Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes

The study of interactions between carbon nanotubes and cellular components, such as membranes and biomolecules, is fundamental for the rational design of nanodevices interfacing with biological systems. In this work, we use molecular dynamics simulations to study the electrophoretic transport of RNA through carbon nanotubes embedded in membranes. Decorated and naked carbon nanotubes are inserted into a dodecane membrane and a dimyristoylphosphatidylcholine lipid bilayer, and the system is subjected to electrostatic potential differences. The transport properties of this artificial pore are determined by the structural modifications of the membrane in the vicinity of the nanotube openings and they are quantified by the nonuniform electrostatic potential maps at the entrance and inside the nanotube. The pore is used to transport electrophoretically a short RNA segment and we find that the speed of translocation exhibits an exponential dependence on the applied potential differences. The RNA is transported while undergoing a repeated stacking and unstacking process, affected by steric interactions with the membrane headgroups and by hydrophobic interaction with the walls of the nanotube. The RNA is structurally reorganized inside the nanotube, with its backbone solvated by water molecules near the axis of the tube and its bases aligned with the nanotube walls. Upon exiting the pore, the RNA interacts with the membrane headgroups and remains attached to the dodecane membrane while it is expelled into the solvent in the case of the lipid bilayer. The results of the simulations detail processes of molecular transport into cellular compartments through manufactured nanopores and they are discussed in the context of applications in biotechnology and nanomedicine.     

The solvation study of carbon, silicon and their mixed nanotubes in water solution

Nanotubes are believed to open the road toward different modern fields, either technological or biological. However, the applications of nanotubes have been badly impeded for the poor solubility in water which is especially essential for studies in the presence of living cells. Therefore, water soluble samples are in demand. Herein, the outcomes of Monte Carlo simulations of different sets of multiwall nanotubes immersed in water are reported. A number of multi wall nanotube samples, comprised of pure carbon, pure silicon and several mixtures of carbon and silicon are the subjects of study. The simulations are carried out in an (N,V,T) ensemble. The purpose of this report is to look at the effects of nanotube size (diameter) and nanotube type (pure carbon, pure silicon or a mixture of carbon and silicon) variation on solubility of multiwall nanotubes in terms of number of water molecules in shell volume. It is found that the solubility of the multi wall carbon nanotube samples is size independent, whereas multi wall silicon nanotube samples solubility varies with diameter of the inner tube. The higher solubility of samples containing silicon can be attributed to the larger atomic size of silicon atom which provides more direct contact with the water molecules. The other affecting factor is the bigger inter space (the space between inner and outer tube) in the case of silicon samples. Carbon type multi wall nanotubes appeared as better candidates for transporting water molecules through a multi wall nanotube structure, while in the case of water adsorption problems it is better to use multi wall silicon nanotubes or a mixture of multi wall carbon/ silicon nanotubes.     

Predicting doxorubicin drug delivery by single-walled carbon nanotube through cell membrane in the absence and presence of nicotine molecules: a molecular dynamics simulation study

Abstract

In order to study the interaction of the anticancer agent Doxorubicin with the single-walled carbon nanotubes with different diameters as drug delivery systems, the molecular dynamics (MD) simulations have been used. Also, for design and development of intracellular Doxorubicin drug delivery systems, a series of steered MD simulations are applied to explore the possibility of encapsulated Doxorubicin–carbon nanotube penetration through a lipid bilayer in presence and absence of Nicotine molecules at different pulling rates. Our simulation results showed that in spite of the adsorption of drug molecules on the outer sidewall of the nanotubes, the spontaneous localization of one Doxorubicin molecule into the cavity of the nanovectors with larger diameters is observed. It is found that the presence of Nicotine molecules in extracellular medium increases the required force for pulling nanotube-encapsulated drug as well as the required time for penetration process, especially at higher velocity. Also, the entering process of the Nicotine molecules into the carbon nanotube causes that the encapsulated drug molecule is fully released in the hydrophobic phase of the lipid bilayer.

Communicated by Ramaswamy H. Sarma     

On the elastic properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites using molecular dynamics simulations

Molecular dynamics simulations are used to study the physical and mechanical properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites. The effects of nanotube atomic structure, diameter, and volume fraction on the polymer density distribution, polymer atom distribution, stress–strain curves of nanocomposites and Young’s, and shear moduli of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites are explored. It is shown that the density of polymer, surrounding the nanotube surface, has a peak near the nanotube surface. However, increasing distance leads to dropping it to the value near the density of pure polymer. It is seen that for armchair nanotubes, the average polymer atoms distances from the single-walled carbon nanotubes are larger than the polymer atom distance from zigzag nanotubes. It further is shown that zigzag nanotubes are better candidates to reinforce poly (ethylene oxide) than their armchair counterparts.     

On the impact of nanotube diameter on biomembrane indentation – Computer simulations study

The influence of the single-walled carbon nanotubes on the phospholipid bilayer has been studied using steered molecular dynamics (SMD) simulations. The impact of different nanotubes on the phospholipid bilayer structure is discussed as well as the speed of indentation. Additionally, a series of simulations with pulling out of the nanotubes from the membrane were performed. The deflection of the membrane in both nanoindenation and extraction processes is also discussed. The self-sealing ability of membrane during this process is examined. Complete degradation of the bilayer was not observed even for the most invasive nanoindentation process studied. The obtained results show that carbon nanotubes can be regarded as potential drug carriers for targeted therapy.     

Ranking the affinity of aromatic residues for carbon nanotubes by using designed surfactant peptides.

A series of surfactant peptides were created to evaluate the affinity of aromatic AAs for single-walled carbon nanotubes in the absence of complications from peptide folding or self-association. Each surfactant peptide has a lipidlike architecture, with two Lys residues at the C-terminus as a hydrophilic head, five Val residues to form a hydrophobic tail, and the testing AA at the N-terminus. Raman and CD spectroscopic studies reveal that the surfactant peptides have a large unordered structural component which is independent of peptide concentration, suggesting that the peptides undergo minimal association under experimental conditions, thus removing this interference from interpretation of the peptide/carbon nanotube interactions. A lack of peptide self-association is also indicated by sedimentation equilibrium ultracentrifugation results. Optical spectroscopy of the peptide/carbon nanotube dispersions indicate that among the three aromatic AAs, tryptophan has the highest affinity for carbon nanotubes (both bundled and individual states) when incorporated into a surfactant peptide, while the Tyr-containing peptide is more selective for individual carbon nanotubes. Phe has the lowest overall affinity for carbon nanotubes. Raman spectra of dispersions made with SPF, SPY and SPW display similar types of nanotubes dispersed, although differences in the relative nanotube populations are observed by optical spectroscopy.     

Molecular simulation of size-selective gas adsorption in idealised carbon nanotubes

Molecular simulations were used to examine the adsorption of diatomic molecules (nitrogen and oxygen) and similarly sized gases (argon and methane) in pores with van der Waals diameters similar in size to the gas diameters. Idealised carbon nanotubes were used to model generic pores, to better understand the effect of pore diameter on guest adsorption in the absence of defects, specific adsorption sites, or variations in pore diameter that often complicate studies of gas adsorption in other porous materials. Molecular dynamics simulations of open nanotubes show that argon and methane are able to enter tubes whose diameters are slightly smaller than the gas diameters. Diatomic gases are able to enter tubes that are significantly smaller than their kinetic diameters with the molecular axis aligned parallel to the nanotube. The results indicate that size-selective adsorption of these gases is theoretically possible, although differences in pore diameters of only a few tenths of an Angstrom are required. Grand canonical Monte Carlo simulations of a 3.38 Å nanotube indicate significant uptake by argon and oxygen, but not nitrogen or methane. The adsorption of nitrogen and methane gradually increases as the nanotube diameter approaches 4.07 Å, and all gases fully saturate a 4.54 Å nanotube. Of the nanotubes studied, the largest adsorption enthalpy for any gas corresponds to the 4.54 Å nanotube, with significantly lower enthalpies seen in the 5.07 Å nanotube. These results suggest an ideal pore diameter for each gas based on the gas–pore van der Waals interaction energies. Trends in the ideal diameter correlate with the minimum tube diameter accessible to each gas.     

Conjugates between photosystem I and a carbon nanotube for a photoresponse device

Photosystem I (PS I) is a large pigment–protein complex embedded in the thylakoid membranes that performs light-driven electron transfer across the thylakoid membrane. Carbon nanotubes exhibit excellent electrical conductivities and excellent strength and stiffness. In this study, we generated PSI–carbon nanotube conjugates dispersed in a solution aimed at application in artificial photosynthesis. PS I complexes in which a carbon nanotube binding peptide was introduced into the middle of the PsaE subunit were conjugated on a single-walled carbon nanotube, orienting the electron acceptor side to the nanotube. Spectral and photoluminescence analysis showed that the PS I is bound to a single-walled carbon nanotube, which was confirmed by transmission electron microscopy. Photocurrent observation proved that the photoexcited electron originated from PSI and transferred to the carbon nanotube with light irradiation, which also confirmed its orientated conjugation. The PS I–carbon nanotube conjugate will be a useful nano-optoelectronic device for the development of artificial systems.     

Morphology of fibroblasts grown on substrates formed by dielectrophoretically aligned carbon nanotubes

Multiwall carbon nanotube templates formed on the surfaces of planar interdigitated microelectrode arrays by means of AC electric field-guided assembly are being explored as potential substrates for tissue engineering. The objective of the present study is to examine whether surface patterns of aligned multiwall carbon nanotubes can have an effect on cell growth, morphology, and alignment. Bovine fibroblasts grown on aligned carbon nanotubes for a period of 2 weeks were found to have raised bodies and pronounced cell extensions for anchoring themselves to the substrate similar to that of the cells found in native tissues. On the other hand, cells grown on various control surfaces had a flat, circular morphology. The cell cultures were visualized by means of SEM imaging and the resulting morphologies were statistically analyzed and compared.     

Insertion of short amino-functionalized single-walled carbon nanotubes into phospholipid bilayer occurs by passive diffusion

Carbon nanotubes have been proposed to be efficient nanovectors able to deliver genetic or therapeutic cargo into living cells. However, a direct evidence of the molecular mechanism of their translocation across cell membranes is still needed. Here, we report on an extensive computational study of short (5 nm length) pristine and functionalized single-walled carbon nanotubes uptake by phospholipid bilayer models using all-atom molecular dynamics simulations. Our data support the hypothesis of a direct translocation of the nanotubes through the phospholipid membrane. We find that insertion of neat nanotubes within the bilayer is a "nanoneedle" like process, which can often be divided in three consecutive steps: landing and floating, penetration of the lipid headgroup area and finally sliding into the membrane core. The presence of functional groups at moderate concentrations does not modify the overall scheme of diffusion mechanism, provided that their deprotonated state favors translocation through the lipid bilayer.     

Molecular insight into adsorption affinities of Carmustine drug on boron and nitrogen doped functionalized single-walled carbon nanotubes using density functional theory including dispersion correction calculations and molecular dynamics simulation

Abstract

We report a quantum mechanics calculation and molecular dynamics simulation study of Carmustine drug (BNU) adsorption on the surface of nitrogen (N) and boron (B) doped-functionalized single-walled carbon nanotubes. The stability of the optimized complexes is determined on the basis of relative adsorption energy (ΔE_ads). The ΔE_ads results claim that drug molecule tends to adsorb on the nitrogen and boron doped functionalized tubes with the energy values in the range of ?61.177 to ?95.806?kJ/mol. Based on the obtained results, it is observed that N-doping compared with B-doping has improved more effectively drug absorption on the surface of functionalized nanotube. The results of Atoms in Molecule calculations indicate that drug adsorbs molecularly via hydrogen bonds interactions on the surface doped-functionalized carbon nanotubes. Moreover, molecular dynamics simulation is performed to investigate the dynamics behavior of the drug molecules on the nitrogen-doped functionalized carbon nanotube (f-NNT) and functionalized carbon nanotube (f-CNT). The higher average calculated electrostatic and van der Waals energies as well as higher number of intermolecular hydrogen bonds in BNU-f-NNT in comparison with BNU-f-CNT model suggest the more effectual interaction between drug molecules and nitrogen-doped functionalized carbon nanotube.

Communicated by Ramaswamy H. Sarma     

Cellular cytotoxic response induced by highly purified multi-wall carbon nanotube in human lung cells

Carbon nanotubes, a promising nanomaterial with unique characteristics, have applications in a variety of fields. The cytotoxic effects of carbon nanotubes are partially due to the induction of oxidative stress; however, the detailed mechanisms of nanotube cytotoxicity and their interaction with cells remain unclear. In this study, the authors focus on the acute toxicity of vapor-grown carbon fiber, HTT2800, which is one of the most highly purified multi-wall carbon nanotubes (MWCNT) by high-temperature thermal treatment. The authors exposed human bronchial epithelial cells (BEAS-2B) to HTT2800 and measured the cellular uptake, mitochondrial function, cellular LDH release, apoptotic signaling, reactive oxygen species (ROS) generation and pro-inflammatory cytokine release. The HTT2800-exposed cells showed cellular uptake of the carbon nanotube, increased cell death, enhanced DNA damage, and induced cytokine release. However, the exposed cells showed no obvious intracellular ROS generation. These cellular and molecular findings suggest that HTT2800 could cause a potentially adverse inflammatory response in BEAS-2B cells.     

High‐Performance Solution‐Processed Double‐Walled Carbon Nanotube Transparent Electrode for Perovskite Solar Cells

Double‐walled carbon nanotubes are between single‐walled carbon nanotubes and multiwalled carbon nanotubes. They are comparable to single‐walled carbon nanotubes with respect to the light optical density, but their mechanical stability and solubility are higher. Exploiting such advantages, solution‐processed transparent electrodes are demonstrated using double‐walled carbon nanotubes and their application to perovskite solar cells is also demonstrated. Perovskite solar cells which harvest clean solar power have attracted a lot of attention as a next‐generation renewable energy source. However, their eco‐friendliness, cost, and flexibility are limited by the use of transparent oxide conductors, which are inflexible, difficult to fabricate, and made up of expensive rare metals. Solution‐processed double‐walled carbon nanotubes can replace conventional transparent electrodes to resolve such issues. Perovskite solar cells using the double‐walled carbon nanotube transparent electrodes produce an operating power conversion efficiency of 17.2% without hysteresis. As the first solution‐processed electrode‐based perovskite solar cells, this work will pave the pathway to the large‐size, low‐cost, and eco‐friendly solar devices.     

Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery

To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.     

Study of carbon nanotube modified biosensor for monitoring total cholesterol in blood

A carbon nanotube modified biosensor for monitoring total cholesterol in blood was studied. This sensor consists of a carbon working electrode and a reference electrode screen-printed on a polycarbonate substrate. Cholesterol esterase, cholesterol oxidase, peroxidase and potassium ferrocyanide were immobilized on the screen-printed carbon electrodes. Multi-walled carbon nanotubes (MWCN) were added to prompt electron transfer. Experimental results show that the carbon nanotube modified biosensor offers a reliable calibration profile and stable electrochemical properties.     

Carbon Nanotube-Encapsulated Drug Penetration Through the Cell Membrane: An Investigation Based on Steered Molecular Dynamics Simulation

Understanding the penetration mechanisms of carbon nanotube (CNTs)-encapsulated drugs through the phospholipid bilayer cell membrane is an important issue for the development of intracellular drug delivery systems. In the present work, steered molecular dynamics (SMD) simulation was used to explore the possibility of penetration of a polar drug, paclitaxel (PTX), encapsulated inside the CNT, through a dipalmitoylphosphatidylcholine bilayer membrane. The interactions between PTX and CNT and between PTX and the confined water molecules inside the CNT had a significant effect on the penetration process of PTX. The results reveal that the presence of a PTX molecule increases the magnitude of the pulling force. The effect of pulling velocity on the penetration mechanism was also investigated by a series of SMD simulations, and it is shown that the pulling velocity had a significant effect on pulling force and the interaction between lipid bilayer and drug molecule.     

Computational study of Au_4 cluster on a carbon nanotube with and without defects using QM/MM methodology

We use ONIOM (QM/MM) methodology to carry out geometry calculations in a 4-atom nanocluster supported by an (8, 8) armchair carbon nanotube with and without defects employing LSDA/SDD for the QM system and UFF for MM. In two particular cases, defects were added in the carbon nanotube wall. These defects are a double oxygenated vacancy (Vac(2)O(2)) and a double vacancy but without oxygen which creates two pentagons and an octagon. Our results show how geometries using QM/MM and energies calculations carried out with QM, change on both the gold nanocluster and the carbon nanotube. In addition, an application of ONIOM methodology in a comparative study to predict behavior of structures as hybrid materials based in carbon nanotubes combined with gold nanoclusters is shown. In this work we examine geometry changes on both the gold nanocluster and the carbon nanotube. A comparison is made with the binding energy resulting values as well as with the orbital energies such as the frontier orbitals HOMO and LUMO.     

Carbon nanotube solar cells

We present proof-of-concept all-carbon solar cells. They are made of a photoactive side of predominantly semiconducting nanotubes for photoconversion and a counter electrode made of a natural mixture of carbon nanotubes or graphite, connected by a liquid electrolyte through a redox reaction. The cells do not require rare source materials such as In or Pt, nor high-grade semiconductor processing equipment, do not rely on dye for photoconversion and therefore do not bleach, and are easy to fabricate using a spray-paint technique. We observe that cells with a lower concentration of carbon nanotubes on the active semiconducting electrode perform better than cells with a higher concentration of nanotubes. This effect is contrary to the expectation that a larger number of nanotubes would lead to more photoconversion and therefore more power generation. We attribute this to the presence of metallic nanotubes that provide a short for photo-excited electrons, bypassing the load. We demonstrate optimization strategies that improve cell efficiency by orders of magnitude. Once it is possible to make semiconducting-only carbon nanotube films, that may provide the greatest efficiency improvement.     

Interaction of a peptide nanotube with a water-membrane interface

Inserting peptide nanotubes into lipid bilayers modulates the permeability properties of the cell wall, thus conferring potential bacteriocidal capability. Interaction of a peptide nanotube formed by eight cyclo[RRKWLWLW] subunits with the surface of a hydrated dimyristoylphosphatidylcholine bilayer is investigated using molecular dynamics simulations. The present sequence of alternated D-L-alpha-amino acids has been shown to yield remarkable antibacterial in vitro activity, and the chosen topoisomer corresponds to the optimum amphipathy of the tubular structure, whereby non-polar and charged side chains are segregated by the aqueous interface. The cohesion of the nanotube is ensured by a scaffold of intermolecular hydrogen bonds between adjacent cyclic peptides, supplemented by favorable like-charged contacts of arginine side chains. It is further reinforced by interactions of charged residues with the lipid head groups and of non-polar residues with the lipid acyl chains. The simulation reveals a partial breaking of the synthetic channel accompanying its early insertion into the lipid bilayer. The latter opens new questions about how peptide nanotubes permeate the membrane, in particular whether or not (i) self-assembly precedes partitioning and (ii) translocation occurs with the complete tubular structure.