Molecular dynamics modelling of an electrical-driven linear nanopump

The dynamics of an electrical-driven linear nanopump, consisting of a carbon nanotube, a C60⁺ molecule and a graphene sheet, has been simulated via the application of the molecular dynamics method. In this nanopump, the nanotube and the graphene sheet are used as the sleeve of the pump and the boundary between the two sides of the nanopump, respectively. By exposing the nanopump to an external alternative electric field, the C60⁺ molecule will be oscillating linearly in the nanotube. We found that the linear oscillating motion of the C60⁺ molecule causes the gas atoms to flow through the nanotube, and a density gradient is generated between the two sides of the nanopump. Also, it was observed that the frequency of the external alternative electric field affected the pump performance in the generation of the density gradient amount. The maximum performance occurred at a specific frequency of the electric field. This specific frequency can be computed by an analytical formula for given materials and temperatures. Moreover, the results indicate that the length of the nanotube can affect the gas pumping.     

Modelling the influence of thermal effects induced by radio frequency electric field on the dynamics of the ATPase nano-biomolecular motors

We model the dynamics of the F₀ component of the F₀F₁-ATPase mitochondrion-based nano-motor operating in a stochastically-fluctuating medium that represents the intracellular environment. The stochastic dynamics are modeled via Langevin equation of motion wherein fluctuations are treated as white noise. We have investigated the influence of an applied alternating electric field on the rotary motion of the F₀ rotor in such an environment. The exposure to the field induces a temperature rise in the mitochondrion’s membrane, within which the F₀ is embedded. The external field also induces an electric potential that promotes a change in the mitochondrion’s transmembrane potential (TMP). Both the induced temperature and the change in TMP contribute to a change in the dynamics of the F₀. We have found that for external fields in the radio frequency (RF) range, normally present in the environment and encountered by biological systems, the contribution of the induced thermal effects, relative to that of the induced TMP, to the dynamics of the F₀ is more significant. The changes in the dynamics of the F₀ part affect the frequency of the rotary motion of the F₀F₁-ATPase protein motor which, in turn, affects the production rate of the ATP molecules.     

Improved phosphate metabolism and biomass production by overexpression of <Emphasis Type="Italic">AtPAP18</Emphasis> in tobacco

Limited availability of phosphate ion (Pi) reduces plant growth in natural ecosystems. Here, we report the functional effects of overexpressing an Arabidopsis thaliana purple acid phosphatase encoding gene, AtPAP18, in Nicotiana tabbacum as a crop model plant. Transgenic tobacco plants exhibited significant increases in acid phosphatase activity, total P and Pi contents leading to improved biomass production in both Pi-deficient and Pi-sufficient conditions. Transient expression of AtPAP18::green fluorescent fusion protein in onion epidermal cells indicated that AtPAP18 is a dual-targeted protein, which is detected mainly in the apoplast of the cells after 24 h and in the vacuole after 72 h. Possibly, AtPAP18 protein confers efficient retrieval of Pi from bonded extracellular compounds as well as expendable intracellular Pi-monoesters and anhydrides. These data clearly indicate that overexpression of AtPAP18 gene offers an effective approach for reducing the consumption of chemical Pi fertilizer through increased acquisition of soil Pi and mobilization of internal resources.     

Effect of external electric fields on the potential energy profile of K+ ions in selective filter of the KcsA potassium channel

In this study, the potential energy profile of potassium ions in the selective filter part of a KcsA channel was investigated via the application of the molecular simulation method. For this purpose, using the molecular dynamics simulation, the effect of an applied electric field, either constant or oscillating, was studied on the dynamics of K ions in the filter. It was found that when the channel is exposed to a constant electric field of strength 0.03 V/nm, the ions experience a hopping motion. Furthermore, it was shown that the application of oscillating electric fields of 1 and 2.5 GHz, can increase the rigidity of the filter atomic bonds. By computing the potential energy of K ion in the filter, it was shown that the depth of the potential wells, corresponding to the filter sites, increased when an alternative field was applied. Therefore, exposing the channel to the GHz oscillating electric field could disturb the passing rate of ions through the filter, which in turn may affect the operation of these kinds of channels.     

Effect of methyl jasmonate on phenolic acids accumulation and the expression profile of their biosynthesis-related genes in Mentha spicata hairy root cultures

Plant Cell, Tissue and Organ Culture (PCTOC) - Mentha spicata L., as a rich source of phenolic acids, is known for its therapeutic importance. Elicitors play a crucial role in biosynthetic pathways...     

A rotary nano ion pump: a molecular dynamics study

The dynamics of a rotary nano ion pump, inspired by the F (0) part of the F(0)F(1)-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.