Abstract: The use of CO2 in oil recovery and in CO2 capture and storage is gaining traction in recent years. These applications involve heat transfer between CO2 and the base fluid, and hence, there arises a need to improve the thermal conductivity of CO2 to increase the process efficiency and reduce cost. One way to improve the thermal conductivity is through nanoparticle addition in the base fluid. The nanofluid model in this study consisted of copper (Cu) nanoparticles in varying concentrations with CO2 as a base fluid. No experimental data are available on thermal conductivity of CO2 based nanofluid. Molecular dynamics (MD) simulations are an increasingly adopted tool to perform preliminary assessments of nanoparticle (NP) fluid interactions. In this study, the effect of the formation of a nanolayer (or molecular layering) at the gas-solid interface on thermal conductivity is investigated using equilibrium MD simulations by varying NP diameter and keeping the volume fraction (1.413%) of nanofluid constant to check the diameter effect of NP on the nanolayer and thermal conductivity. A dense semi-solid fluid layer was seen to be formed at the NP-gas interface, and the thickness increases with increase in particle diameter, which also moves with the NP Brownian motion. Density distribution has been done to see the effect of nanolayer, and its thickness around the NP. These findings are extremely beneficial, especially to industries employed in oil recovery as increased thermal conductivity of CO2 will lead to enhanced oil recovery and thermal energy storage.
Abstract: Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).
Abstract: The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.
Abstract: The aim of this research was to calculate the
mechanical properties of Pd3Rh and PdRh3 ordered alloys. The
molecular dynamics (MD) simulation technique was used to obtain
temperature dependence of the energy, the Yong modulus, the shear
modulus, the bulk modulus, Poisson-s ratio and the elastic stiffness
constants at the isobaric-isothermal (NPT) ensemble in the range of
100-325 K. The interatomic potential energy and force on atoms were
calculated by Quantum Sutton-Chen (Q-SC) many body potential.
Our MD simulation results show the effect of temperature on the
cohesive energy and mechanical properties of Pd3Rh as well as
PdRh3 alloys. Our computed results show good agreement with the
experimental results where they have been available.
Abstract: Viral influenza A subtypes H5N1 and pandemic
H1N1 (pH1N1) have worldwide emerged and transmitted. The most
common anti-influenza drug for treatment of both seasonal and
pandemic influenza viruses is oseltamivir that nowadays becomes
resistance to influenza neuraminidase. The novel long-acting drug,
laninamivir, was discovered for treatment of the patients infected
with influenza B and influenza A viruses. In the present study,
laninamivir complexed with wild-type strain of both H5N1 and
pH1N1 viruses were comparatively determined the structures and
drug-target interactions by means of molecular dynamics (MD)
simulations. The results show that the hydrogen bonding interactions
formed between laninamivir and its binding residues are likely
similar for the two systems. Additionally, the presence of
intermolecular interactions from laninamivir to the residues in the
binding pocket is established through their side chains in accordance
with hydrogen bond interactions.
Abstract: Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.
Abstract: 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the conversion of HMG-CoA to mevalonate using NADPH and the enzyme is involved in rate-controlling step of mevalonate. Inhibition of HMGR is considered as effective way to lower cholesterol levels so it is drug target to treat hypercholesterolemia, major risk factor of cardiovascular disease. To discover novel HMGR inhibitor, we performed structure-based pharmacophore modeling combined with molecular dynamics (MD) simulation. Four HMGR inhibitors were used for MD simulation and representative structure of each simulation were selected by clustering analysis. Four structure-based pharmacophore models were generated using the representative structure. The generated models were validated used in virtual screening to find novel scaffolds for inhibiting HMGR. The screened compounds were filtered by applying drug-like properties and used in molecular docking. Finally, four hit compounds were obtained and these complexes were refined using energy minimization. These compounds might be potential leads to design novel HMGR inhibitor.
Abstract: The aim of this research was to calculate the thermal
properties of Au3Ni Nanowire. The molecular dynamics (MD)
simulation technique was used to obtain the effect of radius size on
the energy, the melting temperature and the latent heat of fusion at
the isobaric-isothermal (NPT) ensemble. The Quantum Sutton-Chen
(Q-SC) many body interatomic potentials energy have been used for
Gold (Au) and Nickel (Ni) elements and a mixing rule has been
devised to obtain the parameters of these potentials for nanowire
stats. Our MD simulation results show the melting temperature and
latent heat of fusion increase upon increasing diameter of nanowire.
Moreover, the cohesive energy decreased with increasing diameter of
nanowire.
Abstract: Every 2-3 years the influenza B virus serves
epidemics. Neuraminidase (NA) is an important target for influenza
drug design. Although, oseltamivir, an oral neuraminidase drug, has
been shown good inhibitory efficiency against wild-type of influenza
B virus, the lower susceptibility to the R152K mutation has been
reported. Better understanding of oseltamivir efficiency and
resistance toward the influenza B NA wild-type and R152K mutant,
respectively, could be useful for rational drug design. Here, two
complex systems of wild-type and R152K NAs with oseltamivir
bound were studied using molecular dynamics (MD) simulations.
Based on 5-ns MD simulation, the loss of notable hydrogen bond and
decrease in per-residue decomposition energy from the mutated
residue K152 contributed to drug compared to those of R152 in wildtype
were found to be a primary source of high-level of oseltamivir
resistance due to the R152K mutation.
Abstract: In this study we investigate the insertion of
pioglitazone, a Thiazolidinedione, into the two different sizes of
Carbon nanotub. It was shown that the insertion of pioglitazone into
the carbon nanotube in a water solute environment could be related
to the diameter of the nanotube and in the flow of the waters via
hydrophilic interactions. This encapsulated drug-carbon nanotube
molecule can be further applicable in other investigations in target
therapy with these agents regarding to reduce their potential toxic
effects.