Methane Storage in Spherical Fullerenes

2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Olumide O. Adisa ◽  
Barry J. Cox ◽  
James M. Hill
Keyword(s):  
Minimum Energy ◽  
Binding Energies ◽  
Methane Molecule ◽  
C60 Fullerene ◽  
Continuum Approximation ◽  
Methane Storage ◽  
Surface Binding ◽  
Jones Potential ◽  
Analytical Formulae ◽  
Dynamics Simulations

In this paper, we investigate methane encapsulation in five spherical fullerenes C60,C240,C540,C960, and C1500. We exploit the 6–12 Lennard-Jones potential function and the continuum approximation to model the surface binding energies between methane and spherical fullerenes of varying sizes. Our results show that for a methane molecule interacting inside a spherical fullerene, the binding energies are minimized at locations which become closer to the fullerene wall as the size of the fullerene increases. However, we find that the methane molecule would require an applied external force to overcome the repulsive energy barrier in order to be encapsulated into a C60 fullerene. The present modeling indicates that the optimal minimum energy for methane storage in any spherical fullerene occurs for a fullerene with radius ≃6.17 Å, with a corresponding potential energy of ≃0.22 eV which occurs for a fullerene bigger than a C60 but slightly smaller than a C240 as the ideal spherical fullerene for methane encapsulation. Overall, our results are in very good agreement with other theoretical studies and molecular dynamics simulations, and show that fullerenes might be good candidates for gas storage. However, the major advantage of the approach adopted here is the derivation of explicit analytical formulae from which numerical results for varying physical scenarios may be readily obtained.

scholarly journals Computational Study on the Interaction and Moving of ssDNA through Nanosheets

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1019
Author(s):  
Mansoor H. Alshehri
Keyword(s):  
Boron Nitride ◽  
Hexagonal Boron Nitride ◽  
Computational Study ◽  
Graphene Nanosheets ◽  
Minimum Energy ◽  
Binding Energies ◽  
Jones Potential ◽  
Boron Nitride Nanosheets ◽  
Continuous Approach ◽  
Energy Location

The adsorption characteristics and moving through nanopores of a single-stranded deoxyribonucleic acid (ssDNA) molecule on monolayers, such ashexagonal boron nitride and graphene nanosheets, were studied using the continuous approach with the 6–12 Lennard–Jones potential function. The ssDNA molecule is assumed to be at a distance l above the sheet, and the relation between the minimum energy location and the perpendicular distance of the ssDNA molecule from the nanosheet surface is found. In addition, by assuming that there is a hole in the surface of the nanosheet as a pore, the interaction energies for the ssDNA molecule moving through the pore in the surface of the nanosheet (used to calculate the radius p of the hole) are obtained, which provides the minimum energies. Furthermore, a comparative study with graphene was performed in order to compare with hexagonal boron nitride nanosheets. Our results indicate that the binding energies of the ssDNA onto graphene and hexagonal boron nitride nanosheets are approximately 15.488 and 17.582 (kcal/mol), corresponding to perpendicular distances of l=20.271 and l=20.231 Å, respectively. In addition, we observe that the ssDNA molecule passes through graphene and hexagonal boron nitride nanopores when the gap radius p>7.5 Å. Our results provide critical insights to understand and develop the interactions and translocation of DNA molecules with and through nanosheets.

Composite Multiwalled Carbon Nanotubes as Memory Devices and Logic Gates

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Richard K. F. Lee ◽  
James M. Hill
Keyword(s):  
Minimum Energy ◽  
Logic Gates ◽  
Memory Device ◽  
Continuum Approximation ◽  
Multiwalled Carbon ◽  
Jones Potential ◽  
Total Interaction ◽  
A Charge ◽  
A Current ◽  
The Continuum

In this study, we propose a new nanocomputer component. We investigate the mechanics of a multiwalled carbon nanotube, comprising two symmetrically placed inner tubes and a moveable tube of radius intermediate to the larger and the two smaller tubes. The larger tube has the two fixed smaller tubes located at its ends, and the moveable tube is assumed to be controlled by an applied voltage difference. The tube radii are purposely chosen so that electrons can jump from one tube to another and a current can flow from the larger tube to the moveable one and finally to one of the smaller tubes. The interaction energy for the system is obtained assuming the Lennard-Jones potential together with the continuum approximation. As expected, the system has two symmetrically placed equal minimum energy locations (i.e., the total interaction energies take on minimum values) and by adopting different electrical circuits, the design gives rise to the possibility of using the device either as a memory device or as logic gates. By applying a voltage input to produce an external electrical field and another voltage input to provide a charge on the moving tube, the moving tube provides an output signal which we assume is registered on a meter that is capable of measuring either voltage or charge. We present the basic design rules for such devices and we establish their feasibility for practical realization.

Modelling the Adsorption of Methane Molecules into Carbon Nanotubes

2011 ◽  
Vol 700 ◽  
pp. 104-107
Author(s):  
Olumide O. Adisa ◽  
Barry J. Cox ◽  
James M. Hill
Keyword(s):  
Carbon Nanotubes ◽  
Interaction Energy ◽  
Gas Storage ◽  
Methane Adsorption ◽  
Methane Molecule ◽  
Methane Storage ◽  
Continuous Approximation ◽  
Jones Potential ◽  
Lennard Jones ◽  
Adsorption Of Methane

We investigate the prospect of methane gas storage in carbon nanotubes, and in particular we determine the interaction energy between a methane molecule and (9, 5), (8, 8) and (10,10) carbon nanotubes. Employing the Lennard-Jones potential together with the continuous approximation, we determine analytically the interaction energy for a methane molecule inside a carbon nanotube. Our results indicate that larger tubes are highly favoured sites for methane storage although smaller tubes might be superior for methane adsorption at higher temperatures, especially in the range 400 − 500 K.

On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment

2020 ◽  
Author(s):  
Robert Stepic ◽  
Lara Jurković ◽  
Ksenia Klementyeva ◽  
Marko Ukrainczyk ◽  
Matija Gredičak ◽  
...  
Keyword(s):  
Active Sites ◽  
Realistic Model ◽  
Binding Energies ◽  
Inhibition Mechanism ◽  
Aqueous Environment ◽  
Binding Modes ◽  
Carboxylate Groups ◽  
Dissolved Ions ◽  
Living Organisms ◽  
Dynamics Simulations

In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth.

scholarly journals Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

2021 ◽  
Vol 11 (9) ◽  
pp. 4052
Author(s):  
Alice Romeo ◽  
Mattia Falconi ◽  
Alessandro Desideri ◽  
Federico Iacovelli
Keyword(s):  
Free Energy ◽  
Double Helix ◽  
Minimum Energy ◽  
Switching Mechanism ◽  
Linker Length ◽  
Energy Profiles ◽  
Functional Dna ◽  
Triplex Forming Oligonucleotide ◽  
Dynamics Simulations ◽  
Free Energy Profiles

The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices.

scholarly journals Tight-Binding Molecular Dynamics Simulations on Point Defects Diffusion and Interactions in Crystalline Silicon

1995 ◽  
Vol 396 ◽  
Author(s):  
M. tang ◽  
L. colombo ◽  
T. Diaz De La Rubia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Point Defects ◽  
Crystalline Silicon ◽  
Tight Binding ◽  
Diffusion Path ◽  
Binding Energies ◽  
Defect Clusters ◽  
Dynamics Simulations

AbstractTight-binding molecular dynamics (TBMD) simulations are performed (i) to evaluate the formation and binding energies of point defects and defect clusters, (ii) to compute the diffusivity of self-interstitial and vacancy in crystalline silicon, and (iii) to characterize the diffusion path and mechanism at the atomistic level. In addition, the interaction between individual defects and their clustering is investigated.

Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

2005 ◽  
Vol 1 (4) ◽  
pp. 204-209
Author(s):  
O.B. Malcıoğlu ◽  
Ş. Erkoç
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binary Systems ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Atomic Interactions ◽  
Dynamics Simulations ◽  
Three Body ◽  
Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

scholarly journals Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations

2020 ◽  
Vol 26 (42) ◽  
pp. 7598-7622 ◽  
Author(s):  
Xiao Hu ◽  
Irene Maffucci ◽  
Alessandro Contini
Keyword(s):  
Drug Discovery ◽  
Binding Free Energy ◽  
Docking Studies ◽  
Free Energy Calculations ◽  
Binding Energies ◽  
New Drugs ◽  
Water Molecules ◽  
Open Questions ◽  
Dynamics Simulations ◽  
Computational Drug Discovery

Background: The inclusion of direct effects mediated by water during the ligandreceptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. Objective: In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. Results: Here, we analyse the software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. Conclusions: Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon.

scholarly journals APPLICATION OF THE LENNARD-JONES POTENTIAL IN MODELLING ROBOT MOTION

2019 ◽  
Vol 9 (4) ◽  
pp. 14-17
Author(s):  
Piotr Wójcicki ◽  
Tomasz Zientarski
Keyword(s):  
Interaction Strength ◽  
Robot Motion ◽  
Lennard Jones Potential ◽  
Ordered Group ◽  
Jones Potential ◽  
Lennard Jones ◽  
Optimal Value ◽  
Potential Impact ◽  
Moving Groups ◽  
Dynamics Simulations

The article proposes a method of controlling the movement of a group of robots with a model used to describe the interatomic interactions. Molecular dynamics simulations were carried out in a system consisting of a moving groups of robots and fixed obstacles. Both the obstacles and the group of robots consisted of uniform spherical objects. Interactions between the objects are described using the Lennard-Jones potential. During the simulation, an ordered group of robots was released at a constant initial velocity towards the obstacles. The objects’ mutual behaviour was modelled only by changing the value of the interaction strength of the potential. The computer simulations showed that it is possible to find the optimal value of the potential impact parameters that enable the implementation of the assumed robotic behaviour scenarios. Three possible variants of behaviour were obtained: stopping, dispersing and avoiding an obstacle by a group of robots.

Computational Discovery of SARS-CoV-2 NSP 16 Drug Candidates Based on Pharmacophore Modeling and Molecular Dynamics Simulation

2021 ◽  
Vol 20 (04) ◽  
pp. 377-390
Author(s):  
Zahra Hesari ◽  
Samaneh Zolghadri ◽  
Sajad Moradi ◽  
Mohsen Shahlaei ◽  
Elham Tazikeh-Lemeski
Keyword(s):  
Molecular Dynamics ◽  
Study Drug ◽  
Pharmacophore Modeling ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Structural Protein ◽  
Drug Candidates ◽  
Computational Discovery ◽  
Approved Drugs ◽  
Dynamics Simulations

Non-Structural Protein 16 (NSP-16) is one of the most suitable targets for discovery of drugs for corona viruses including SARS-CoV-2. In this study, drug discovery of SARS-CoV-2 nsp-16 has been accomplished by pharmacophore-based virtual screening among some analogs (FDA approved drugs) and marine natural plants (MNP). The comparison of the binding energies and the inhibition constants was determined using molecular docking method. Three compounds including two FDA approved (Ibrutinib, Idelalisib) and one MNP (Kumusine) were selected for further investigation using the molecular dynamics simulations. The results indicated that Ibrutinib and Idelalisib are oral medications while Kumusine, with proper hydrophilic and solubility properties, is an appropriate candidate for nsp-16 inhibitor and can be effective to control COVID-19 disease.

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