skip to main content


Title: Data‐driven reduced‐order model of microtubule mechanics
Abstract

A beam element is constructed for microtubules based upon data reduction of the results from atomistic simulation of the carbon backbone chain of‐tubulin dimers. The database of mechanical responses to various types of loads from atomistic simulation is reduced to dominant modes. The dominant modes are subsequently used to construct the stiffness matrix of a beam element that captures the anisotropic behavior and deformation mode coupling that arises from a microtubule's spiral structure. In contrast to standard Euler–Bernoulli or Timoshenko beam elements, the link between forces and node displacements results not from hypothesized deformation behavior, but directly from the data obtained by molecular scale simulation. Differences between the resulting microtubule data‐driven beam model (MTDDBM) and standard beam elements are presented, with a focus on coupling of bending, stretch, shear deformations. The MTDDBM is just as economical to use as a standard beam element, and allows accurate reconstruction of the mechanical behavior of structures within a cell as exemplified in a simple model of a component element of the mitotic spindle.

 
more » « less
NSF-PAR ID:
10047407
Author(s) / Creator(s):
 ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
Cytoskeleton
Volume:
75
Issue:
2
ISSN:
1949-3584
Page Range / eLocation ID:
p. 45-60
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Phyllosilicate minerals, due to their sheets structure and morphology, are known to cause anisotropy in bulk rock properties and make the bulk rock more compliant. Accurately characterizing the micromechanical behavior of phyllosilicate minerals from laboratory observations, which eventually translates to the bulk rock behavior, is still challenging due to their fine‐grained nature. Recent advances in atomistic simulations open the possibility of theoretically investigating such mineral mechanical behavior. We compare the elastic properties of biotites recovered by spherical nanoindentation with those predicted from density functional theory (DFT) simulations to investigate to what extent theoretical predictions reproduce actual phyllosilicate properties. Spherical nanoindentation was conducted using schist rocks from Poorman Formation, South Dakota, USA, to recover continuous indentation stress‐strain curves. Loading in the layer‐normal orientation shows an average indentation modulus () of about 35 GPa, while loading in the layer‐parallel orientation gives a higher average of about 95 GPa. To facilitate comparison, the elastic stiffness constants (cij) determined from DFT were converted to indentation modulus () using solutions proposed in this study. The majority of the nanoindentation modulus results are below the values inferred from the simulation results representing ideal defect‐free minerals. We suggest that crystal defects present at the nano‐scale, potentially ripplocations, are the dominant cause of the lower indentation modulus recovered from nanoindentation compared to those inferred from DFT simulations. Results highlight the importance of acknowledging the defects that exist down to the nano‐scale as it modifies the mechanical properties of phyllosilicates compared to its pure defect‐free form.

     
    more » « less
  2. Abstract

    We report the Earth's rate of radiogenic heat production and (anti)neutrino luminosity from geologically relevant short‐lived radionuclides (SLR) and long‐lived radionuclides (LLR) using decay constants from the geological community, updated nuclear physics parameters, and calculations of theβspectra. We track the time evolution of the radiogenic power and luminosity of the Earth over the last 4.57 billion years, assuming an absolute abundance for the refractory elements in the silicate Earth and key volatile/refractory element ratios (e.g., Fe/Al, K/U, and Rb/Sr) to set the abundance levels for the moderately volatile elements. The relevant decays for the present‐day heat production in the Earth (19.9 ± 3.0 TW) are from40K,87Rb,147Sm,232Th,235U, and238U. Given element concentrations in kg‐element/kg‐rock and densityρin kg/m3, a simplified equation to calculate the present‐day heat production in a rock isurn:x-wiley:ggge:media:ggge22244:ggge22244-math-0001

    The radiogenic heating rate of Earth‐like material at solar system formation was some 103to 104times greater than present‐day values, largely due to decay of26Al in the silicate fraction, which was the dominant radiogenic heat source for the first10 Ma. Assuming instantaneous Earth formation, the upper bound on radiogenic energy supplied by the most powerful short‐lived radionuclide26Al (t1/2= 0.7 Ma) is 5.5×1031 J, which is comparable (within a factor of a few) to the planet's gravitational binding energy.

     
    more » « less
  3. Abstract

    Sound waves generated by erupting volcanoes can be used to infer important source dynamics, yet acoustic source‐time functions may be distorted during propagation, even at local recording distances (15 km). The resulting uncertainty in source estimates can be reduced by improving constraints on propagation effects. We aim to quantify potential distortions caused by wave steepening during nonlinear propagation, with the aim of improving the accuracy of volcano‐acoustic source predictions. We hypothesize that wave steepening causes spectral energy transfer away from the dominant source frequency. To test this, we apply a previously developed single‐point, frequency domain, quadspectral density‐based nonlinearity indicator to 30 acoustic signals from Vulcanian explosion events at Sakurajima Volcano, Japan, in an 8‐day data set collected by five infrasound stations in 2013 with 2.3‐ to 6.2‐km range. We model these results with a 2‐D axisymmetric finite‐difference method that includes rigid topography, wind, and nonlinear propagation. Simulation results with flat ground indicate that wave steepening causes up to2 dB (1% of source level) of cumulative upward spectral energy transfer for Sakurajima amplitudes. Correction for nonlinear propagation may therefore provide a valuable second‐order improvement in accuracy for source parameter estimates. However, simulations with wind and topography introduce variations in the indicator spectra on order of a few decibels. Nonrandom phase relationships generated during propagation or at the source may be misinterpreted as nonlinear spectral energy transfer. The nonlinearity indicator is therefore best suited to small source‐receiver distances (e.g.,2 km) and volcanoes with simple sources (e.g., gas‐rich strombolian explosions) and topography.

     
    more » « less
  4. Abstract

    Infrasound observations are increasingly used to constrain properties of volcanic eruptions. In order to better interpret infrasound observations, however, there is a need to better understand the relationship between eruption properties and sound generation. Here we perform two‐dimensional computational aeroacoustic simulations where we solve the compressible Navier‐Stokes equations for pure‐air with a large‐eddy simulation approximation. We simulate idealized impulsive volcanic eruptions where the exit velocity is specified and the eruption is pressure‐balanced with the atmosphere. Our nonlinear simulation results are compared with the commonly used analytical linear acoustics model of a compact monopole source radiating acoustic waves isotropically in a half space. The monopole source model matches the simulations for low exit velocities (m/s orwhereis the Mach number); however, the two solutions diverge as the exit velocity increases with the simulations developing lower peak amplitude, more rapid onset, and anisotropic radiation with stronger infrasound signals recorded above the vent than on Earth's surface. Our simulations show that interpreting ground‐based infrasound observations with the monopole source model can result in an underestimation of the erupted volume for eruptions with sonic or supersonic exit velocities. We examine nonlinear effects and show that nonlinear effects during propagation are relatively minor for the parameters considered. Instead, the dominant nonlinear effect is advection by the complex flow structure that develops above the vent. This work demonstrates the need to consider anisotropic radiation patterns and jet dynamics when interpreting infrasound observations, particularly for eruptions with sonic or supersonic exit velocities.

     
    more » « less
  5. Abstract

    The effect of initial texture on cyclic deformation behavior of extruded ZK60 magnesium (Mg) alloy was experimentally investigated under strain‐controlled loading with the strain amplitudes at 4%, 1%, and 0.35%. The testing specimens were taken from extrusion direction (ED), transverse direction (TD), and a material precompressed to 9.4% along the ED (ED−9.4%). At a high strain amplitude of 4%, the cyclic deformation modes of ED and ED−9.4%specimens are similar, and they experience twinning exhaustion → slip and detwinning exhaustion → slip during each loading cycle. At a medium strain amplitude of 1%, twinning‐detwinning is involved in the cyclic deformation, but different deformation mechanisms were observed in the 3 different specimens. Partial twinning‐complete detwinning mode dominates the cyclic deformation in the ED specimen, while partial detwinning‐retwinning mode occurs in the ED−9.4%specimen. For the TD specimen, both basal slip andtension twinning occur during cyclic deformation. At a low strain amplitude of 0.35%, dislocation slips dominate the deformation for the ED specimen with a few observable tension twins. For the ED−9.4%specimen, initially twined texture increases the ductility of the material and enhances fatigue life as compared with the other 2 specimens.

     
    more » « less