Abstract: In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.
Abstract: In this work, adsorption of chlorophylls a and b pigments in aqueous solution on the inner and outer surfaces of single-walled carbon nanotube (SWCNT) has been studied using molecular dynamics simulation. The linear interaction energy algorithm has been used to calculate the binding free energy. The results show that the adsorption of two pigments is fine on the both positions. Although there is the close similarity between these two pigments, their interaction with the nanotube is different. This result is useful to separate these pigments from one another. According to interaction energy between the pigments and carbon nanotube, interaction between these pigments-SWCNT on the inner surface is stronger than the outer surface. The interaction of SWCNT with chlorophylls phytol tail is stronger than the interaction of SWCNT with porphyrin ring of chlorophylls.
Abstract: Surface characteristics of Bacillus megaterium strain
were investigated; zeta potential, FTIR and contact angle were
measured. Surface energy components including Lifshitz-van der
Waals, Hamaker constant, and acid/base components (Lewis
acid/Lewis base) were calculated from the contact angle data. The
results showed that the microbial cells were negatively charged over
all pH regions with high values at alkaline region. A hydrophilic
nature for the strain was confirmed by contact angle and free energy
of adhesion between microbial cells. Adsorption affinity of the strain
toward dolomite was studied at different pH values. The results
showed that the cells had a high affinity to dolomite at acid pH
comparing to neutral and alkaline pH. Extended DLVO theory was
applied to calculate interaction energy between B. megaterium cells
and dolomite particles. The adsorption results were in agreement with
the results of Extended DLVO approach. Surface changes occurred
on dolomite surface after the bio-treatment were monitored; contact
angle decreased from 69° to 38° and the mineral’s floatability
decreased from 95% to 25% after the treatment.
Abstract: This research work presents the surface
thermodynamics approach to M-TB/HIV-Human sputum
interactions. This involved the use of the Hamaker coefficient
concept as a surface energetics tool in determining the interaction
processes, with the surface interfacial energies explained using van
der Waals concept of particle interactions. The Lifshitz derivation for
van der Waals forces was applied as an alternative to the contact
angle approach which has been widely used in other biological
systems. The methodology involved taking sputum samples from
twenty infected persons and from twenty uninfected persons for
absorbance measurement using a digital Ultraviolet visible
Spectrophotometer. The variables required for the computations with
the Lifshitz formula were derived from the absorbance data. The
Matlab software tools were used in the mathematical analysis of the
data produced from the experiments (absorbance values). The
Hamaker constants and the combined Hamaker coefficients were
obtained using the values of the dielectric constant together with the
Lifshitz Equation. The absolute combined Hamaker coefficients
A132abs and A131abs on both infected and uninfected sputum samples
gave the values of A132abs = 0.21631x10-21Joule for M-TB infected
sputum and Ã132abs = 0.18825x10-21Joule for M-TB/HIV infected
sputum. The significance of this result is the positive value of the
absolute combined Hamaker coefficient which suggests the existence
of net positive van der waals forces demonstrating an attraction
between the bacteria and the macrophage. This however, implies that
infection can occur. It was also shown that in the presence of HIV,
the interaction energy is reduced by 13% conforming adverse effects
observed in HIV patients suffering from tuberculosis.
Abstract: Electrostatic interaction energy (ΔEEDL) is a part of the Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, which, together with van der Waals (ΔEVDW) and acid base (ΔEAB) interaction energies, has been extensively used to investigate the initial adhesion of bacteria to surfaces. Electrostatic or electrical double layer interaction energy is considerably affected by surface potential; however it cannot be determined experimentally and is usually replaced by zeta (ζ) potential via electrophoretic mobility. This paper focusses on the effect of ionic concentration as a function of pH and the effect of mineral grain size on ζ potential. It was found that both ionic strength and mineral grain size play a major role in determining the value of ζ potential for the adhesion of P. putida to hematite and quartz surfaces. Higher ζ potential values lead to higher electrostatic interaction energies and eventually to higher total XDLVO interaction energy resulting in bacterial repulsion.
Abstract: In this paper, we summarize recent work of the authors on nanocomputing memory devices. We investigate two memory devices, each comprising a charged metallofullerene and carbon nanotubes. The first device involves two open nanotubes of the same radius that are joined by a centrally located nanotube of a smaller radius. A metallofullerene is then enclosed inside the structure. The second device also involves a etallofullerene that is located inside a closed carbon nanotube. Assuming the Lennard-Jones interaction energy and the continuum approximation, for both devices, the metallofullerene has two symmetrically placed equal minimum energy positions. On one side the metallofullerene represents the zero information state and by applying an external electrical field, it can overcome the energy barrier, and pass from one end of the tube to the other, where the metallofullerene then represents the one information state.
Abstract: The electrical interaction between two axisymmetric
spheroidal particles in an electrolyte solution is examined numerically.
A Galerkin finite element method combined with a Newton-Raphson
iteration scheme is proposed to evaluate the spatial variation in the
electrical potential, and the result obtained used to estimate the
interaction energy between two particles. We show that if the surface
charge density is fixed, the potential gradient is larger at a point, which
has a larger curvature, and if surface potential is fixed, surface charge
density is proportional to the curvature. Also, if the total interaction
energy against closest surface-to-surface curve exhibits a primary
maximum, the maximum follows the order (oblate-oblate) >
(sphere-sphere)>(oblate-prolate)>(prolate-prolate), and if the curve
has a secondary minimum, the absolute value of the minimum follows
the same order.
Abstract: Hypertension is characterized with stress on the heart and blood vessels thus increasing the risk of heart attack and renal diseases. The Renin angiotensin system (RAS) plays a major role in blood pressure control. Renin is the enzyme that controls the RAS at the rate-limiting step. Our aim is to develop new drug-like leads which can inhibit renin and thereby emerge as therapeutics for hypertension. To achieve this, molecular dynamics (MD) simulation and receptor-based pharmacophore modeling were implemented, and three rennin-inhibitor complex structures were selected based on IC50 value and scaffolds of inhibitors. Three pharmacophore models were generated considering conformations induced by inhibitor. The compounds mapped to these models were selected and subjected to drug-like screening. The identified hits were docked into the active site of renin. Finally, hit1 satisfying the binding mode and interaction energy was selected as possible lead candidate to be used in novel renin inhibitors.
Abstract: In order to find the particular interaction energy
between cylcloguanil and the amino acids surrounding the pocket of
wild type and quadruple mutant type PfDHFR enzymes, the MP2
method with basis set 6-31G(d,p) level of calculations was
performed. The obtained interaction energies found that Asp54 has
the strongest interaction energy to both wild type and mutant type of -
12.439 and -11.250 kcal/mol, respectively and three amino acids;
Asp54, Ile164 and Ile14 formed the H-bonding with cycloguanil
drug. Importantly, the mutation at Ser108Asn was the key important
of cycloguanil resistant with showing repulsive interaction energy.
Abstract: Molar excess Volumes, VE ijk and speeds of sound , uijk of 2-pyrrolidinone (i) + benzene or toluene (j) + ethanol (k) ternary mixture have been measured as a function of composition at 308.15 K. The observed speeds of sound data have been utilized to determine excess isentropic compressiblities, ( E S κ )ijk of ternary (i + j + k) mixtures. Molar excess volumes, VE ijk and excess isentropic compressibilities, ( E S κ )ijk data have fitted to the Redlich-Kister equation to calculate ternary adjustable parameters and standard deviations. The Moelywn-Huggins concept (Huggins in Polymer 12: 389-399, 1971) of connectivity between the surfaces of the constituents of binary mixtures has been extended to ternary mixtures (using the concept of a connectivity parameter of third degree of molecules, 3ξ , which inturn depends on its topology) to obtain an expression that describes well the measured VE ijk and ( E S κ )ijk data.