scholarly journals A Review on the Application of Molecular Dynamics to the Study of Coalbed Methane Geology

2021 ◽  
Vol 9 ◽  
Author(s):  
Song Yu ◽  
Jiang Bo ◽  
Wei Chongtao ◽  
Dai Xuguang ◽  
Quan Fangkai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Diffusion Coefficients ◽  
Coalbed Methane ◽  
Md Simulation ◽  
Numerical Models ◽  
Positive Trend ◽  
Coal Pyrolysis ◽  
Coal Swelling ◽  
Analytical Approaches

Over the last three decades, molecular dynamics (MD) has been extensively utilized in the field of coalbed methane geology. These uses include but are not limited to 1) adsorption of gaseous molecules onto coal, 2) diffusion of gaseous molecules into coal, 3) gas adsorption-induced coal matrix swelling and shrinkage, and 4) coal pyrolysis and combustion. With the development of computation power, we are entering a period where MD can be widely used for the above higher level applications. Here, the application of MD for coalbed methane study was reviewed. Combining GCMC (grand canonical Monte Carlo) and MD simulation can provide microscopic understanding of the adsorption of gaseous molecules onto coal. The experimental observations face significant challenges when encountering the nanoscale diffusion process due to coal structure heterogeneity. Today, all types of diffusion coefficients, such as self-, corrected-, and transport-diffusion coefficients can be calculated based on MD and the Peng-Robinson equation. To date, the MD simulation for both pure and multi-components has reached a situation of unprecedented success. Meanwhile, the swelling deformation of coal has been attracting an increasing amount of attention both via experimental and mimetic angles, which can be successfully clarified using MD and a poromechanical model incorporating the geothermal gradient law. With the development of computational power and physical examination level, simulation sophistication and improvements in MD, GCMC, and other numerical models will provide more opportunities to go beyond the current informed approach, gaining researcher confidence in the engagement in the estimation of coal-swelling deformation behaviors. These reactive MD works have clarified the feasibility and capability of the reactive force field ReaxFF to describe initial reactive events for coal pyrolysis and combustion. In future, advancing MD simulation (primarily characterized by the ReaxFF force field) will allow the exploration of the more complex reaction process. The reaction mechanism of pyrolysis and spontaneous combustion should also be a positive trend, as well as the potential of MD for both visualization and microscopic mechanisms for more clean utilization processes of coal. Thus, it is expected that the availability of MD will continue to increase and be added to the extensive list of advanced analytical approaches to explore the multi-scaled behaviors in coalbed methane geology.

scholarly journals Molecular Dynamics Simulation of Diffusion Behavior of CH4, CO2, and N2 in Mid-Rank Coal Vitrinite

Energies ◽  
2019 ◽  
Vol 12 (19) ◽  
pp. 3744
Author(s):  
Jing Liu ◽  
Shike Li ◽  
Yang Wang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Coalbed Methane ◽  
Peak Pressure ◽  
The Self ◽  
Dynamics Simulation ◽  
Diffusion Activation Energy ◽  
Gas Concentration ◽  
Diffusion Characteristics ◽  
Diffusion Activation

The diffusion characteristics of CH4, CO2, and N2 in coal are important for the study of CO2-enhanced coalbed methane (CO2-ECBM) recovery, which has become the most potential method for carbon sequestration and natural gas recovery. However, quantitative research on the diffusion characteristics of CH4 and the invasive gases (CO2 and N2) in coal, especially those in micropores, still faces enormous challenges. In this paper, the self-, Maxwell’s, and transport diffusions of CO2, CH4, and N2 in mid-rank coal vitrinite (MRCV) macromolecules were simulated based on the molecular dynamics method. The effects of the gas concentration, temperature, and pressure on the diffusion coefficients were examined via the comparison of various ranks. The results indicated that the diffusion coefficients have the order of D(N2) > D(CO2) > D(CH4) in their saturated adsorption states. However, when MRCV adsorbed the same amounts of CH4, CO2, and N2, the self- and transport diffusion coefficients followed the order of DS(N2) > DS(CO2) > DS(CH4) and Dt(CO2) > Dt(N2) > Dt(CH4), respectively. Independent of the gas species, all these diffusion coefficients decreased with increasing gas concentration and increased with increasing temperature. In the saturated adsorption state, the diffusion activation energies of CH4, CO2, and N2 were ordered as CH4 (27.388 kJ/mol) > CO2 (11.832 kJ/mol) > N2 (10.396 kJ/mol), indicating that the diffusion processes of CO2 and N2 occur more easily than CH4. The increase of temperature was more conducive to the swelling equilibrium of coal. For the pressure dependence, the diffusion coefficients first increased until the peak pressure (3 MPa) and then decreased with increasing pressure. In contrast, the diffusion activation energy first decreased and then increased with increasing pressure, in which the peak pressure was also 3 MPa. The swelling rate changed more obviously in high-pressure conditions.

Effect of w/c ratio and cement content on diffusivity of chloride ion in concrete: A molecular dynamics study

2019 ◽  
Vol 10 (4) ◽  
pp. 83
Author(s):  
Rokonuzzaman Rokon ◽  
Md. Shafiqul Islam ◽  
Nusrat E. Mursalin
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Cement Content ◽  
Chloride Ion ◽  
Simulation Method ◽  
Chloride Induced Corrosion ◽  
Simulation Results ◽  
And Performance

When a reinforced structure is exposed to marine environments, chloride-induced corrosion occurs and it decreases the durability and performance of the structure. The degree of humidity, the presence of cracks, environmental conditions, w/c ratio, and cement content are the influencing factors for chloride ion ingress into concrete. All of them, w/c ratio and cement content are treated as the most crucial factors on diffusion. This paper focus on Molecular Dynamics (MD) simulation method to determine the diffusion coefficient of chloride ion in concrete. The effect of w/c ratio and cement content on the diffusivity of chloride ion is also evaluated. The diffusion coefficients are obtained 2.88x10-12 m2/s, 3.13x10-12 m2/s, and 3.61x10-12 m2/s respectively for different w/c ratio of 0.40, 0.45 and 0.50 with constant cement content. Again the diffusion coefficient are calculated 4.6x10-12 m2/s, 3.13x10-12 m2/s, 2.78x10-12 m2/s respectively for different cement content of 300 kg/m3, 350 kg/m3 and 400 kg/m3 with constant w/c ratio. The simulation results clearly indicate that the diffusion coefficient of chlorine was affected by w/c ratio and cement content significantly.

Molecular Dynamics Study of Contact Line Dynamics of Water Droplets on PTFE Surfaces

2016 ◽  
Author(s):  
Lei Zhao ◽  
Jiangtao Cheng
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Force Field ◽  
Contact Line ◽  
Md Simulation ◽  
Dimensionless Number ◽  
Water Droplets ◽  
Ptfe Surface ◽  
Static Contact ◽  
Wetting Dynamics

Although wetting dynamics of liquids on solid surfaces has been studied for decades, via both experimental investigation and theoretical analyses, the physical mechanism still remains obscure. One of the major difficulties is that wetting dynamics is actually dominated by interfacial reactions at the molecular level. In this study, the dynamic contact angle and contact line deformation of a water droplet on a well-confined amorphous polytetrafluoroethylene (PTFE) surface was examined by molecular dynamics (MD) simulation. The force field parameters of PTFE structures were based on the OPLSAA force field in Gromacs 5.1.2. Our MD simulation yielded a satisfactory glass transition temperature of 118.8°C. A confined-layer method was used to construct a flat PTFE surface by smoothing out the intrusion or extrusion-induced roughness. Four cases for water droplets with different diameters were simulated. The static contact angle of water droplets was found to be ∼110.6° on PTFE. An exponential relationship was verified to describe the contact area development in the wetting process. By comparing our MD results with the hydrodynamics theory and molecular kinetics (MKT) theory, the viscous and molecular friction coefficients were determined to be on the order of 10−4kg/m · s. The MKT theory demonstrates excellent agreement with our MD results in the whole range of contact line velocity, while slight deviation exists in fitting hydrodynamics theory to high contact line velocity region. For the first time, a dimensionless number Nt was proposed to quantify the relative fluctuations of contact line velocity in this study.

Molecular Dynamics Simulation of Gas Transport in Polyisoprene Matrix

2013 ◽  
Vol 844 ◽  
pp. 209-213
Author(s):  
Natthida Rakkapao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Model ◽  
Material Properties ◽  
Diffusion Coefficients ◽  
Potential Application ◽  
Md Simulation ◽  
Gas Transport ◽  
Dynamics Simulation ◽  
Membrane Properties

Molecular Dynamics (MD) simulation was employed to study the diffusivity of biogas in a PI matrix with the aim to verify simulations as a useful tool to predict PI membrane properties for biogas treatment. The simulation model of PI numerical was reliable and accurate in predicting both the material properties and the diffusivity of gases in PI matrix. The diffusion coefficients (D) of the major components in biogas, namely CH4, CO2, H2O, O2, and N2, were computed by simulating trajectories of each gas in PI matrix at 300 K. The simulations gave DCO2 that was 6 times larger than DCH4, and this agrees well with permeabilities reported in the literature. This suggests that PI membranes could be used to treat biogas by separating CO2 and CH4. However, the diffusivities of N2, H2O, and CH4 are closely similar, so PI membranes are not capable of separating these. The potential application of PI membrane to CO2/CH4 separation seems worth further exploration.

scholarly journals Developing a molecular dynamics force field for both folded and disordered protein states

2018 ◽  
Vol 115 (21) ◽  
pp. E4758-E4766 ◽  
Author(s):  
Paul Robustelli ◽  
Stefano Piana ◽  
David E. Shaw
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Md Simulation ◽  
State Of The Art ◽  
Force Fields ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Disordered Protein ◽  
Data Points ◽  
Folded Proteins

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields.

Dopant Clustering and Correlated Oxygen Migration in Conditionally Stabilized Zirconia Electrolytes

2015 ◽  
Vol 12 (2) ◽  
Author(s):  
Steven P. Miller ◽  
Brett I. Dunlap ◽  
Amy S. Fleischer
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Oxygen Diffusion ◽  
Md Simulation ◽  
Cubic Phase ◽  
Correlation Effects ◽  
Stabilized Zirconia ◽  
Oxygen Ions ◽  
Oxygen Migration

Molecular dynamics (MD) simulation of yttria/scandia-stabilized zirconia (SSZ) with variably distributed Y/Sc dopant ions shows that energy is minimized when the dopants are uniformly spread apart, provided that the lattice maintains cubic fluorite symmetry. In contrast, highly clustered dopants are found to destabilize the cubic phase due to the presence of large regions of dopant-free zirconia. Computed oxygen diffusion coefficients and conductivity values consistently show that the Haven ratio is always less than one, indicating that correlation effects influence the motion of oxygen ions and vacancies. In addition, it is seen that the conductivity of crystals with noncubic symmetry is markedly anisotropic.

Translational and rotational dynamics in supercritical methanol from molecular dynamics simulation

2004 ◽  
Vol 76 (1) ◽  
pp. 203-213 ◽  
Author(s):  
Michalis Chalaris ◽  
J. Samios
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Time Correlation ◽  
The Self ◽  
Dynamics Simulation ◽  
Supercritical Methanol ◽  
Reorientational Motion ◽  
Self Diffusion ◽  
Theoretical Predictions

The purpose of this paper is to review our latest molecular dynamics (MD) simulation studies on the temperature and density dependence of the translational and reorientational motion in supercritical (SC) methanol. In the present treatment, Jorgensen's [W. L. Jorgensen. J. Phys. Chem. A102, 8641 (1998)] transferable potential model, tested in a recent MD study of hydrogen bonds in this fluid [M. Chalaris and J. Samios, J. Phys. Chem. B103, 1161 (1999)], was employed to simulate the dynamics of the system. The simulations were performed in the canonical (NVT) ensemble along the isotherms 523, 623, and 723 K and densities corresponding to the pressures from 10 to 30 MPa. Several dynamical properties of the fluid have been obtained and analyzed in terms of appropriate time-correlation functions (CFs). With respect to the translational dynamics, the self-diffusion coefficients obtained have been used to test the applicability of the well-known Chapman-Enskog kinetic theory. We have found that the theoretical predictions for the self-diffusion coefficients are only in qualitative agreement with the MD results over the whole temperature and density range studied. Finally, the inspection of the reorientational CFs and their corresponding correlation times lead to the conclusion that the reorientational motion of the SC methanol molecules in the sample is anisotropic.

Thermophysical Properties of Anti-Parallel β-Sheets with Bombyx mori Silk Nanostructures [Gly-Ser-Gly-Ala-Gly-Ala]n and [Gly-Ala]n

2016 ◽  
Vol 856 ◽  
pp. 70-73
Author(s):  
Baki Aksakal ◽  
Seçkin D. Günay ◽  
Ünsal Akdere ◽  
Tahir Çağın ◽  
Çetin Tasseven
Keyword(s):  
Molecular Dynamics ◽  
Thermal Expansion ◽  
Force Field ◽  
Bombyx Mori ◽  
Thermophysical Properties ◽  
Md Simulation ◽  
Field Method ◽  
Bombyx Mori Silk ◽  
Charmm Force Field ◽  
Β Sheets

Thermal expansion of anti-parallel beta pleated sheets with Bombyx mori silk nanostructures [Gly-Ser-Gly-Ala-Gly-Ala]n and commonly used model of [Gly-Ala]n have been investigated through molecular dynamics (MD) simulation calculations in conjunction with interatomic interactions modeled by CHARMM force field method between the temperature range of 300K-700K. Preliminary results indicate significant differences on thermal expansion of two structures that was observed on directions of chain and the direction perpendicular to plates.

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