A Theoretical and Computational Study of Superlubricity and the Role of the Roughness Exponent

2005 ◽  
Author(s):  
Martin H. Mu¨ser ◽  
Carlos Campana
Keyword(s):  
Friction Velocity ◽  
Computational Study ◽  
Absolute Magnitude ◽  
Flat Surfaces ◽  
Coulomb’S Friction ◽  
Fractal Surfaces ◽  
Elastic Interactions ◽  
Roughness Exponent ◽  
Dynamics Simulations

Superlubricity can only be achieved if the intra-bulk elastic interactions dominate interfacial shear forces at every single length-scale in a contact. Otherwise, there will be some type of plucking motion which will lead to friction-velocity relationships akin of Coulomb’s friction law. For nominally flat surfaces, it has been predicted theoretically and demonstrated experimentally that plucking motion and hence kinetic friction can be avoided under certain circumstances. We present theoretical arguments, why these findings may extend to fractal surfaces. The theories are checked by molecular dynamics simulations. It turns out that the roughness exponent and the absolute magnitude of the roughness both play a crucial role in determining whether there can be superlubricity.

scholarly journals Computational investigation on the role of C-Terminal of human albumin on the dimerization of Aβ1-42 peptide

2020 ◽  
Vol 10 (1) ◽  
pp. 4944-4955 ◽  
Keyword(s):  
Computational Study ◽  
Binding Free Energy ◽  
Conformational Dynamics ◽  
Human Albumin ◽  
Potential Of Mean Force ◽  
Amber Force Field ◽  
Aβ Aggregation ◽  
The Difference ◽  
Dynamics Simulations

Alzheimer’s disease (AD) is characterized by the presence of Amyloid-beta (Aβ) peptide, which has the propensity to fold into β-sheets under stress forming aggregated amyloid plaques. Nowadays many studies have focused on the development of novel, specific therapeutic strategies to slow down Aβ aggregation or control preformed aggregates. Albumin, the most abundant protein in the cerebrospinal fluid, was reported to bind Aβ impeding its aggregation. Recently, it has been reported that C-terminal (CTerm) of Human Albumin binds with Aβ1-42, impairs Aβ aggregation and promotes disassembly of Aβ aggregates protecting neurons. In this computational study, we have investigated the effect of CTerm on the conformational dynamics and the aggregation propensity of Aβ1-42 peptide. We have performed molecular dynamics simulations on the Aβ1-42-Aβ1-42 homodimer and Aβ1-42-CTerm of albumin heterodimer using the AMBER force field ff99SBildn. From the Potential of mean force (PMF) study and Binding free energy (BFE) analysis, we observed the association of Aβ1-42 peptide monomer with itself in the form of homodimer to be stronger than its association with the CTerm in the heterodimer complex. The difference in the number of residues in the Aβ1-42 peptide monomer (42 AAs) and CTerm (35 AAs) may be probable reason for the difference in association between the monomeric units in corresponding homodimer and heterodimer complexes. But even then CTerm shows a significant effect on the dimerization of Aβ1-42 peptide. Our findings therefore suggest that CTerm can be used for the disassembly of Aβ1-42 peptide monomer.

scholarly journals Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation

Cellulose ◽  
2022 ◽  
Author(s):  
Eivind Bering ◽  
Jonathan Ø. Torstensen ◽  
Anders Lervik ◽  
Astrid S. de Wijn
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Interactions ◽  
Computational Study ◽  
Pure Water ◽  
Solvent Mixture ◽  
Dissolution Mechanism ◽  
Dynamics Simulations ◽  
External Forces

Abstract We investigate the dissolution mechanism of cellulose using molecular dynamics simulations in both water and a mixture solvent consisting of water with Na$$^+$$ + , OH$$^-$$ - and urea. As a first computational study of its kind, we apply periodic external forces that mimic agitation of the suspension. Without the agitation, the bundles do not dissolve, neither in water nor solvent. In the solvent mixture the bundle swells with significant amounts of urea entering the bundle, as well as more water than in the bundles subjected to pure water. We also find that the mixture solution stabilizes cellulose sheets, while in water these immediately collapse into bundles. Under agitation the bundles dissolve more easily in the solvent mixture than in water, where sheets of cellulose remain that are bound together through hydrophobic interactions. Our findings highlight the importance of urea in the solvent, as well as the hydrophobic interactions, and are consistent with experimental results. Graphical abstract

scholarly journals A Theoretical Approach to Demystify the Role of Copper Salts and O2 in the Mechanism of C-N Bond Cleavage and Nitrogen Transfer

2021 ◽  
Author(s):  
Boyli Ghosh ◽  
Ambar Banerjee ◽  
Lisa Roy ◽  
Rounak Nath ◽  
Rabindra Nath Manna Manna ◽  
...  
Keyword(s):  
Computational Study ◽  
Bond Cleavage ◽  
Nitrogen Transfer ◽  
Copper Salts ◽  
Cyanide Anion ◽  
Aryl Aldehydes ◽  
Bond Scission ◽  
Dynamics Simulations ◽  
Experimental Findings

<b>C≡N bond scission accomplished by protonation, reductive cleavage and metathesis techniques are well-known to execute nitrogen transfer reactions. Herein, we have conducted an extensive computational study, using DFT and molecular dynamics simulations, to unravel the mechanistic pathways traversed in CuCN and CuBr<sub>2</sub> promoted splitting of coordinated cyanide anion under a dioxygen atmosphere, which enables nitrogen transfer to various aldehydes. Our detailed electronic structure analysis using <i>ab initio</i> multi-reference CASSCF calculations reveal that both the promoters facilitate radical pathways, in agreement with the experimental findings. This is a unique instance of oxygen activation initiated by single electron transfer from the nitrile carbon, while the major driving force is the operation of the Cu<sup>II/I </sup>redox cycle. Our study reveals that the copper salts act as the “electron pool” in this unique nitrogen transfer reaction forming aryl nitrile from aryl aldehydes.</b><br>

scholarly journals A Theoretical Approach to Demystify the Role of Copper Salts and O2 in the Mechanism of C-N Bond Cleavage and Nitrogen Transfer

2021 ◽  
Author(s):  
Boyli Ghosh ◽  
Ambar Banerjee ◽  
Lisa Roy ◽  
Rounak Nath ◽  
Rabindra Nath Manna Manna ◽  
...  
Keyword(s):  
Computational Study ◽  
Bond Cleavage ◽  
Nitrogen Transfer ◽  
Copper Salts ◽  
Cyanide Anion ◽  
Aryl Aldehydes ◽  
Bond Scission ◽  
Dynamics Simulations ◽  
Experimental Findings

<b>C≡N bond scission accomplished by protonation, reductive cleavage and metathesis techniques are well-known to execute nitrogen transfer reactions. Herein, we have conducted an extensive computational study, using DFT and molecular dynamics simulations, to unravel the mechanistic pathways traversed in CuCN and CuBr<sub>2</sub> promoted splitting of coordinated cyanide anion under a dioxygen atmosphere, which enables nitrogen transfer to various aldehydes. Our detailed electronic structure analysis using <i>ab initio</i> multi-reference CASSCF calculations reveal that both the promoters facilitate radical pathways, in agreement with the experimental findings. This is a unique instance of oxygen activation initiated by single electron transfer from the nitrile carbon, while the major driving force is the operation of the Cu<sup>II/I </sup>redox cycle. Our study reveals that the copper salts act as the “electron pool” in this unique nitrogen transfer reaction forming aryl nitrile from aryl aldehydes.</b><br>

scholarly journals Computational Study of the Dissolution of Cellulose into Single Chains: the Role of the Solvent and Agitation

2021 ◽  
Author(s):  
Eivind Bering ◽  
Jonathan Torstensen ◽  
Anders Lervik ◽  
Astrid S. de Wijn
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Interactions ◽  
Computational Study ◽  
Pure Water ◽  
Solvent Mixture ◽  
Dissolution Mechanism ◽  
Dynamics Simulations ◽  
External Forces

Abstract We investigate the dissolution mechanism of cellulose using molecular dynamics simulations in both water and a mixture solvent consisting of water with Na + , OH - and urea. As a first computational study of its kind, we apply periodic external forces that mimic agitation of the suspension. Without the agitation, the bundles do not dissolve, neither in water nor solvent. In the solvent mixture the bundle swells up with significant amounts of urea entering the bundle, as well as more water than in the bundles subjected to pure water. We also find that the mixture solution stabilizes cellulose sheets, while in water these immediately collapse into bundles. Under agitation the bundles dissolve more easily in the solvent mixture than in water, where sheets of cellulose remain that are bound together through hydrophobic interactions. Our findings highlight the importance of urea in the solvent, as well as the hydrophobic interactions, and are consistent with experimental results.

scholarly journals A computational study of the interface interaction between SARS-CoV-2 RBD and ACE2 from human, cat, dog and ferret.

2021 ◽  
Author(s):  
William Sote ◽  
Eduardo Franca ◽  
Aline Hora ◽  
Moacyr Comar
Keyword(s):  
Animal Species ◽  
Computational Study ◽  
Infection Process ◽  
Point Of View ◽  
Cellular Receptor ◽  
Angiotensin Converting Enzyme 2 ◽  
Dynamics Simulations ◽  
Key Residues ◽  
Total Impact

The total impact of the worldwide COVID-19 pandemic is still emerging, changing all relationships as a result, including those with pet animals. In the infection process, the use of Angiotensin-converting enzyme 2 (ACE2) as a cellular receptor to the spike protein of the new coronavirus is a fundamental step. In this sense, understanding which residue plays what role in the interaction between SARS-CoV-2 spike glycoprotein and ACE2 from cats, dogs, and ferrets is an important guide for helping to choose which animal model can be used to study the pathology of COVID-19 and if there are differences between these interactions and those occurring in the human system. Hence, trying to help to answer these questions, we performed classical molecular dynamics simulations to evaluate, from an atomistic point of view, the interactions in these systems. Our results show that there are significant differences in the interacting residues between the systems from different animal species, and the role of ACE2 key residues are different in each system and can assist in the search for different inhibitors for each animal.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Liquid dibromomethane under pressure: a computational study

2021 ◽  
Vol 23 (4) ◽  
pp. 2964-2971
Author(s):  
Bernadeta Jasiok ◽  
Mirosław Chorążewski ◽  
Eugene B. Postnikov ◽  
Claude Millot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Computational Study ◽  
Thermal Expansivity ◽  
Dynamics Simulations ◽  
Isobaric Thermal Expansivity

Thermophysical properties of liquid dibromomethane are investigated by molecular dynamics simulations between 268 and 328 K at pressures up to 3000 bar. Notably, the isotherms of the isobaric thermal expansivity cross around 800 bar.

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