skip to main content

Search for: All records

Creators/Authors contains: "Xu, Da"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Free, publicly-accessible full text available April 12, 2024
  2. Free, publicly-accessible full text available December 27, 2023
  3. Free, publicly-accessible full text available December 1, 2023
  4. Billions of years ago, the Earth’s atmosphere had very little oxygen. It was only after some bacteria and early plants evolved to harness energy from sunlight that oxygen began to fill the Earth’s environment. Oxygen is highly reactive and can interfere with enzymes and other molecules that are essential to life. Organisms living at this point in history therefore had to adapt to survive in this new oxygen-rich world. An ancient family of enzymes known as ribonucleotide reductases are used by all free-living organisms and many viruses to repair and replicate their DNA. Because of their essential role in managing DNA, these enzymes have been around on Earth for billions of years. Understanding how they evolved could therefore shed light on how nature adapted to increasing oxygen levels and other environmental changes at the molecular level. One approach to study how proteins evolved is to use computational analysis to construct a phylogenetic tree. This reveals how existing members of a family are related to one another based on the chain of molecules (known as amino acids) that make up each protein. Despite having similar structures and all having the same function, ribonucleotide reductases have remarkably diverse sequences of amino acids. This makes it computationally very demanding to build a phylogenetic tree. To overcome this, Burnim, Spence, Xu et al. created a phylogenetic tree using structural information from a part of the enzyme that is relatively similar in many modern-day ribonucleotide reductases. The final result took seven continuous months on a supercomputer to generate, and includes over 6,000 members of the enzyme family. The phylogenetic tree revealed a new distinct group of ribonucleotide reductases that may explain how one adaptation to increasing levels of oxygen emerged in some family members, while another adaptation emerged in others. The approach used in this work also opens up a new way to study how other highly diverse enzymes and other protein families evolved, potentially revealing new insights about our planet’s past. 
    more » « less
  5. Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known a priori . To address this issue, the REGALS method (regularized alternating least squares) is introduced, which incorporates simple expectations about the data as prior knowledge, and utilizes parameterization and regularization to provide robust deconvolution solutions. The restraints used by REGALS are general properties such as smoothness of profiles and maximum dimensions of species, making it well suited for exploring datasets with unknown species. Here, REGALS is applied to the analysis of experimental data from four types of SAXS experiment: anion-exchange (AEX) coupled SAXS, ligand titration, time-resolved mixing and time-resolved temperature jump. Based on its performance with these challenging datasets, it is anticipated that REGALS will be a valuable addition to the SAXS analysis toolkit and enable new experiments. The software is implemented in both MATLAB and Python and is available freely as an open-source software package. 
    more » « less
  6. Abstract

    Optical transmission and scattering spectroscopic microscopy at the visible and adjacent wavelengths denote one of the most informative and inclusive characterization methods in material research. Unfortunately, restricted by the diffraction limit of light, it cannot resolve the nanoscale variation in light absorption and scattering, diagnostics of the local inhomogeneity in material structure and properties. Moreover, a large quantity of nanomaterials has anisotropic optical properties that are appealing yet hard to characterize through conventional optical methods. There is an increasing demand to extend the optical hyperspectral imaging into the nanometer length scale. In this work, we report a super-resolution hyperspectral imaging technique that uses a nanoscale white light source generated by superfocusing the light from a tungsten-halogen lamp to simultaneously obtain optical transmission and scattering spectroscopic images. A 6-nm spatial resolution in the visible to near-infrared wavelength regime (415–980 nm) is demonstrated on an individual single-walled carbon nanotube (SW-CNT). Both the longitudinal and transverse optical electronic transitions are measured, and the SW-CNT chiral indices can be identified. The band structure modulation in a SW-CNT through strain engineering is mapped.

    more » « less
  7. Abstract Silver nanowires (AgNWs) hold great promise for applications in wearable electronics, flexible solar cells, chemical and biological sensors, photonic/plasmonic circuits, and scanning probe microscopy (SPM) due to their unique plasmonic, mechanical, and electronic properties. However, the lifetime, reliability, and operating conditions of AgNW-based devices are significantly restricted by their poor chemical stability, limiting their commercial potentials. Therefore, it is crucial to create a reliable oxidation barrier on AgNWs that provides long-term chemical stability to various optical, electrical, and mechanical devices while maintaining their high performance. Here we report a room-temperature solution-phase approach to grow an ultra-thin, epitaxial gold coating on AgNWs to effectively shield the Ag surface from environmental oxidation. The Ag@Au core-shell nanowires (Ag@Au NWs) remain stable in air for over six months, under elevated temperature and humidity (80 °C and 100% humidity) for twelve weeks, in physiological buffer solutions for three weeks, and can survive overnight treatment of an oxidative solution (2% H 2 O 2 ). The Ag@Au core-shell NWs demonstrated comparable performance as pristine AgNWs in various electronic, optical, and mechanical devices, such as transparent mesh electrodes, surface-enhanced Raman spectroscopy (SERS) substrates, plasmonic waveguides, plasmonic nanofocusing probes, and high-aspect-ratio, high-resolution atomic force microscopy (AFM) probes. These Au@Ag core-shell NWs offer a universal solution towards chemically-stable AgNW-based devices without compromising material property or device performance. 
    more » « less
  8. null (Ed.)