Network Theoretic Approach to Atomistic Material Modeling Using Spectral Sparsification

Network theory is used to formulate an atomistic material network. Spectral sparsification is applied to the network as a method for approximating the interatomic forces. Local molecular forces and the total force balance is quantified when the internal forces are approximated. In particular, we compare spectral sparsification to conventional thresholding (radial cut-off distance) of molecular forces for a Lennard-Jones potential and a Coulomb potential. The spectral sparsification for the Lennard-Jones potential yields comparable results while spectral sparsification of the Coulomb potential outperforms the thresholding approach. The results show promising opportunities which may accelerate molecular simulations containing long-range electrical interactions which are relevant to many multifunctional materials.

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Relativistic Molecular Dynamics Simulations of Laser Ablation Process on the Xenon Solid

Journal of Heat Transfer ◽

10.1115/1.3056607 ◽

2009 ◽

Vol 131 (3) ◽

Cited By ~ 1

Author(s):

Yun-Che Wang ◽

Jing-Wen Chen ◽

Lun-De Liao ◽

Hong-Chang Lin ◽

Chi-Chuan Hwang

Keyword(s):

Molecular Dynamics ◽

Laser Ablation ◽

Special Relativity ◽

Coulomb Potential ◽

Charged Particles ◽

Lennard Jones Potential ◽

Ablation Process ◽

Jones Potential ◽

Lennard Jones ◽

Laser Ablation Process

The phenomena of Coulomb explosion require the consideration of special relativity due to the involvement of high energy electrons or ions. It is known that laser ablation processes at high laser intensities may lead to the Coulomb explosion, and their released energy is in the regime of kEV to MeV. In contrast to conventional molecular dynamics (MD) simulations, we adopt the three-dimensional relativistic molecular dynamics (RMD) method to consider the effects of special relativity in the conventional MD simulation for charged particles in strong electromagnetic fields. Furthermore, we develop a Coulomb force scheme, combined with the Lennard-Jones potential, to calculate interactions between charged particles, and adopt a Verlet list scheme to compute the interactions between each particle. The energy transfer from the laser pulses to the solid surface is not directly simulated. Instead, we directly assign ion charges to the surface atoms that are illuminated by the laser. By introducing the Coulomb potential into the Lennard-Jones potential, we are able to mimic the laser energy being dumped into the xenon (Xe) solid, and track the motion of each Xe atom. In other words, the laser intensity is simulated by using the repulsive forces from the Coulomb potential. Both nonrelativistic and relativistic simulations are performed, and the RMD method provides more realistic results, in particular, when high-intensity laser is used. In addition, it is found that the damage depth does not increase with repeated laser ablation when the pulse frequency is comparable to the duration of the pulse. Furthermore, we report the time evolution of energy propagation in space in the laser ablation process. The temporal-spatial distribution of energy indirectly indicates the temperature evolution on the surface of the Xe solid under intense laser illumination.

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Virial Coefficients of Modified Lennard-Jones Potential

Ukrainian Journal of Physics ◽

10.15407/ujpe59.02.0172 ◽

2014 ◽

Vol 59 (2) ◽

pp. 172-178 ◽

Cited By ~ 10

Author(s):

Ushcats M.V. Ushcats M.V. ◽

Keyword(s):

Virial Coefficients ◽

Lennard Jones Potential ◽

Jones Potential ◽

Lennard Jones

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Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential

International Journal of Molecular Sciences ◽

10.3390/ijms22115914 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5914

Author(s):

Mengsheng Zha ◽

Nan Wang ◽

Chaoyang Zhang ◽

Zheng Wang

Keyword(s):

Single Cell ◽

Loss Function ◽

Gaussian Function ◽

Three Dimensional ◽

Lennard Jones Potential ◽

Jones Potential ◽

Cubic Lattice ◽

Lennard Jones ◽

3D Fish ◽

Well Depth

Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis–Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.

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