scholarly journals On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives

2021 ◽  
Vol 5 (2) ◽  
pp. 55
Author(s):  
Krishnamurthy Prasad ◽  
Mostafa Nikzad ◽  
Shammi Sultana Nisha ◽  
Igor Sbarski
Keyword(s):  
Molecular Dynamics ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Md Simulations ◽  
Thermomechanical Properties ◽  
Current State ◽  
Physico Chemical ◽  
Carbohydrate Complex ◽  
Dynamics Simulations

The use of Molecular Dynamics (MD) simulations for predicting subtle structural, thermomechanical and related characteristics of lignocellulosic systems is studied. A historical perspective and the current state of the art are discussed. The use of parameterised MD force fields, scaling up simulations via high performance computing and intrinsic molecular mechanisms influencing the mechanical, thermal and chemical characteristics of lignocellulosic systems and how these can be predicted and modelled using MD is shown. Individual discussions on the MD simulations of the lignin, cellulose, lignin-carbohydrate complex (LCC) and how MD can elucidate the role of water on the surface and microstructural characteristics of these lignocellulosic systems is shown. In addition, the use of MD for unearthing molecular mechanisms behind lignin-enzyme interactions during precipitation processes and the deforming/structure weakening brought about by cellulosic interactions in some lignocellulosic systems is both predicted and quantified. MD results from relatively smaller systems comprised of several hundred to a few thousand atoms and massive multi-million atom systems are both discussed. The versatility and effectiveness of MD based on its ability to provide viable predictions from both smaller and massive starting systems is presented in detail.

Molecular Dynamics simulations of displacement cascades: role of the interatomic potentials and of the potential hardening

2000 ◽  
Vol 650 ◽  
Author(s):  
C.S. Becquart ◽  
C. Domain ◽  
A. Legris ◽  
J.C. van Duysen
Keyword(s):  
Molecular Dynamics ◽  
Thermal Characteristics ◽  
Md Simulations ◽  
Interatomic Potentials ◽  
Static Properties ◽  
Displacement Cascades ◽  
Energy Transfers ◽  
Primary Damage ◽  
Dynamics Simulations

ABSTRACTThe role of the interatomic potentials on the primary damage has been investigated by Molecular Dynamics (MD) simulations of displacement cascades with three different interatomic potentials dedicated to α-Fe. The primary damage, caused by the neutron interaction with the matter, has been found to be potential sensitive. We have investigated the equilibrium parts of the potential as well as the “short distance interactions” which appear to have a strong influence on the cascade morphology and defects distribution at the end of the cascade. The static properties as well as dynamical (thermal) characteristics of the potentials have been considered; the kinetic and potential energy transfers during the collisions have also been studied.

scholarly journals Three-dimensional structure of Megabalanus rosa Cement Protein 20 revealed by multi-dimensional NMR and molecular dynamics simulations

2019 ◽  
Vol 374 (1784) ◽  
pp. 20190198 ◽  
Author(s):  
Harini Mohanram ◽  
Akshita Kumar ◽  
Chandra S. Verma ◽  
Konstantin Pervushin ◽  
Ali Miserez
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bonds ◽  
Molecular Mechanisms ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Md Simulations ◽  
Dimensional Structure ◽  
Nmr Studies ◽  
Dynamics Simulations ◽  
Cement Protein

Barnacles employ a protein-based cement to firmly attach to immersed substrates. The cement proteins (CPs) have previously been identified and sequenced. However, the molecular mechanisms of adhesion are not well understood, in particular, because the three-dimensional molecular structure of CPs remained unknown to date. Here, we conducted multi-dimensional nuclear magnetic resonance (NMR) studies and molecular dynamics (MD) simulations of recombinant Megabalanus rosa Cement Protein 20 ( r MrCP20). Our NMR results show that r MrCP20 contains three main folded domain regions intervened by two dynamic loops, resulting in multiple protein conformations that exist in equilibrium. We found that 12 out of 32 Cys in the sequence engage in disulfide bonds that stabilize the β -sheet domains owing to their placement at the extremities of β -strands. Another feature unveiled by NMR is the location of basic residues in turn regions that are exposed to the solvent, playing an important role for intermolecular contact with negatively charged surfaces. MD simulations highlight a highly stable and conserved β -motif ( β 7- β 8), which may function as nuclei for amyloid-like nanofibrils previously observed in the cured adhesive cement. To the best of our knowledge, this is the first report describing the tertiary structure of an extracellular biological adhesive protein at the molecular level. This article is part of the theme issue ‘Transdisciplinary approaches to the study of adhesion and adhesives in biological systems’.

THE ROLE OF SUBSTRATE IN PACKING STRUCTURES OF SEXITHIOPHENES ON AG (111) SURFACE: MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM CHEMICAL CALCULATIONS

2009 ◽  
Vol 08 (04) ◽  
pp. 677-690 ◽  
Author(s):  
JIN WEN ◽  
JING MA
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Md Simulations ◽  
Site Preference ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Dynamics Simulations

Packing structures and orientation of sexithiophene (6T) molecules on Ag (111) surface are investigated by molecular dynamics (MD) simulations and quantum chemical calculations. Both the cluster and the slab models are employed. The density functional theory and molecular mechanism calculations demonstrate a weak physisorption and little site-preference in thiophene/ Ag (111) system. The MD simulations show that in the first layer close to the surface, the nearly coplanar 6T strips lie parallel with long axes deviating from [Formula: see text] direction about 20° – 30° and 75° – 90°. The average adsorption height of the monolayer is about 3.2 Å with most of the sulfur atoms in thienyl rings sitting on the bridge site of Ag (111) surface. The 6T molecules tend to take tilted orientations when they are far away from the surface. The packing structures of 6T layers deposited on the surface resulted from the competition between the molecule–substrate and intermolecular interactions.

Role of nanoparticle network in polymer mechanical reinforcement: Insights from molecular dynamics simulations

2021 ◽  
Author(s):  
Xiu Li ◽  
Ziwei Li ◽  
Jianxiang Shen ◽  
Zijian Zheng ◽  
Jun Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Nanocomposites ◽  
High Performance ◽  
Polymer Matrices ◽  
Coarse Grained ◽  
Mechanical Reinforcement ◽  
High Performance Polymer ◽  
Dynamics Simulations

Fully understanding the mechanism by which nanoparticles (NPs) strengthen polymer matrices is crucial for fabricating high-performance polymer nanocomposites (PNCs). Herein, coarse-grained molecular dynamics simulations were adopted to explicitly investigate the...

Isolating the role of hydrogen bonding in hydroxyl-functionalized ionic liquids by means of vaporization enthalpies, infrared spectroscopy and molecular dynamics simulations

2019 ◽  
Vol 21 (36) ◽  
pp. 20308-20314 ◽  
Author(s):  
Dzmitry H. Zaitsau ◽  
Jan Neumann ◽  
Thomas Niemann ◽  
Anne Strate ◽  
Dietmar Paschek ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Infrared Spectroscopy ◽  
Ir Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Dispersion Interaction ◽  
Dynamics Simulations

Hydrogen bonding in hydroxyl-functionalized ionic liquids (right) prevents favourable dispersion interaction between cation and anion (left). We analyze this subtle balance of interactions by combining calorimetry, IR spectroscopy and MD simulations.

scholarly journals Molecular Mechanisms on the Selectivity Enhancement of Ascorbic Acid, Dopamine, and Uric Acid by Serine Oligomers Decoration on Graphene Oxide: A Molecular Dynamics Study

2021 ◽  
Author(s):  
Threravee Sanglao ◽  
Pattanan Oungkanitanon ◽  
Piyapong Asanithi ◽  
Thana Sutthibutpong
Keyword(s):  
Molecular Dynamics ◽  
Ascorbic Acid ◽  
Uric Acid ◽  
Graphene Oxide ◽  
Molecular Mechanisms ◽  
Simultaneous Detection ◽  
Md Simulations ◽  
Bond Forming ◽  
Solvent Environment

The selectivity in the simultaneous detection of ascorbic acid (AA), dopamine (DA), and uric acid (UA) has been an open problem in the biosensing field. Many surface modification methods were carried out for glassy carbon electrodes (GCE), including the use of graphene oxide and amino acids as a selective layer. In this work, molecular dynamics (MD) simulations were performed to investigate the role of serine oligomers on the selectivity of the AA, DA, UA analytes. Our models consisted of a graphene oxide (GO) sheet under a solvent environment. Serine tetramers were added into the simulation box and were adsorbed on the GO surface. Then, the adsorption of each analyte on the mixed surface was monitored from MD trajectories. It was found that the adsorption of AA was preferred by serine oligomers due to the largest number of hydrogen-bond forming functional groups of AA, while UA was the least preferred due to its highest aromaticity. Finally, the role of hydrogen bonds on the electron transfer selectivity of biosensors was discussed with some previous studies.

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

Exploring secondary interactions and the role of temperature in moisture-contaminated polymer networks through molecular simulations

Soft Matter ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. 2942-2956
Author(s):  
Rishabh D. Guha ◽  
Ogheneovo Idolor ◽  
Katherine Berkowitz ◽  
Melissa Pasquinelli ◽  
Landon R. Grace
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Temperature Variation ◽  
Polymer Networks ◽  
Molecular Simulations ◽  
Effect Of Temperature ◽  
Secondary Interactions ◽  
Dynamics Simulations ◽  
Secondary Bonding

We investigated the effect of temperature variation on the secondary bonding interactions between absorbed moisture and epoxies with different morphologies using molecular dynamics simulations.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

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