ACTION-DERIVED AB INITIO MOLECULAR DYNAMICS

2009 ◽  
Vol 01 (03) ◽  
pp. 469-482 ◽  
Author(s):  
S. JUN ◽  
S. PENDURTI ◽  
I.-H. LEE ◽  
S. Y. KIM ◽  
H. S. PARK ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Energy Surface ◽  
Atomic System ◽  
Minimum Energy ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Least Action Principle ◽  
Least Action ◽  
Long Time

Action-derived molecular dynamics (ADMD) is a numerical method to search for minimum-energy dynamic pathways on the potential-energy surface of an atomic system. The method is based on Hamilton's least-action principle and has been developed for problems of activated processes, rare events, and long-time simulations. In this paper, ADMD is further extended to incorporate ab initio total-energy calculations, which enables the detailed electronic analysis of transition states as well as the exploration of energy landscapes. Three numerical examples are solved to demonstrate the capability of this action-derived ab initio molecular dynamics (MD). The proposed approach is expected to circumvent the severe time-scale limitation of conventional ab intio MD simulations.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

Energetics and diffusion of liquid water and hydrated ions through nanopores in graphene: ab initio molecular dynamics simulation

2017 ◽  
Vol 19 (31) ◽  
pp. 20551-20558 ◽  
Author(s):  
Raúl Guerrero-Avilés ◽  
Walter Orellana
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Functional Theory ◽  
Hydrated Ions ◽  
And Diffusion

The energetics and diffusion of water molecules and hydrated ions (Na+, Cl−) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations.

scholarly journals Exploring the free energy surface using ab initio molecular dynamics

2016 ◽  
Vol 144 (16) ◽  
pp. 164101 ◽  
Author(s):  
Amit Samanta ◽  
Miguel A. Morales ◽  
Eric Schwegler
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Energy Surface ◽  
Ab Initio Molecular Dynamics ◽  
Free Energy Surface

scholarly journals Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

2019 ◽  
Vol 3 (4) ◽  
pp. 24
Author(s):  
Marie-Anne Hervé du Penhoat ◽  
Anis Hamila ◽  
Marie-Pierre Gaigeot ◽  
Rodolphe Vuilleumier ◽  
Kentaro Fujii ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
X Rays ◽  
Auger Decay ◽  
Hydration Layer ◽  
The Core ◽  
Dynamics Simulations

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

scholarly journals The Effect of Hydrogen on the Stress-Strain Response in Fe3Al: An ab initio Molecular-Dynamics Study

Materials ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4155
Author(s):  
Petr Šesták ◽  
Martin Friák ◽  
Mojmír Šob
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Intrinsic Property ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Uniaxial Deformation ◽  
Ambient Conditions ◽  
Hydrogen Atoms ◽  
Octahedral Sites

We performed a quantum-mechanical molecular-dynamics (MD) study of Fe3Al with and without hydrogen atoms under conditions of uniaxial deformation up to the point of fracture. Addressing a long-lasting problem of hydrogen-induced brittleness of iron-aluminides under ambient conditions, we performed our density-functional-theory (DFT) MD simulations for T = 300 K (room temperature). Our MD calculations include a series of H concentrations ranging from 0.23 to 4 at. % of H and show a clear preference of H atoms for tetrahedral-like interstitial positions within the D03 lattice of Fe3Al. In order to shed more light on these findings, we performed a series of static lattice-simulations with the H atoms located in different interstitial sites. The H atoms in two different types of octahedral sites (coordinated by either one Al and five Fe atoms or two Al and four Fe atoms) represent energy maxima.Our structural relaxation of the H atoms in the octahedral sites lead to minimization of the energy when the H atom moved away from this interstitial site into a tetrahedral-like position with four nearest neighbors representing an energy minimum. Our ab initio MD simulations of uniaxial deformation along the ⟨001⟩ crystallographic direction up to the point of fracture reveal that the hydrogen atoms are located at the newly-formed surfaces of fracture planes even for the lowest computed H concentrations. The maximum strain associated with the fracture is then lower than that of H-free Fe3Al. We thus show that the hydrogen-related fracture initiation in Fe3Al in the case of an elastic type of deformation as an intrinsic property which is active even if all other plasticity mechanism are absent. The newly created fracture surfaces are partly non-planar (not atomically flat) due to thermal motion and, in particular, the H atoms creating locally different environments.

scholarly journals Combined ReaxFF and Ab Initio MD Simulations of Brown Coal Oxidation and Coal–Water Interactions

Entropy ◽  
2021 ◽  
Vol 24 (1) ◽  
pp. 71
Author(s):  
Shi Yu ◽  
Ruizhi Chu ◽  
Xiao Li ◽  
Guoguang Wu ◽  
Xianliang Meng
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Brown Coal ◽  
Water Adsorption ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Coal Oxidation ◽  
Simulation Results

In this manuscript, we use a combination of Car–Parrinello molecular dynamics (CPMD) and ReaxFF reactive molecular dynamics (ReaxFF-MD) simulations to study the brown coal–water interactions and coal oxidation. Our Car–Parrinello molecular dynamics simulation results reveal that hydrogen bonds dominate the water adsorption process, and oxygen-containing functional groups such as carboxyl play an important role in the interaction between brown coal and water. The discrepancy in hydrogen bonds formation between our simulation results by ab initio molecular dynamics (CPMD) and that by ReaxFF-MD indicates that the ReaxFF force field is not capable of accurately describing the diffusive behaviors of water on lignite at low temperatures. The oxidations of brown coal for both fuel rich and fuel lean conditions at various temperatures were investigated using ReaxFF-MD simulations through which the generation rates of major products were obtained. In addition, it was observed that the density decrease significantly enhances the generation of gaseous products due to the entropy gain by reducing system density. Although the ReaxFF-MD simulation of complete coal combustion process is limited to high temperatures, the combined CPMD and ReaxFF-MD simulations allow us to examine the correlation between water adsorption on brown coal and the initial stage of coal oxidation.

Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: an ab initio molecular dynamics study

2015 ◽  
Vol 17 (17) ◽  
pp. 11615-11626 ◽  
Author(s):  
Philippe Carbonniere ◽  
Claude Pouchan ◽  
Roberto Improta
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Ab Initio ◽  
Gas Phase ◽  
Ground State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
State Decay ◽  
State Recovery

MD simulations provide the first atomistic insights into the IVR processes of photoexcited uracil soon after ground state recovery.

scholarly journals CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

Geofluids ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Yuan Mei ◽  
Weihua Liu ◽  
A. A. Migdiov ◽  
Joël Brugger ◽  
A. E. Williams-Jones
Keyword(s):  
Molecular Dynamics ◽  
Water Molecule ◽  
Ab Initio ◽  
Hydration Number ◽  
Hydration Shell ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Low Density ◽  
Fluid Density ◽  
Hydration Numbers

We investigated the hydration of the CuCl0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H2O-Cu-Cl]0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm3 (fH2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.

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