scholarly journals Hybrid Plasma/Molecular-Dynamics Approach for Efficient XFEL Radiation Damage Simulations

Crystals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 478 ◽  
Author(s):  
Alexander Kozlov ◽  
Andrew V. Martin ◽  
Harry M. Quiney

X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb forces. The accurate simulation of these dynamical effects is critical in designing feasible XFEL experiments and interpreting the results. Current molecular dynamics simulations are, however, computationally intensive, particularly when they treat unbound electrons as classical point particles. On the other hand, plasma simulations are computationally efficient but do not model atomic motion. Here we present a hybrid approach to XFEL damage simulation that combines molecular dynamics for the nuclear motion and plasma models to describe the evolution of the low-energy electron continuum. The plasma properties of the unbound electron gas are used to define modified inter-ionic potentials for the molecular dynamics, including Debye screening and drag forces. The hybrid approach is significantly faster than damage simulations that treat unbound electrons as classical particles, enabling simulations to be performed on large sample volumes.

CrystEngComm ◽  
2016 ◽  
Vol 18 (38) ◽  
pp. 7297-7304 ◽  
Author(s):  
Linjun Wang ◽  
David Beljonne

We report on a first-principle theoretical investigation of the optical absorption and emission spectra of poly(3-hexylthiophene) (P3HT) aggregates by means of a multiscale all-atom hybrid approach, which combines molecular dynamics simulations, quantum-chemical calculations, and solving of a Frenkel–Holstein model.


2020 ◽  
Vol 8 (43) ◽  
pp. 15436-15449
Author(s):  
Julia E. Medvedeva ◽  
Bishal Bhattarai

Microscopic mechanisms of the formation of H defects and their role in passivation of under-coordinated atoms, short- and long-range structural transformations, and the resulting electronic properties of amorphous In–Ga–O with In : Ga = 6 : 4 are investigated using computationally-intensive ab initio molecular dynamics simulations and accurate density-functional calculations.


Author(s):  
Sumith Yd ◽  
Shalabh C. Maroo

It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating the time evolution of contact angle. This is a tedious effort to do manually or with image processing algorithms. In this work we propose a new algorithm to estimate contact angle from MD simulations directly and in a computationally efficient way. This algorithm segregates the droplet molecules from the vapor molecules using Mahalanobis distance (MND) technique. Then the density is smeared onto a 2D grid using 4th order B-spline interpolation function. The vapor liquid interface data is estimated from the grid using density filtering. With the interface data a circle is fitted using Landau method. The equation of this circle is solved for obtaining the contact angle. This procedure is repeated by rotating the droplet about the vertical axis. We have applied this algorithm to a number of studies (different potentials and thermostat methods) which involves the MD simulation of water.


2020 ◽  
Vol 20 (6) ◽  
pp. 201-212
Author(s):  
Bojana Koteska ◽  
Anastas Mishev ◽  
Ljupco Pejov

AbstractCombining a computationally efficient and affordable molecular dynamics approach, based on atom-centered density matrix propagation scheme, with the density functional tight binding semiempirical quantum mechanics, we study the vibrational dynamics of a single molecule at series of finite temperatures, spanning quite wide range. Data generated by molecular dynamics simulations are further analyzed and processed using time series analytic methods, based on correlation functions formalism, leading to both vibrational density of states spectra and infrared absorption spectra at finite temperatures. The temperature-induced dynamics in structural intramolecular parameters is correlated to the observed changes in the spectral regions relevant to molecular detection. In particular, we consider a case when an intramolecular X-H stretching vibrational states are notably dependent on the intramolecular torsional degree of freedom, the dynamics of which is, on the other hand, strongly temperature-dependent.


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