A molecular dynamics study of chirality transfer: The impact of a chiral solute on an achiral solvent

2008 ◽  
Vol 129 (5) ◽  
pp. 054507 ◽  
Author(s):  
Shihao Wang ◽  
N. M. Cann
Keyword(s):  
Molecular Dynamics ◽  
Chirality Transfer ◽  
The Impact

scholarly journals The Impact of the Electric Field on Surface Condensation of Water Vapor: Insight from Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu
Keyword(s):  
Molecular Dynamics ◽  
Water Vapor ◽  
Electric Field ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Attraction Force ◽  
Condensation Rate ◽  
Shape Transformation ◽  
The Impact

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.

Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

Molecular Dynamics Study on the Impact of the Cutting Depth to the Titanium Nanometric Cutting

2014 ◽  
Vol 536-537 ◽  
pp. 1431-1434 ◽  
Author(s):  
Ying Zhu ◽  
Yin Cheng Zhang ◽  
Shun He Qi ◽  
Zhi Xiang
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Cutting Force ◽  
Simulation Study ◽  
Cutting Process ◽  
Work Piece ◽  
Cutting Depth ◽  
Nanometric Cutting ◽  
The Impact

Based on the molecular dynamics (MD) theory, in this article, we made a simulation study on titanium nanometric cutting process at different cutting depths, and analyzed the changes of the cutting depth to the effects on the work piece morphology, system potential energy, cutting force and work piece temperature in this titanium nanometric cutting process. The results show that with the increase of the cutting depth, system potential energy, cutting force and work piece temperature will increase correspondingly while the surface quality of machined work piece will decrease.

Study on the effect of temperature and strain rate on Ni2FeCrCuAl high entropy alloy: a molecular dynamics study

2021 ◽  
Vol 3 (4) ◽  
pp. 045042
Author(s):  
S Gowthaman ◽  
T Jagadeesha
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Point Defects ◽  
Tensile Deformation ◽  
Variable Temperature ◽  
Effect Of Temperature ◽  
High Entropy Alloy ◽  
High Entropy ◽  
Beneficial Impact ◽  
The Impact

Abstract High entropy alloy has offered significant attention in various material science applications, due to its excellent material features. In this investigation, the mechanical characteristics of Ni2FeCrCuAl High Entropy Alloy (HEA) have been examined under variable temperature and strain rates to analyze its influence over the material features of high entropy alloy through Molecular Dynamics (MD) simulation and it is stated that the formation of various point defects and dislocations are the major cause for the augmentation of tensile deformation which impacts the tensile behavior of high entropy alloy. Moreover, the Radial Distribution Function (RDF) has been examined throughout tensile deformation, to investigate the impact of applied stress over the de-bonding of various atoms and it is found that the strain rate has a greater beneficial impact over the material feature trailed by the temperature outcome, owed to its superior impact on the formation of point defects and shear strain during tensile characterization.

On the impact of lattice parameter accuracy of atomistic simulations on the microstructure of Ni-Ti shape memory alloys

2021 ◽  
Author(s):  
Lorenzo La Rosa ◽  
Francesco Maresca
Keyword(s):  
Molecular Dynamics ◽  
Shape Memory Alloys ◽  
Shape Memory ◽  
Shape Memory Effect ◽  
Memory Effect ◽  
Lattice Parameter ◽  
Lattice Parameters ◽  
Atomistic Simulations ◽  
Interatomic Potentials ◽  
The Impact

Abstract Ni-Ti is a key shape memory alloy (SMA) system for applications, being cheap and having good mechanical properties. Recently, atomistic simulations of Ni-Ti SMAs have been used with the purpose of revealing the nano-scale mechanisms that control superelasticity and the shape memory effect, which is crucial to guide alloying or processing strategies to improve materials performance. These atomistic simulations are based on molecular dynamics modelling that relies on (empirical) interatomic potentials. These simulations must reproduce accurately the mechanism of martensitic transformation and the microstructure that it originates, since this controls both superelasticity and the shape memory effect. As demonstrated by the energy minimization theory of martensitic transformations [Ball, James (1987) Archive for Rational Mechanics and Analysis, 100:13], the microstructure of martensite depends on the lattice parameters of the austenite and the martensite phases. Here, we compute the bounds of possible microstructural variations based on the experimental variations/uncertainties in the lattice parameter measurements. We show that both density functional theory and molecular dynamics lattice parameters are typically outside the experimental range, and that seemingly small deviations from this range induce large deviations from the experimental bounds of the microstructural predictions, with notable cases where unphysical microstructures are predicted to form. Therefore, our work points to a strategy for benchmarking and selecting interatomic potentials for atomistic modelling of shape memory alloys, which is crucial to modelling the development of martensitic microstructures and their impact on the shape memory effect.

scholarly journals Structural Properties of G,T-Parallel Duplexes

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Anna Aviñó ◽  
Elena Cubero ◽  
Raimundo Gargallo ◽  
Carlos González ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Theoretical Calculations ◽  
Md Simulations ◽  
Theoretical Studies ◽  
Duplex Structure ◽  
Strong Stabilization ◽  
The Stability ◽  
The Impact

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

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