under accession code WP_009116906. Atomic coordinates and structure factors for the reported crystal structures are deposited in the Protein Data Bank under accession codes 5L26 (substrate-bound inward-facing, CNT ), 5L27 (intermediate 1, CNT N149L-1), 5L24 (intermediate 2, CNT N149L-2), 5U9W (intermediate 3, CNT N149L-3), 5L2A (outward-facing, CNT N149S,F366A) and 5L2B (outward-facing, CNT N149S,E332A).
News Article | May 8, 2017
These materials generate electricity whenever mechanical pressure is applied to them, and they've helped shape how we use and interact with technology today. Piezoelectric devices can be found everywhere, from consumer electronics like wearable fitness trackers and smart clothing, to medical devices and motors. Now researchers at the U.S. Department of Energy's (DOE) Argonne National Laboratory have developed a new approach for studying piezoelectric materials by using ultrafast 3-D X-ray imaging and computer modeling. Their integrated approach, reported in Nano Letters, can help us better understand material behavior and engineer more powerful and energy-efficient technologies. "Our approach reveals a wealth of information about the underlying mechanisms that regulate the transfer of energy in such materials, as well as how stable these materials are under extreme conditions," said Argonne computational scientist and co-author Subramanian Sankaranarayanan. "Using experimental data, we make informed models which in turn make predictions at space and time scales that experiments cannot reach," said Mathew Cherukara, the lead author of the study. The researchers applied their new approach to the study of zinc oxide, a material that can generate electricity when twisted, bent or deformed in other ways. With its desirable piezoelectric and semiconducting properties, zinc oxide has emerged as a promising material for generating electricity in small-scale devices. In their experimental approach, known as ultrafast X-ray coherent imaging, researchers took a nanocrystal of zinc oxide and exposed it to intense, short X-ray and optical laser pulses at Argonne's Advanced Photon Source, a DOE Office of Science User Facility. The ultrafast laser pulses excited the crystal, and the X-ray pulses imaged the crystal structure as it changed over time. This enabled researchers to capture very small changes in the material at a high resolution in both time and space. "Unlike an optical microscope, which enables you to see an object but doesn't allow you to see what's happening inside of it, X-ray coherent diffractive imaging lets us see inside materials as they're bending, twisting and deforming, in full 3-D," said Argonne physicist and co-author Ross Harder. This is the first time such a time-resolved study has been performed at a synchrotron source. Researchers identified the deformation modes – meaning new ways in which the material could bend, twist, rotate, etc. – from this experimental approach, and used this insight to build a model that would describe the behavior of the nanocrystal. "By integrating theory and modeling with experiments, we're providing a more complete picture of the material behavior," said Argonne postdoctoral researcher and lead theory author Kiran Sasikumar. "Modeling provides additional insight into the problem – insights that experiments alone cannot probe." With this model, researchers discovered additional twisting modes that can generate 50 percent more electricity than the bending modes of the crystal. "Now we can use this information to create devices that exploit these twisting modes," Cherukara said. "This additional insight generated from the theory demonstrates how experimentation and theory together can enable us to make more accurate and useful predictions." Combining modeling and experimental approaches can also help researchers explore various other material systems and processes, such as corrosion and heat management across thermal devices. Such work will also be advanced with the upgrade of the Advanced Photon Source, which will increase the flux of the facility's high-energy coherent X-ray beams by one hundred fifty-fold, the researchers said. "With this upgrade, we'll be able to apply coherent imaging techniques to a wider class of materials, with less data acquisition time and even higher spatial resolution," said Argonne physicist and co-author Haidan Wen. The study, titled "Ultrafast Three-Dimensional X-ray Imaging of Deformation Modes in ZnO Nanocrystals" was published in Nano Letters. More information: Mathew J. Cherukara et al. Ultrafast Three-Dimensional X-ray Imaging of Deformation Modes in ZnO Nanocrystals, Nano Letters (2017). DOI: 10.1021/acs.nanolett.6b04652
News Article | April 20, 2017
Focused Ion Beam Milling (FIB) uses a tiny beam of highly energetic particles to cut and analyse materials smaller than one thousandth of a stand of human hair. This remarkable capability transformed scientific fields ranging from materials science and engineering to biology and earth sciences. FIB is now an essential tool for a number of applications including; researching high performance alloys for aerospace engineering, nuclear and automotive applications and for prototyping in micro-electronics and micro-fluidics. FIB was previously understood to cause structural damage within a thin surface layer (tens of atoms thick) of the material being cut. Until now it was assumed that the effects of FIB would not extend beyond this thin damaged layer. Ground-breaking new results from the University of Oxford demonstrate that this is not the case, and that FIB can in fact dramatically alter the material's structural identity. This work was carried out in collaboration with colleagues from Argonne National Laboratory, USA, LaTrobe University, Australia, and the Culham Centre for Fusion Energy, UK. In research newly published in the journal Scientific Reports, the team studied the damage caused by FIB using a technique called coherent synchrotron X-ray diffraction. This relies on ultra-bright high energy X-rays, available only at central facilities such as the Advanced Photon Source at Argonne National Lab, USA. These X-rays can probe the 3-D structure of materials at the nano-scale. The results show that even very low FIB doses, previously thought negligible, have a dramatic effect. Felix Hofmann, Associate Professor in Oxford's Department of Engineering Science and lead author on the study, said, "Our research shows that FIB beams have much further-reaching consequences than first thought, and that the structural damage caused is considerable. It affects the entire sample, fundamentally changing the material. Given the role FIB has come to play in science and technology, there is an urgent need to develop new strategies to properly understand the effects of FIB damage and how it might be controlled." Prior to the development of FIB, sample preparation techniques were limited, only allowing sections to be prepared from the material bulk, but not from specific features. FIB transformed this field by making it possible to cut out tiny coupons from specific sites in a material. This progression enabled scientists to examine specific material features using high-resolution electron microscopes. Furthermore it has made mechanical testing of tiny material specimens possible, a necessity for the study of dangerous or extremely precious materials. Although keen for his peers to heed the serious consequence of FIB, Professor Hofmann said, "The scientific community has been aware of this issue for a while now, but no one (myself included) realised the scale of the problem. There is no way we could have known that FIB had such invasive side effects. The technique is integral to our work and has transformed our approach to prototyping and microscopy, completely changing the way we do science. It has become a central part of modern life." Moving forward, the team is keen to develop awareness of FIB damage. Furthermore, they will build on their current work to gain a better understanding of the damage formed and how it might be removed. Professor Hofmann said, "We're learning how to get better. We have gone from using the technique blindly, to working out how we can actually see the distortions caused by FIB. Next we can consider approaches to mitigate FIB damage. Importantly the new X-ray techniques that we have developed will allow us to assess how effective these approaches are. From this information we can then start to formulate strategies for actively managing FIB damage." Explore further: Testing the thermal tolerance of the fusion reactors of the future More information: Felix Hofmann et al. 3D lattice distortions and defect structures in ion-implanted nano-crystals, Scientific Reports (2017). DOI: 10.1038/srep45993
News Article | February 15, 2017
Researchers are taking rough, defective diamonds and using high temperatures to perfect them for quantum sensing WASHINGTON, D.C., February 14, 2017 -- Quantum mechanics, the physics that governs nature at the atomic and subatomic scale, contains a host of new physical phenomena to explore quantum states at the nanoscale. Though tricky, there are ways to exploit these inherently fragile and sensitive systems for quantum sensing. One nascent technology in particular makes use of point defects, or single-atom misplacements, in nanoscale materials, such as diamond nanoparticles, to measure electromagnetic fields, temperature, pressure, frequency and other variables with unprecedented precision and accuracy. Quantum sensing could revolutionize medical diagnostics, enable new drug development, improve the design of electronic devices and more. For use in quantum sensing, the bulk nanodiamond crystal surrounding the point defect must be highly perfect. Any deviation from perfection, such as additional missing atoms, strain in the crystalline lattice of the diamond, or the presence of other impurities, will adversely affect the quantum behavior of the material. Highly perfect nanodiamonds are also quite expensive and difficult to make. A cheaper alternative, say researchers at Argonne National Laboratory and the University of Chicago, is to take defect-ridden, low-quality, commercially manufactured diamonds, and then "heal" them. In a paper published this week in APL Materials, from AIP Publishing, the researchers describe a method to heal diamond nanocrystals under high-temperature conditions, while visualizing the crystals in three dimensions using an X-ray imaging technique. "Quantum sensing is based on the unique properties of certain optically active point defects in semiconductor nanostructures," said F. Joseph Heremans, an Argonne National Laboratory staff scientist and co-author on the paper. These defects, such as the nitrogen-vacancy (NV) centers in diamond, are created when a nitrogen atom replaces a carbon atom adjacent to a vacancy in the diamond lattice structure. They are extremely sensitive to their environment, making them useful probes of local temperatures, as well as electric and magnetic fields, with a spatial resolution more than 100 times smaller than the thickness of a human hair. Because diamonds are biologically inert, quantum sensors based on diamond nanoparticles, which can operate at room temperature and detect several factors simultaneously, could even be placed within living cells, where they could, according to Heremans, "image systems from the inside out." Heremans and his colleagues, including Argonne's Wonsuk Cha and Paul Fuoss, as well as David Awschalom of the University of Chicago, set out to map the distribution of the crystal strain in nanodiamonds and to track the healing of these imperfections by subjecting them to high temperatures, up to 800 degrees Celsius in an inert helium environment. "Our idea of the 'healing' process is that gaps in the lattice are filled as the atoms move around when the crystal is heated to high temperatures, thereby improving the homogeneity of the crystal lattice," said Stephan Hruszkewycz, also a staff scientist at Argonne and lead author on the paper. This nanodiamond healing was monitored with a 3-D microscopy method called Bragg coherent diffraction imaging, performed by subjecting the crystals to a coherent X-ray beam at the Advanced Photon Source at Argonne. The X-ray beam that scatters off the nanodiamonds was detected and used to reconstruct the 3-D shape of the nanocrystal, "and, more importantly, the strain state of the crystal," Hruszkewycz said. The researchers found that nanodiamonds "shrink" during the high-temperature annealing process, and surmise that this occurs because of a phenomenon called graphitization. This phenomenon occurs when the surface of the material is converted from the normal diamond lattice arrangement into graphite, a single layer of chicken-wire-like arranged carbon atoms. The study marks the first time that Bragg coherent diffraction imaging has been shown to be useful at such high temperatures, a capability that, Hruszkewycz said, "enables the exploration of structural changes in important nanocrystalline materials at high temperatures that are difficult to access with other microscopy techniques." Hruszkewycz added that the research represents "a significant step towards developing scalable methods of processing inexpensive, commercial nanodiamonds for quantum sensing and information processing." The article, "In-situ study of annealing-induced strain relaxation in diamond nanoparticles using Bragg coherent diffraction imaging," is authored by Stephan O. Hruszkewycz, Wonsuk Cha, Paolo Andrich, Christopher P. Anderson, Andrew Ulvestad, Ross Harder, Paul Fuoss, David D. Awschalom and F. Joseph P. Heremans. The article appeared in the journal APL Materials Feb. 14, 2017 (DOI: 10.1063/1.49748651) and can be accessed at http://aip. . APL Materials is a new open access journal featuring original research on significant topical issues within the field of functional materials science. See http://aplmaterials. .
News Article | February 15, 2017
About 4.6 billion years ago, an enormous cloud of hydrogen gas and dust collapsed under its own weight, eventually flattening into a disk called the solar nebula. Most of this interstellar material contracted at the disk's center to form the sun, and part of the solar nebula's remaining gas and dust condensed to form the planets and the rest of our solar system. Now scientists from MIT and their colleagues have estimated the lifetime of the solar nebula -- a key stage during which much of the solar system evolution took shape. This new estimate suggests that the gas giants Jupiter and Saturn must have formed within the first 4 million years of the solar system's formation. Furthermore, they must have completed gas-driven migration of their orbital positions by this time. "So much happens right at the beginning of the solar system's history," says Benjamin Weiss, professor of earth, atmospheric, and planetary sciences at MIT. "Of course the planets evolve after that, but the large-scale structure of the solar system was essentially established in the first 4 million years." Weiss and MIT postdoc Huapei Wang, the first author of this study, report their results today in the journal Science. Their co-authors are Brynna Downey, Clement Suavet, and Roger Fu from MIT; Xue-Ning Bai of the Harvard-Smithsonian Center for Astrophysics; Jun Wang and Jiajun Wang of Brookhaven National Laboratory; and Maria Zucolotto of the National Museum in Rio de Janeiro. By studying the magnetic orientations in pristine samples of ancient meteorites that formed 4.563 billion years ago, the team determined that the solar nebula lasted around 3 to 4 million years. This is a more precise figure than previous estimates, which placed the solar nebula's lifetime at somewhere between 1 and 10 million years. The team came to its conclusion after carefully analyzing angrites, which are some of the oldest and most pristine of planetary rocks. Angrites are igneous rocks, many of which are thought to have erupted onto the surface of asteroids very early in the solar system's history and then quickly cooled, freezing their original properties -- including their composition and paleomagnetic signals -- in place. Scientists view angrites as exceptional recorders of the early solar system, particularly as the rocks also contain high amounts of uranium, which they can use to precisely determine their age. "Angrites are really spectacular," Weiss says. "Many of them look like what might be erupting on Hawaii, but they cooled on a very early planetesimal." Weiss and his colleagues analyzed four angrites that fell to Earth at different places and times. "One fell in Argentina, and was discovered when a farm worker was tilling his field," Weiss says. "It looked like an Indian artifact or bowl, and the landowner kept it by this house for about 20 years, until he finally decided to have it analyzed, and it turned out to be a really rare meteorite." The other three meteorites were discovered in Brazil, Antarctica, and the Sahara Desert. All four meteorites were remarkably well-preserved, having undergone no additional heating or major compositional changes since they originally formed. The team obtained samples from all four meteorites. By measuring the ratio of uranium to lead in each sample, previous studies had determined that the three oldest formed around 4.563 billion years ago. The researchers then measured the rocks' remnant magnetization using a precision magnetometer in the MIT Paleomagnetism Laboratory. "Electrons are little compass needles, and if you align a bunch of them in a rock, the rock becomes magnetized," Weiss explains. "Once they're aligned, which can happen when a rock cools in the presence of a magnetic field, then they stay that way. That's what we use as records of ancient magnetic fields." When they placed the angrites in the magnetometer, the researchers observed very little remnant magnetization, indicating there was very little magnetic field present when the angrites formed. The team went a step further and tried to reconstruct the magnetic field that would have produced the rocks' alignments, or lack thereof. To do so, they heated the samples up, then cooled them down again in a laboratory-controlled magnetic field. "We can keep lowering the lab field and can reproduce what's in the sample," Weiss says. "We find only very weak lab fields are allowed, given how little remnant magnetization is in these three angrites." Specifically, the team found that the angrites' remnant magnetization could have been produced by an extremely weak magnetic field of no more than 0.6 microteslas, 4.563 billion years ago, or, about 4 million years after the start of the solar system. In 2014, Weiss' group analyzed other ancient meteorites that formed within the solar system's first 2 to 3 million years, and found evidence of a magnetic field that was about 10-100 times stronger -- about 5-50 microtesla. "It's predicted that once the magnetic field drops by a factor of 10-100 in the inner solar system, which we've now shown, the solar nebula goes away really quickly, within 100,000 years," Weiss says. "So even if the solar nebula hadn't disappeared by 4 million years, it was basically on its way out." The researchers' new estimate is much more precise than previous estimates, which were based on observations of faraway stars. "What's more, the angrites' paleomagnetism constrains the lifetime of our own solar nebula, while astronomical observations obviously measure other faraway solar systems," Wang adds. "Since the solar nebula lifetime critically affects the final positions of Jupiter and Saturn, it also affects the later formation of the Earth, our home, as well as the formation of other terrestrial planets." Now that the scientists have a better idea of how long the solar nebula persisted, they can also narrow in on how giant planets such as Jupiter and Saturn formed. Giant planets are mostly made of gas and ice, and there are two prevailing hypotheses for how all this material came together as a planet. One suggests that giant planets formed from the gravitational collapse of condensing gas, like the sun did. The other suggests they arose in a two-stage process called core accretion, in which bits of material smashed and fused together to form bigger rocky, icy bodies. Once these bodies were massive enough, they could have created a gravitational force that attracted huge amounts of gas to ultimately form a giant planet. According to previous predictions, giant planets that form through gravitational collapse of gas should complete their general formation within 100,000 years. Core accretion, in contrast, is typically thought to take much longer, on the order of 1 to several million years. Weiss says that if the solar nebula was around in the first 4 million years of solar system formation, this would give support to the core accretion scenario, which is generally favored among scientists. "The gas giants must have formed by 4 million years after the formation of the solar system," Weiss says. "Planets were moving all over the place, in and out over large distances, and all this motion is thought to have been driven by gravitational forces from the gas. We're saying all this happened in the first 4 million years." This research was supported, in part, by NASA and a generous gift from Thomas J. Peterson, Jr. Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov. NOTE: This news release was issued on February 9, 2017 by MIT News. Physicist Jun Wang and former postdoc (now scientific associate) Jiajun Wang of the U.S. Department of Energy's (DOE) Brookhaven National Laboratory contributed to the research. Using transmission x-ray microscopy (TXM) nanoimaging, they identified and characterized the chemical composition and the grain size of magnetic particles within ancient igneous meteorites. The analyses provided accurate estimates of the intensities of the early solar system's magnetic fields (as preserved in the meteorites); this information is key to setting the time scale of the evolution of the solar nebula--the cloud of dust and gas particles thought to be behind the development of our solar system--and the formation of planets. The TXM data were collected at Brookhaven's National Synchrotron Light Source (NSLS) and the Advanced Photon Source (APS) at DOE's Argonne National Laboratory through the NSLS-II TXM transition program. The TXM instrument was temporarily relocated to APS in 2015 when NSLS was replaced by NSLS-II. The instrument will remain at APS until its new beamline at NSLS-II is constructed. NSLS-II (and the former NSLS) and APS are DOE Office of Science User Facilities.
News Article | February 15, 2017
Researchers may have developed a cheaper and easier alternative to improving defect-ridden, low-quality, commercially manufactured diamonds by simply heating them up. A team from Argonne National Laboratory in Illinois and the University of Chicago, have devised a method to heal diamond nanocrystals under high-temperature conditions, while visualizing the crystals in three dimensions using an X-ray imaging technique. “Quantum sensing is based on the unique properties of certain optically active point defects in semiconductor nanostructures,” F. Joseph Heremans, an Argonne National Laboratory staff scientist and co-author on the paper, said in a statement. The use of quantum sensing could be a revolutionary in advancing medical diagnostics, enabling new drug development and improving the design of electronic devices. However, for use in quantum sensing, the bulk nanodiamond crystal surrounding the point defect must be basically perfect and any deviation from perfection—which includes missing atoms, strains in the crystalline lattice of the diamond or the presence of other impurities—will negatively affect the quantum behavior of the material. These defects, including the nitrogen-vacancy centers in diamonds, are created when a nitrogen atom replaces a carbon atom adjacent to a vacancy in the diamond lattice structure. They are extremely sensitive to their environment, making them useful probes of local temperatures as well as electric and magnetic fields with a spatial resolution more than 100 times smaller than the thickness of a human hair. While perfection is needed, highly perfect nanodiamonds are currently both expensive and difficult to make. Diamonds are biologically inert, meaning quantum sensors based on diamond nanoparticules—which can operate at room temperature and detect several factors simultaneously—could even be placed within living cells where they could, according to Heremans, "image systems from the inside out." The science team was able to map the distribution of the crystal strain in nanodiamonds and to track the healing of these imperfections by subjecting them to up to 800 degrees Celsius in an inert helium environment. “Our idea of the 'healing' process is that gaps in the lattice are filled as the atoms move around when the crystal is heated to high temperatures, thereby improving the homogeneity of the crystal lattice,” Stephan Hruszkewycz, also a staff scientist at Argonne and lead author on the paper, said in a statement. The research team monitored the nanodiamond healing with a 3D microscopy method caked Bragg coherent diffraction imaging, which is performed by subjecting the crystals to a coherent X-ray beam at the Advanced Photon Source at Argonne. The X-ray beam that scatters off the nanodiamonds was detected and used to reconstruct the 3D shape of the nanocrystal and the strain state of the crystal, according to Hruszkewycz. The experiments showed that nanodiamonds shrunk during the high-temperature annealing process, which is believed to have occurred because of a phenomenon called graphitization, which occurs when the surface of the material is converted from the normal diamond lattice arrangement into graphite, a single layer of chicken-wire-like arranged carbon atoms. According to Hruszkewycz, this marks the first time that Bragg coherent diffraction imaging has been shown to be useful at high temperatures, which enables the exploration of structural changes in important nanocrystalline materials at high temperatures that are difficult to access with other microscopy techniques. Hruszkewycz said the research represents a significant step towards developing scalable methods of processing inexpensive, com