scholarly journals Size Dependence of the Dissociation Process of Spherical Hydrate Particles via Microsecond Molecular Dynamics Simulations

Author(s):  
Stephan Mohr ◽  
Rémi Pétuya ◽  
Jonathan Wylde ◽  
Juan Sarria ◽  
Nirupam Purkayastha ◽  
...  

The dissociation process of spherical sII mixed methane-propane hydrate particles in liquid hydrocarbon was investigated via microsecond-long Molecular Dynamics simulations. A strong dependence of the melting temperature on the particle...

2020 ◽  
pp. 2150005
Author(s):  
Shouqi Cao ◽  
Haochen Zuo ◽  
He Xin ◽  
Lixin Zhou

The coalescence of particles extensively exists in the industrial production and nature, which is of great research significance. This paper examined the alloying process of Cu/Au nanoparticles with different sizes by molecular dynamics (MDs) simulations. The coalescence process presents three stages which can be divided by the contact and fusion. The alloying processes of Cu/Au nanoparticles with different sizes had contacted with each other before the heating at 300 K. The Au atoms diffused through the outer area of the sintering neck before the nanoparticles were fused into one particle. The coalescence had become severe after the systems reached the melting temperature. The different systems showed different sintering rate.


Author(s):  
Jithu Paul ◽  
A. K. Madhu ◽  
U. B. Jayadeep ◽  
C. B. Sobhan

Nanofluids — colloidal suspensions of nanoparticles in base fluids — are known to possess superior thermal properties compared to the base fluids. Various theoretical models have been suggested to explain the often anomalous enhancement of these properties. Liquid layering around the nanoparticle is one of such reasons. The effect of the particle size on the extent of liquid layering around the nanoparticle has been investigated in the present study. Classical molecular dynamics simulations have been performed in the investigation, considering the case of a copper nanoparticle suspended in liquid argon. The results show a strong dependence of thickness of the liquid layer on the particle size, below a particle diameter of 4nm. To establish the role of liquid layering in the enhancement of thermal conductivity, simulations have been performed at constant volume fraction for different particle sizes using Green Kubo formalism. The thermal conductivity results show 100% enhancement at 3.34% volume fraction for particle size of 2nm. The results establish the dominant role played by liquid layering in the enhanced thermal conductivity of nanofluids at the low particle sizes used. Contrary to the previous findings, the molecular dynamics simulations also predict a strong dependence of the liquid layer thickness on the particle size in the case of small particles.


2019 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot

AbstractA recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed. Here, we express three main concerns about that study. In addition, we show that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.


eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L de Groot

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.


Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 256 ◽  
Author(s):  
Alina Remeeva ◽  
Vera V. Nazarenko ◽  
Ivan M. Goncharov ◽  
Anna Yudenko ◽  
Anastasia Smolentseva ◽  
...  

Light-oxygen-voltage (LOV) domains are ubiquitous photosensory modules found in proteins from bacteria, archaea and eukaryotes. Engineered versions of LOV domains have found widespread use in fluorescence microscopy and optogenetics, with improved versions being continuously developed. Many of the engineering efforts focused on the thermal stabilization of LOV domains. Recently, we described a naturally thermostable LOV domain from Chloroflexus aggregans. Here we show that the discovered protein can be further stabilized using proline substitution. We tested the effects of three mutations, and found that the melting temperature of the A95P mutant is raised by approximately 2 °C, whereas mutations A56P and A58P are neutral. To further evaluate the effects of mutations, we crystallized the variants A56P and A95P, while the variant A58P did not crystallize. The obtained crystal structures do not reveal any alterations in the proteins other than the introduced mutations. Molecular dynamics simulations showed that mutation A58P alters the structure of the respective loop (Aβ-Bβ), but does not change the general structure of the protein. We conclude that proline substitution is a viable strategy for the stabilization of the Chloroflexus aggregans LOV domain. Since the sequences and structures of the LOV domains are overall well-conserved, the effects of the reported mutations may be transferable to other proteins belonging to this family.


2015 ◽  
Vol 17 (34) ◽  
pp. 21894-21901 ◽  
Author(s):  
Matthew Becton ◽  
Xianqiao Wang

Molecular dynamics simulations are performed to investigate the mechanical properties and failure mechanism of polycrystalline boron nitride sheet with various grain sizes.


RSC Advances ◽  
2015 ◽  
Vol 5 (15) ◽  
pp. 11297-11308 ◽  
Author(s):  
Hamed Akbarzadeh ◽  
Mohsen Abbaspour

In this paper we have extended the equation of state (EoS) in terms of particle size for Ne nanoclusters using an effective two-body Hartree–Fock dispersion (HFD)-like potential by molecular dynamics simulations.


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