MD Simulation of Ionic Crystal under Strong Gravitational Field

2015 ◽  
Vol 363 ◽  
pp. 151-155
Author(s):  
Takahiro Kinoshita ◽  
Takashi Kawakami ◽  
Katsuyuki Kawamura ◽  
Tsutomo Mashimo

Molecular dynamics (MD) simulations were performed to investigate unique crystalline states of typical ionic crystal at condition of a strong gravitational field (one million G). The simulation results showed that lattice vibration spectra of anion and cation along the gravity direction were different from the spectra along normal directions of the gravity. It is also shown that the shapes of spectra along the gravity are obviously different from the others along normal directions of the gravity. In addition, the peaks of spectra along the gravity were shifted. The simulation results showed that anisotropic lattice vibration spectra were induced by strong gravitational field, and it is insisted that the unique crystalline states and physical properties are induced by strong gravitational field.

Author(s):  
Takahiro KINOSHITA ◽  
Takashi KAWAKAMI ◽  
Katsuyuki KAWAMURA ◽  
Tsutomu MASHIMO

2009 ◽  
Vol 289-292 ◽  
pp. 357-360 ◽  
Author(s):  
Tsutomu Mashimo ◽  
Yusuke Iguchi ◽  
Rabaya Bagum ◽  
Tomokazu Sano ◽  
S. Takeda ◽  
...  

A visible four-layers structure with anomalous nano-sturucture was formed from a homogeneous -phase Bi3Pb7 intermetallic compound under a strong gravitational field (1.02x106 G, 130°C, 100 hours). In the 4th layer (lowest-gravity region), pure Bi particles precipitate. In the 2nd 3rd layers, composition graded structures, where Pb content increased along the gravity direction, were formed. It was found that the very broad XRD peak appeared in the 2nd layer, which indicated that an amorphous structure was contained.


2006 ◽  
Vol 05 (01) ◽  
pp. 131-144 ◽  
Author(s):  
JIHUA GOU ◽  
BIN FAN ◽  
GANGBING SONG ◽  
AURANGZEB KHAN

In the processing of carbon nanotube/polymer composites, the interactions between the nanotube and polymer matrix will occur at the molecular level. Understanding their interactions before curing is crucial for nanocomposites processing. In this study, molecular dynamics (MD) simulations were employed to reveal molecular interactions between (10, 10) single-walled nanotube and two kinds of epoxy resin systems. The two kinds of resin systems were EPON 862/EPI-CURE W curing agent (DETDA) and DGEBA (diglycidylether of bisphenol A)diethylenetriamine (DETA) curing agent. The MD simulation results show that the EPON 862, DETDA and DGEBA molecules had strong attractive interactions with single-walled nanotubes and their molecules changed their conformation to align their aromatic rings parallel to the nanotube surface due to π-stacking effect, whereas the DETA molecule had a repulsive interaction with the single-walled nanotubes. The interaction energies of the molecular systems were also calculated. Furthermore, an affinity index (AI) of the average distance between the atoms of the resin molecule and nanotube surface was defined to quantify the affinities between the nanotubes and resin molecules. The MD simulation results show that the EPON 862/EPI-CURE W curing agent system has good affinities with single-walled nanotubes.


2013 ◽  
Vol 328 ◽  
pp. 684-689
Author(s):  
Qi Xin Liu ◽  
Zhi Yong Cai ◽  
Xiao Ping Yu

Now the non-equilibrium MD simulations are frequently used to study the gas flow characteristic at nanoscale. In the non-equilibrium MD simulations, one force which is several magnitude orders larger than the actual force was added on all gas molecules. Its very necessary to study whether such large force added in non-equilibrium MD simulation will affect the simulation results. The present paper carried out the comparative studies on the simulation results of gas flow in nanopores by non-equilibrium and equilibrium MD. The gas number density profile and the gas molecular mean free path are studied in this paper, our simulation results indicate that both non-equilibrium and equilibrium MD produce no obvious difference on simulation results of the gas number density profile and the gas molecular mean free path. It could be concluded that even the force added on every gas molecules is very large in non-equilibrium MD simulation; the added force doesnt obviously affect the simulation results.


2021 ◽  
Author(s):  
Shixun Bai ◽  
Jan Kubelka ◽  
Mohammad Piri

Abstract Wettability is a key factor influencing oil production, particularly from the oil-wet carbonate reservoirs where the recoveries are often low. This is a serious problem for the oil industry as significant portion of the world's hydrocarbon reserves resides in carbonate formations. Since the wettability has its roots in the inter-molecular interactions between the oil and the mineral, our objectives are, first, to provide the molecular-level understanding of the carbonate wettability and, second, to apply this understanding to devise effective approaches for wettability alteration. Specifically, we focused on chemical additives such as surfactants and ions, which have demonstrated potential as wettability reversal agents. Molecular dynamics (MD) simulations were used as the primary method to study the wettability properties on newly-developed model calcite and dolomite surfaces that mimic experimentally-known mineral properties. Wettability reversal by cationic, anionic, and non-ionic surfactants, as well as by divalent ions (Ca2+, Mg2+, and SO42-) were investigated. A systematic approach for maximizing the surfactant efficiency by tuning the cationic surfactant head-group chemistry was proposed. To validate the MD simulation results, experimental contact angle measurements on dolomite chips were conducted. The MD simulation results demonstrated that, in the absence of asphaltenes, the oil-wetness of the carbonate minerals arises from the electrostatic attraction between the (negatively charged) oil carboxylates and the (positive) surfaces. Due to this electrostatic nature, the wettability could be reversed only by the cationic (positive) surfactants, which screen the oil-surface attraction. Other surfactant types had negligible effect, in agreement with the experimental contact angle measurements. Moreover, the wettability alteration efficiency of the cationic surfactants was directly related to their molecular charge distributions, offering guidelines for the practical design of the most potent wettability-reversing molecules. The simulations of the wettability alteration by Mg2+, Ca2+, and SO42- ions were likewise consistent with the contact angle measurements. The roles of individual ions in the multiple ion exchange (MIE) mechanism were deduced, and the known strong temperature dependence of their wettability alteration effect explained by the stability of the ion hydration shells. Finally, the simulations also exposed differences between the wettability reversal mechanisms on calcite and dolomite minerals, which may have important practical impact. Our results offer a novel perspective on the carbonate wettability and its reversal from the standpoint of atomic-level interactions and molecular mechanisms. New models for the carbonate surfaces were developed for reliable simulations of the wetting properties, which led to new insights into the origins of carbonate oil-wetness and the mechanisms of its reversal in two types of minerals. Lastly, the MD simulations demonstrated their utility as a powerful tool for the practical design and evaluation of potential chemical agents for EOR from carbonate reservoirs.


Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 366 ◽  
Author(s):  
G. Sainath ◽  
Sunil Goyal ◽  
A. Nagesha

The deformation behaviour of twinned FCC nanowires has been extensively investigated in recent years. However, the same is not true for their BCC counterparts. Very few studies exist concerning the deformation behaviour of twinned BCC nanowires. In view of this, molecular dynamics (MD) simulations have been performed to understand the deformation mechanisms in twinned BCC Fe nanowires. The twin boundaries (TBs) were oriented parallel to the loading direction [110] and the number of TBs is varied from one to three. MD simulation results indicate that deformation under the compressive loading of twinned BCC Fe nanowires is dominated by a unique de-twinning mechanism involving the migration of a special twin–twin junction. This de-twinning mechanism results in the complete annihilation of pre-existing TBs along with reorientation of the nanowire. Further, it has been observed that the annihilation of pre-existing TBs has occurred through two different mechanisms, one without any resolved shear stress and other with finite and small resolved shear stress. The present study enhances our understanding of de-twinning in BCC nanowires.


2021 ◽  
Author(s):  
Aman Yadav ◽  
Amit Kumar ◽  
Kamal Sharma

Abstract The effect of carboxyl (–COOH) functionalized graphene (FG) on the mechanical properties of its epoxy-based nanocomposites has been investigated by Molecular Dynamics (MD) simulations. Simulations cells of nanocomposites with varying wt% of FG (1, 2 & 3 wt%) were constructed using Material Studio 6.0. Obtained MD simulation results show improved mechanical properties such as elastic modulus, bulk modulus, shear modulus, and the Poisson ratio of the FG/epoxy nanocomposites than that of pure epoxy. Moreover, the computational results of nanocomposites have also been validated well with existing experimental data. Therefore, the current MD simulation shows a decent computational sign for the existing experimental and simulation outcomes on mechanical properties of FG/epoxy nanocomposites.


2018 ◽  
Vol 28 (01n02) ◽  
pp. 1-5
Author(s):  
Akira Takeuchi

The present paper discusses the simulation results, performed by classical molecular dynamics (MD), for vermiculite. The kinetic process of the [Formula: see text] ions in water that are adsorbed into vermiculite [Formula: see text] was investigated with classical MD simulations utilizing Coulomb and Born–Mayer–Huggins potentials. A monoclinic vermiculite crystal with a [Formula: see text] supercell was placed into 8461 molecules of water to form a rectangular supercell of [Formula: see text]. The water was placed into contact with both sides of the [Formula: see text]–[Formula: see text] planes of the vermiculite crystal, along the [Formula: see text]-axis only. The rectangular supercells, which were prepared with the vermiculite in water with and without an additional 200 [Formula: see text] ions, were simulated. The MD conditions included a constant pressure ensemble for 1 ps at a constant step of 0.1 fs. The results revealed an increase in the distances of the [Formula: see text] layers at the interface between the vermiculite and water. This increase in the separation of the [Formula: see text] layers was suitable for the uptake of [Formula: see text] ions by the vermiculite. The accelerated MD simulation which replaced the interfacial [Formula: see text] ions with [Formula: see text] ions tended to include the [Formula: see text] ions into the vermiculite by excluding the [Formula: see text] ions.


Author(s):  
Rameez Jabeer Khan ◽  
Rajat Kumar Jha ◽  
Gizachew Muluneh Amera ◽  
Jayaraman Muthukumaran ◽  
Rashmi Prabha Singh ◽  
...  

Introduction: Lactoperoxidase (LPO) is a member of mammalian heme peroxidase family and is an enzyme of innate immune system. It possesses a covalently linked heme prosthetic group (a derivative of protoporphyrin IX) in its active site. LPO catalyzes the oxidation of halides and pseudohalides in the presence of hydrogen peroxide (H2O2) and shows a broad range of antimicrobial activity. Methods: In this study, we have used two pharmaceutically important drug molecules, namely dapsone and propofol, which are earlier reported as potent inhibitors of LPO. Whereas the stereochemistry and mode of binding of dapsone and propofol to LPO is still not known because of the lack of the crystal structure of LPO with these two drugs. In order to fill this gap, we utilized molecular docking and molecular dynamics (MD) simulation studies of LPO in native and complex forms with dapsone and propofol. Results: From the docking results, the estimated binding free energy (ΔG) of -9.25 kcal/mol (Ki = 0.16 μM) and -7.05 kcal/mol (Ki = 6.79 μM) was observed for dapsone, and propofol, respectively. The standard error of Auto Dock program is 2.5 kcal/mol; therefore, molecular docking results alone were inconclusive. Conclusion: To further validate the docking results, we performed MD simulation on unbound, and two drugs bounded LPO structures. Interestingly, MD simulations results explained that the structural stability of LPO-Propofol complex was higher than LPO-Dapsone complex. The results obtained from this study establish the mode of binding and interaction pattern of the dapsone and propofol to LPO as inhibitors.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.


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