skip to main content

Explore Research Products in the NSF-PAR

  • NSF Public Access
  • Search Results
  • Annealing‐Induced Changes in the Atomic Structure of Amorphous Silica, Germania, and Tantala Using Accelerated Molecular Dynamics
Title: Annealing‐Induced Changes in the Atomic Structure of Amorphous Silica, Germania, and Tantala Using Accelerated Molecular Dynamics
  more » « less
Award ID(s):
2011706 2011571 1707870 2011770 1707964 2011776
NSF-PAR ID:
10230479
Author(s) / Creator(s):
 ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
physica status solidi (b)
Volume:
258
Issue:
9
ISSN:
0370-1972
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ( , Physical Chemistry Chemical Physics)
    null (Ed.)
    Pulsed electron paramagnetic resonance (EPR) based distance measurements using the recently developed Cu 2+ -DPA label present a promising strategy for measuring DNA backbone distance constraints. Herein we develop force field parameters for Cu 2+ -DPA in order to understand the features of this label at an atomic level. We perform molecular dynamics (MD) simulations using the force field parameters of Cu 2+ -DPA on four different DNA duplexes. The distance between the Cu 2+ centers, extracted from the 2 μs MD trajectories, agrees well with the experimental distance for all the duplexes. Further analyses of the trajectory provide insight into the orientation of the Cu 2+ -DPA inside the duplex that leads to such agreement with experiments. The MD results also illustrate the ability of the Cu 2+ -DPA to report on the DNA backbone distance constraints. Furthermore, measurement of fluctuations of individual residues showed that the flexibility of Cu 2+ -DPA in a DNA depends on the position of the label in the duplex, and a 2 μs MD simulation is not sufficient to fully capture the experimental distribution in some cases. Finally, the MD trajectories were utilized to understand the key aspects of the double electron electron resonance (DEER) results. The lack of orientational selectivity effects of the Cu 2+ -DPA at Q-band frequency is rationalized in terms of fluctuations in the Cu 2+ coordination environment and rotameric fluctuations of the label linker. Overall, a combination of EPR and MD simulations based on the Cu 2+ -DPA labelling strategy can contribute towards understanding changes in DNA backbone conformations during protein–DNA interactions. 
    more » « less
  2. ; ( , Frontiers in Molecular Biosciences)
    null (Ed.)
    Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportunities for Molecular Dynamics (MD) simulations. With the ability to describe the biomolecular dynamics at the atomic level, MD can extend the capabilities of cryo-EM, capturing the conformational variability and predicting biologically relevant short-lived conformational states. Here, we report about the state-of-the-art MD procedures that are currently used to refine, reconstruct and interpret cryo-EM maps. We show the capability of MD to predict short-lived conformational states, finding remarkable confirmation by cryo-EM structures subsequently solved. This has been the case of the CRISPR-Cas9 genome editing machinery, whose catalytically active structure has been predicted through both long-time scale MD and enhanced sampling techniques 2 years earlier than cryo-EM. In summary, this contribution remarks the ability of MD to complement cryo-EM, describing conformational landscapes and relating structural transitions to function, ultimately discerning relevant short-lived conformational states and providing mechanistic knowledge of biological function. 
    more » « less
  3. ; ; ( , The Journal of Physical Chemistry B)
    The abundance and isotopic composition of noble gases dissolved in water have many applications in the geosciences. In recent years, new analytical techniques have opened the door to the use of high-precision measurements of noble gas isotopes as tracers for groundwater hydrology, oceanography, mantle geochemistry, and paleoclimatology. These analytical advances have brought about new measurements of solubility equilibrium isotope effects (SEIEs) in water (i.e., the relative solubilities of noble gas isotopes) and their sensitivities to the temperature and salinity. Here, we carry out a suite of classical molecular dynamics (MD) simulations and employ the theoretical method of quantum correction to estimate SEIEs for comparison with experimental observations. We find that classical MD simulations can accurately predict SEIEs for the isotopes of Ar, Kr, and Xe to order 0.01‰, on the scale of analytical uncertainty. However, MD simulations consistently overpredict the SEIEs of Ne and He by up to 40% of observed values. We carry out sensitivity tests at different temperatures, salinities, and pressures and employ different sets of interatomic potential parameters and water models. For all noble gas isotopes, the TIP4P water model is found to reproduce observed SEIEs more accurately than the SPC/E and TIP4P/ice models. Classical MD simulations also accurately capture the sign and approximate magnitude of temperature and salinity sensitivities of SEIEs for heavy noble gases. We find that experimental and modeled SEIEs generally follow an inverse-square mass dependence, which implies that the mean-square force experienced by a noble gas atom within a solvation shell is similar for all noble gases. This inverse-square mass proportionality is nearly exact for Ar, Kr, and Xe isotopes, but He and Ne exhibit a slightly weaker mass dependence. We hypothesize that the apparent dichotomy between He–Ne and Ar–Kr–Xe SEIEs may result from atomic size differences, whereby the smaller noble gases are more likely to spontaneously fit within cavities of water without breaking water–water H-bonds, thereby experiencing softer collisions during translation within a solvation shell. We further speculate that the overprediction of simulated He and Ne SEIEs may result from the neglection of higher-order quantum corrections or the overly stiff representation of van der Waals repulsion by the widely used Lennard-Jones 6–12 potential model. We suggest that new measurements of SEIEs of heavy and light noble gases may represent a novel set of constraints with which to refine hydrophobic solvation theories and optimize the set of interatomic potential models used in MD simulations of water and noble gases. 
    more » « less
  4. ; ; ; ; ; ( , Composite Interfaces)
    The objective of this paper is to predict the fiber/matrix interfacial debond strength in composites. Atomic force microscopy (AFM) images of the surface topography of a de-sized carbon fiber reveal that there are surface asperities present at various length scales ranging from a nanometer to several microns. These asperities are likely caused by shrinkage of the polyacrylonitrile (PAN) precursor during the graphitization process. In order to bridge the length scales, a Fourier series-decomposition covering a range of asperity wavelengths and amplitudes is necessary to effectively capture the roughness of the fiber surface at different length scales. Further, once a surface asperity profile has been resolved into individual subcomponents using Fourier-decomposition, MD simulations can then be employed to obtain the interfacial shear strength of the subcomponent asperity of a given amplitude and wavelength. Finally, by recombining the peak interfacial shear force obtained from each of these subcomponents into the overall shear force for the fiber surface profile, the length-scale -averaged shear strength can be obtained for any given asperity. The objective of this paper is to use this novel approach to determine the interfacial shear strength of de-sized carbon fiber embedded in an epoxy matrix and compare predicted results with experimental data. 
    more » « less
  5. ; ; ; ; ( , Physical Chemistry Chemical Physics)
    Recently, 2D tellurene (Te) structures have been experimentally synthesized. These structures possess high carrier mobility and stability which make them ideal candidates for applications in electronics, optoelectronics and energy devices. We performed density functional theory (DFT) and molecular dynamics (MD) simulations to investigate the stability and electronic structure of 2D α- and β-Te sheets, and hydrogen, oxygen, and fluorine functionalized counterparts, including spin–orbit coupling effects. Our calculations show that bare α and β-Te sheets are stable with band gaps of 0.44 eV and 1.02 eV respectively. When functionalized, α and β monolayers exhibit metallic properties, except for hydrogenated β-Te, which exhibits semiconducting properties with a band gap of 1.37 eV. We see that H, O and F destabilize the structure of α-Te. We also find that F and H cause β-Te layers to separate into functionalized atomic chains and O causes β-Te to transform into a Te 3 O 2 -like structure. We also studied single atom and molecule binding on the Te surface, the effects of adatom coverage, and the effects of functionalized Te on a GaSe substrate. Our results indicate that tellurene monolayers and functionalized counterparts are not only suitable for future optoelectronic devices, but can be used as metallic contacts in nanoscale junctions. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email