scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

Molecular Dynamics Study of the Interfacial Thermal Conductance at the Graphene/Paraffin Interface in Solid and Liquid Phases

2013 ◽  
Author(s):  
Hasan Babaei ◽  
Pawel Keblinski ◽  
J. M. Khodadadi
Keyword(s):  
Molecular Dynamics ◽  
Solid Phase ◽  
Thermal Conductance ◽  
Md Simulations ◽  
Interfacial Thermal Conductance ◽  
A Value ◽  
Number Of Layers ◽  
Liquid Phases ◽  
Phase Systems ◽  
Parallel Configuration

By utilizing molecular dynamics (MD) simulations, we study the interfacial thermal conductance at the interface of graphene and paraffin. In doing so, we conduct non-equilibrium heat source and sink simulations on systems of parallel and perpendicular configurations in which the heat flow is parallel and perpendicular to the surface of graphene, respectively. For the perpendicular configuration, graphene with different number of layers are considered. The results show that the interfacial thermal conductance decreases with the number of layers and converges to a value which is equal to the obtained conductance by using the parallel configuration. We also study the conductance for the solid phase paraffin. The results indicate that solid paraffin-graphene interfaces have higher conductance values with respect to the corresponding liquid phase systems.

scholarly journals A hierarchical Bayesian framework for force field selection in molecular dynamics simulations

2016 ◽  
Vol 374 (2060) ◽  
pp. 20150032 ◽  
Author(s):  
S. Wu ◽  
P. Angelikopoulos ◽  
C. Papadimitriou ◽  
R. Moser ◽  
P. Koumoutsakos
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Force Field ◽  
Computational Cost ◽  
Md Simulations ◽  
Bayesian Framework ◽  
Underlying Structure ◽  
Hierarchical Bayesian ◽  
Wide Range ◽  
Selection Of

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5853
Author(s):  
Sulejman Skoko ◽  
Matteo Ambrosetti ◽  
Tommaso Giovannini ◽  
Chiara Cappelli
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Force Field ◽  
Absorption Spectra ◽  
Computational Study ◽  
Md Simulations ◽  
Quantum Mechanical ◽  
Hydrogen Bonding Interactions

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

Molecular simulation study on the flexibility in the interpenetrated metal–organic framework LMOF-201 using reactive force field

2020 ◽  
Vol 8 (32) ◽  
pp. 16385-16391
Author(s):  
Ankit Agrawal ◽  
Mayank Agrawal ◽  
Donguk Suh ◽  
Yunsheng Ma ◽  
Ryotaro Matsuda ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Structural Changes ◽  
Metal Organic Framework ◽  
Reactive Force ◽  
Grand Canonical Monte Carlo ◽  
Reactive Force Field ◽  
Metal Organic ◽  
Dynamics Simulations ◽  
Grand Canonical

The guest-induced structural changes in LMOF-201 were demonstrated by using reactive force field combined with Grand Canonical Monte Carlo and molecular dynamics simulations.

Force field development and simulations of senior dialkyl sulfoxides

2016 ◽  
Vol 18 (15) ◽  
pp. 10507-10515 ◽  
Author(s):  
Vitaly V. Chaban
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Md Simulations ◽  
Field Development ◽  
Force Field Development ◽  
Structure And Dynamics ◽  
Ethyl Methyl ◽  
Methyl Sulfoxide ◽  
Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

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