On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives
Abstract
:1. Introduction
1.1. Molecular Dynamics and Associated Force Fields
- Simulating the motions of particles (atoms, molecules, granules, etc.) via a classical approach;
1.2. Molecular Dynamics Ensembles
- Total number of atoms (N);
- Volume (V);
- Temperature (T);
- Pressure (P);
- Total energy (E).
- The Microcanonical ensemble or the NVE set up. Here, the particle number (N), volume (V) and total energy (E) (sum of Kinetic and Potential Energies) are constant, and Temperature (T) and Pressure (P) are unregulated.
- The Canonical ensemble or the NVT set up. Here, N, V are constant, T is regulated by a thermostat and P is unregulated.
- The Isothermal-Isobaric ensemble or the NPT set up. This is similar to NVT except that P is regulated while V and E are the observables to be calculated.
- Stochastic Langevin thermostat;
- Andersen thermostat;
- Isokinetic/Gaussian thermostat;
- Berendsen thermostat;
- Nose-Hoover thermostat.
- Berendsen barostat;
- Parrinello–Rahman barostat.
1.3. Lignocellulosics: Structure, Compostion and Uses
- Production of polyhydroxyalkanoates (PHA) through lignocellulosic vaporization. These PHAs then find applications in packaging, medical implant and drug delivery sectors.
- Energy recovery through biogas generation.
- Biodiesel production.
- Sustainable chemicals and polymers synthesis including bioethanol and biobutanol production.
- Pulp and paper making.
2. Molecular Dynamics Simulations of Lignocellulosics
2.1. Validations of Subtle Structural Characteristics and Attempts in Upscaling MD Simulations of Lignocellulosics
- The first attempts at lignocellulosic MD simulations, the various force fields that have been tried for this purpose and the validation methodologies used.
- The types of structural/molecular characteristics of lignocellulosics that were uncovered using MD and the insights gained thereof.
- Scales of the various initial simulations in terms of number of atoms, structural complexity and upscaling using high performance parallel computing systems.
2.2. Mechanical Behavior Prediction of Lignocelluloics Using MD
2.2.1. Cellulosics
2.2.2. Lignins
2.2.3. Combined Lignocellulosic and Lignin Carbohydrate Complexes
3. Conclusions
- Using a parameterized force field that can accurately recreate the inter and intra molecular interactions in the built MD system. These so-called parameterized force fields can be validated using physical properties such as density and crystalline unit cell parameters and compared with experimentally obtained properties of model compounds.
- The use of massive systems comprised of typically several million atoms effectively simulating all the atoms represented in the real-life structures.
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Cell Dimension | Experimental Data from X-ray Structural Analysis | MD Data from Ganster and Blackwell [22] |
---|---|---|
a (Å) | 8.01 | 7.80 |
b (Å) | 9.04 | 9.31 |
c (Å) | 10.36 | 10.74 |
α (°) | 90 | 90 |
β (°) | 90 | 90 |
γ (°) | 117.1 | 116.6 |
Density (g/cm3) | 1.61 | 1.54 |
Cell Dimension | Experimental Data | MD Data from Petridis and Smith [23] |
---|---|---|
a (Å) | 8.69 | 8.73 ± 0.02 |
b (Å) | 8.90 | 8.93 ± 0.01 |
c (Å) | 13.11 | 13.68 ± 0.03 |
α (°) | 73.85 | 74.48 ± 0.05 |
β (°) | 86.15 | 86.30 ± 0.01 |
γ (°) | 83.06 | 83.06 ± 0.02 |
Cell volume (cubic Å) | 966 | 1020 |
Strain Rate | 10−4/ps | 10−3/ps | 10−2/ps | ||||||
---|---|---|---|---|---|---|---|---|---|
Deformation Direction | X | Y | Z | X | Y | Z | X | Y | Z |
Elastic Modulus (GPa) | 21.6 | 7.6 | 107.8 | 22.7 | 7.1 | 113.5 | 24.4 | 6.5 | 112.9 |
Yield Stress (GPa) | 0.3 | 0.2 | 4.6 | 0.4 | 0.3 | 5.4 | 0.6 | 0.4 | 6.6 |
Yield Strain (%) | 1.3 | 2.3 | 4.3 | 1.8 | 4.1 | 4.9 | 2.5 | 5.9 | 5.9 |
Ultimate Stress (GPa) | 0.4 | 0.3 | 5.4 | 0.7 | 0.4 | 6.0 | 0.9 | 0.5 | 7.2 |
Ultimate Strain (%) | 3.0 | 7.5 | 5.1 | 4.6 | 9.4 | 5.4 | 6.2 | 11.3 | 6.7 |
System | Simulated Density (g/cm3) | Experimental Density (g/cm3) | Simulated Glass Transition Temperature- Tg (°C) | Experimental Glass Transition Temperature- Tg (°C) | Simulated Young’s Modulus (GPa) | Experimental Young’s Modulus through Nanoindentation (GPa) |
---|---|---|---|---|---|---|
Lignin | 1.26 ± 0.02 | 1.33 | 140.26 | 97–171 | 5.90 ± 0.37 | 2–6.7 |
Property | Value for Simulated LCC [62] |
---|---|
Simulated density (g/cm3) | 1.34 ± 0.02 |
Simulated glass transition temperature- Tg (°C) | 166.11 |
Simulated Young’s Modulus (GPa) | 6.93 ± 0.31 |
Property | Microfibril | S2 | ||||
---|---|---|---|---|---|---|
x | y | z | x | y | z | |
Young’s Modulus (dry, GPa) | 5.01 | 5.21 | 76.80 | 1.42 | 1.61 | 58.70 |
Young’s Modulus (saturated, GPa) | 0.86 | 0.99 | 61.80 | 0.36 | 0.27 | 44.70 |
Shear Modulus (dry, GPa) | 1.85 | 4.74 | 4.31 | 0.63 | 1.34 | 0.88 |
Shear Modulus (saturated, GPa) | 0.31 | 1.85 | 0.98 | 0.01 | 0.17 | 0.01 |
Dry density (g/cm3) | 1.352 | 1.342 |
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Prasad, K.; Nikzad, M.; Nisha, S.S.; Sbarski, I. On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives. J. Compos. Sci. 2021, 5, 55. https://doi.org/10.3390/jcs5020055
Prasad K, Nikzad M, Nisha SS, Sbarski I. On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives. Journal of Composites Science. 2021; 5(2):55. https://doi.org/10.3390/jcs5020055
Chicago/Turabian StylePrasad, Krishnamurthy, Mostafa Nikzad, Shammi Sultana Nisha, and Igor Sbarski. 2021. "On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives" Journal of Composites Science 5, no. 2: 55. https://doi.org/10.3390/jcs5020055
APA StylePrasad, K., Nikzad, M., Nisha, S. S., & Sbarski, I. (2021). On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives. Journal of Composites Science, 5(2), 55. https://doi.org/10.3390/jcs5020055