Collaboratory for Advanced Computing and Simulations

Los Angeles, CA, United States

Collaboratory for Advanced Computing and Simulations

Los Angeles, CA, United States

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Ngo V.A.,University of Southern California | Kalia R.K.,Collaboratory for Advanced Computing and Simulations | Kalia R.K.,University of Southern California | Nakano A.,Collaboratory for Advanced Computing and Simulations | And 2 more authors.
Journal of Physical Chemistry C | Year: 2012

We use million-atom molecular dynamics simulations to study body-centered cubic (BCCS) and face-centered cubic (FCCS) supercrystals of DNA-functionalized gold nanoparticles, which are solvated with water and neutralized with sodium ions. The two supercrystals contain 2.77 and 5.05 million atoms. Having large numbers of DNAs and hexanethiols attached to 3 nm diameter gold nanoparticles, we observe smooth changes of the averaged DNA structures over the simulation time. We find that, after 10 ns, the DNA structures are different from the canonical B-DNA structures in terms of root-mean-square deviations, base-base stacking structures, and hydrogen bonds. We also examine ion distributions around DNAs and estimate the melting temperature increases for the supercrystals from the ion distributions, which are ΔT BCCS = 12.9 K and ΔT FCCS = 8.0 K. The radial distribution functions for the correlation between ions and DNA show that ions bind stronger in BCCS than FCCS. This correlation explains the higher melting temperature increase in BCCS and supports that there are more entropic effects in FCCS than in BCCS. We also report the Young's and bulk moduli of the supercrystals, which resemble those of water. The Possion ratios for both supercrystals (∼0.39) are close to the ideal value (=1/3). © 2012 American Chemical Society.


Rountree C.L.,CEA Saclay Nuclear Research Center | Rountree C.L.,Louisiana State University | Rountree C.L.,Collaboratory for Advanced Computing and Simulations | Bonamy D.,CEA Saclay Nuclear Research Center | And 7 more authors.
Physics and Chemistry of Glasses: European Journal of Glass Science and Technology Part B | Year: 2010

Through a joint molecular dynamics (MD) simulation of dynamic fracture and atomic force microscopy (AFM) study of stress corrosion fracture, we provide evidence for a unified scenario of damage spreading in pure amorphous silica (a-SiO2). Over the whole range of velocities, the crack progresses through the growth and coalescence of nanoscale damage cavities. The cavitation process is shown to set the process zone size. Both cavity size and the process zone size variations with respect to crack velocity are presented and discussed.


Wu Z.,Collaboratory for Advanced Computing and Simulations | Wu Z.,University of Southern California | Wu Z.,Anhui University of Science and Technology | Mou W.,Collaboratory for Advanced Computing and Simulations | And 7 more authors.
International Journal of Energetic Materials and Chemical Propulsion | Year: 2015

Vibrational and thermodynamic properties of TATB have been investigated within the quasiharmonic approximation and density functional theory using three exchange-correlation functionals: local density approximation (LDA), generalized gradient approximation (GGA), and GGA with an empirical van der Waals correction (GGA + vdW). We find that GGA provides a reasonable description of only the heat capacity and thermal expansion, while it fails to reproduce the experimental bulk modulus and volume. Van der Waals correction improves the lattice constants, volume, and bulk modulus, but it fails badly in describing thermal expansion and heat capacity. In contrast, LDA accurately describes all the thermodynamic properties of TATB considered here. For example, the equilibrium volume calculated with LDA is only 4.6% smaller than the experimental value after including vi-brational contributions. It is therefore essential to include phonon contributions when comparing the calculated volume with experimental data at ambient conditions. We show that an accurate equation of state of TATB is obtained by simply multiplying the volume calculated with LDA by a factor of 1.046, because LDA predicts the bulk modulus well in the entire pressure range. Therefore, LDA is a satisfactory exchange-correlation functional for TATB because only LDA correctly predicts the volume dependence ofvibrational frequencies. All calculations exhibit an abrupt change of the compressibility at a critical pressure, Pc ~ 0.5-1.0 GPa. Below Pc, the volume reduction by pressure is mainly due to the lattice contraction along the c axis, whereas above Pc the lattice contracts significantly along all three axes. © 2015 by Begell House, Inc.

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