Interaction of Pristine and Functionalized Carbon Nanotubes with Lipid Membranes

Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly

Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable filter. Supported dense-packed 2D-crystals of single-walled carbon nanotube (CNT) porins with ∼1 nm wide pores could, in principle, meet these challenges. However, such CNT membranes cannot currently be synthesized at high pore density. Here, we use computer simulations to explore lipid-mediated self-assembly as a route toward densely packed CNT membranes, motivated by the analogy to membrane-protein 2D crystallization. In large-scale coarse-grained molecular dynamics (MD) simulations, we find that CNTs in lipid membranes readily self-assemble into large clusters. Lipids trapped between the CNTs lubricate CNT repacking upon collisions of diffusing clusters, thereby facilitating the formation of large ordered structures. Cluster diffusion follows the Saffman-Delbrück law and its generalization by Hughes, Pailthorpe, and White. On longer time scales, we expect the formation of close-packed CNT structures by depletion of the intervening shared annular lipid shell, depending on the relative strength of CNT-CNT and CNT-lipid interactions. Our simulations identify CNT length, diameter, and end functionalization as major factors for the self-assembly of CNT membranes.

Exploring CVD Method for Synthesizing Carbon-Carbon Composites as Materials to Contact with Nerve Tissue

The main purpose of these studies was to obtain carbon-carbon composites with a core built of carbon fibers and a matrix in the form of pyrolytic carbon (PyC), obtained by using the chemical vapor deposition (CVD) method with direct electrical heating of a bundle of carbon fibers as a potential electrode material for nerve tissue stimulation. The methods used for the synthesis of PyC proposed in this paper allow us, with the appropriate selection of parameters, to obtain reproducible composites in the form of rods with diameters of about 300 µm in 120 s (CF_PyC_120). To evaluate the materials, various methods such as scanning electron microscopy (SEM), scanning transmission electron microscope (STEM), high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and tensiometer techniques were used to study their microstructural, structural, chemical composition, surface morphology, and surface wettability. Assessing their applicability for contact with nervous tissue cells, the evaluation of cytotoxicity and biocompatibility using the SH-SY5Y human neuroblastoma cell line was performed. Viability and cytotoxicity tests (WST-1 and LDH release) along with cell morphology examination demonstrated that the CF_PyC_120 composites showed high biocompatibility compared to the reference sample (Pt wire), and the best adhesion of cells to the surface among all tested materials.

Coarse-grained modeling of polystyrene-modified CNTs and their interactions with lipid bilayers

In the present work, we describe Martini3 coarse-grained models of polystyrene and carboxyl-terminated polystyrene functionalized carbon nanotubes (CNTs) and investigate their interactions with lipid bilayers with and without cholesterol (CHOL) using molecular dynamics simulations. By changing the polystyrene chain length and grafting density at the end ring of the CNTs at two different nanotube concentrations, we observe the translocation of nanoparticles as well as changes in the lipid bilayer properties. Our results show that all developed models passively diffuse into the membranes without causing any damage to the membrane integrity, although high concentrations of CNTs induce structural and elastic changes in lipid bilayers. In the presence of CHOL, increasing CNT concentration results in decreased rates of CHOL transmembrane motions. On the other hand, CNTs are prone to lipid and polystyrene blockage, which affects their equilibrated configurations, and tilting behavior within the membranes. Hence, we demonstrate that polystyrene-functionalized CNTs are promising drug-carrier agents. However, polystyrene chain length and grafting density are important factors to consider to enhance the efficiency of drug delivery.

HRMAS-NMR and simulation study of the self-assembly of surfactants on carbon nanotubes

Polyethoxylated surfactants, such as those of the Tween and Pluronic series, are commonly used to disperse carbon nanotubes (CNTs) and other nanoparticles. However, the current understanding of the nature of interactions between these surfactants and CNTs is limited. The nature of the interactions between surfactants (Tween-80 [T80] and Pluronic F68 [PF68]) and CNTs was investigated using high-resolution magic angle spinning nuclear magnetic resonance (HRMAS-NMR) and coarse-grained molecular dynamics (MD) simulations. HRMAS-NMR revealed that T80 molecules interact with single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) via the oleyl chain, whereas PF68 molecules interact with the surface of SWCNTs and MWCNTs via the polypropylene oxide residues. The polyethylene oxide chains were oriented towards the external aqueous environment. The HRMAS-NMR results were supported by MD simulations, and the latter provided further insights into the nature of the interactions.

Facilitating CG Simulations with MAD: The MArtini Database Server

The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.

Organic Bioelectronics for In Vitro Systems

Bioelectronics have made strides in improving clinical diagnostics and precision medicine. The potential of bioelectronics for bidirectional interfacing with biology through continuous, label-free monitoring on one side and precise control of biological activity on the other has extended their application scope to in vitro systems. The advent of microfluidics and the considerable advances in reliability and complexity of in vitro models promise to eventually significantly reduce or replace animal studies, currently the gold standard in drug discovery and toxicology testing. Bioelectronics are anticipated to play a major role in this transition offering a much needed technology to push forward the drug discovery paradigm. Organic electronic materials, notably conjugated polymers, having demonstrated technological maturity in fields such as solar cells and light emitting diodes given their outstanding characteristics and versatility in processing, are the obvious route forward for bioelectronics due to their biomimetic nature, among other merits. This review highlights the advances in conjugated polymers for interfacing with biological tissue in vitro, aiming ultimately to develop next generation in vitro systems. We showcase in vitro interfacing across multiple length scales, involving biological models of varying complexity, from cell components to complex 3D cell cultures. The state of the art, the possibilities, and the challenges of conjugated polymers toward clinical translation of in vitro systems are also discussed throughout.

The nanotube express: Delivering a stapled peptide to the cell surface

HYPOTHESIS

Carbon nanotubes (CNTs) represent a novel platform for cellular delivery of therapeutic peptides. Chemically-functionalized CNTs may enhance peptide uptake by improving their membrane targeting properties.

EXPERIMENTS

Using coarse-grained (CG) molecular dynamics (MD) simulations, we investigate membrane interactions of a peptide conjugated to pristine and chemically-modified CNTs. As proof of principle, we focus on their interactions with PM2, an amphipathic stapled peptide that inhibits the E3 ubiquitin ligase HDM2 from negatively regulating the p53 tumor suppressor. CNT interaction with both simple planar lipid bilayers as well as spherical lipid vesicles was studied, the latter as a surrogate for curved cellular membranes.

FINDINGS

Membrane permeation was rapid and spontaneous for both pristine and oxidized CNTs when unconjugated. This was slowed upon addition of a noncovalently attached peptide surface "sheath", which may be an effective way to slow CNT entry and avert membrane rupture. The CNT conjugates were observed to "desheath" their peptide layer at the bilayer interface upon insertion, leaving their cargo behind in the outer leaflet. This suggests that a synergy may exist to optimize CNT safety whilst enhancing the delivery efficiency of "hitchhiking" therapeutic molecules.

Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation

Macrophage recognition and phagocytosis of crystals is critical for the associated fibrosis and cancer. Of note, multi-walled carbon nanotubes (MWCNTs), the highly representative products of nanotechnology, induce macrophage NLRP3 inflammasome activation and cause asbestosis-like pathogenesis. However, it remains largely unknown how macrophages efficiently recognize MWCNTs on their cell surfaces. Here, we identify by a targeted screening of phagocyte receptors the phosphatidylserine receptors T cell immunoglobulin mucin 4 (Tim4) and Tim1 as the pattern-recognition receptors for carbon crystals. Docking simulation studies reveal spatiotemporally stable interfaces between aromatic residues in the extracellular IgV domain of Tim4 and one-dimensional carbon crystals. Further, CRISPR-Cas9-mediated deletion of Tim4 and Tim1 reveals that Tim4, but not Tim1, critically contributes to the recognition of MWCNTs by peritoneal macrophages and to granuloma development in a mouse model of direct mesothelium exposure to MWCNTs. These results suggest that Tim4 recognizes MWCNTs through aromatic interactions and mediates phagocytosis leading to granulomas.

Investigating the interactions of corona-free SWCNTs and cell membrane models using sum-frequency generation

The understanding of the interactions between biomolecules and nanomaterials is of great importance in many areas of nanomedicine and bioapplications. Numerous studies in this area have been performed. However, toxicological aspects involving the interaction between phospholipids and carbon nanotubes (CNTs) remain undefined, especially for those cases in which a protein corona is not formed around the nanomaterial (corona-free nanomaterials). This study focuses on the interaction of Langmuir films of dipalmitoylphosphatidylglycerol (DPPG) and dipalmitoylphosphatidylcholine (DPPC) with corona-free, single-walled CNTs. Surface pressure-area isotherms and sum-frequency generation (SFG) vibrational spectroscopy, a non-linear optical technique used to study surfaces and interfaces, were used to investigate the lipid tail orientation and conformation, aiming to understand the interactions between phospholipids and single walled carbon nanotubes functionalized by carboxylic acid (SWCNTs-COOH) at the air-water interface under low ionic strength conditions. Data from isotherms and SFG spectra revealed that the SWCNT adsorption at the air-water interface is induced by the presence of both lipids, although at a lesser extent for DPPG due to its anionic head group, which could result in repulsion of SWCNTs-COOH that also bear a negative charge. Furthermore, lipid monolayers remained conformationally ordered, indicating insertion of SWCNTs into the lipid monolayer. Our results corroborate previous works and simulations in the literature, but made it possible to perform an in-depth investigation of the interaction of these nanomaterials with components of phospholipid membranes.

Nanomaterial Effects on Viral Infection

The potential for environmental and occupational exposures of populations to nanomaterials (NMs) has fostered concerns of associated adverse health effects, with a particular emphasis on pulmonary injury and disease. Many studies have revealed that several types of NMs can evoke a variety of biological responses, such as pulmonary inflammation and oxidative stress, which contribute to allergy, fibrosis, and granuloma formation. Less attention has been paid to health effects that may result from exposure to NMs and additional stressors such as pathogens, with a particular focus on susceptibility to viral infection. This chapter will summarize the current body of literature related to NMs and viral exposures with a primary focus on immune modulation. A summary of the studies performed and major findings to date will be discussed, highlighting proposed molecular mechanisms behind NM-driven host susceptibility, challenges, limitations, and future research needs. Specific mechanisms discussed include direct interaction between NMs and biological molecules, activation of pattern recognition receptors (PRRs) and related signaling pathways, production of oxidative stress and mitochondrial dysfunction, inflammasome activation, and modulation of lipid signaling networks.

Efficient water disinfection using hybrid polyaniline/graphene/carbon nanotube nanocomposites

Pathogens, such as Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), contaminate water resources and are the main causes of diseases, not just waterborne diseases. The present study aims to fabricate hybrid materials composed of polyaniline (PANI), graphene nanosheets (GNs), and carbon nanotubes (CNTs) and utilize the materials for water disinfection. Thus, a new class of hybrid nanocomposites (PANI/GN/CNTs_a-e) was fabricated under ultrasonic conditions following a well-known in situ oxidative polymerization technique in an aqueous acidic solution. A homogeneous mixture of GNs and CNTs (40/60 weight %) prepared at 2, 5, 10, 20 and 30% fixed ratios of GNs/CNTs was utilized in the fabrication of the nanocomposites. The structure of this new hybrid class of materials was confirmed by various characterization techniques that were utilized to corroborate their assembly. Column removal studies with bacteria indicated that the removal percentages of S. aureus and E. coli were 99.5 and 99.2%, respectively, using PANI/GN/CNTs_e. The bacterial count is an indication of bacterial removal after and before adsorption. Additionally, the data indicated clear synergic effects among the nanocomposites. Reuse studies revealed that the same percentage of adsorption was obtained for four cycles, which shows the PANI/GN/CNTs_e nanocomposites can be reused and recycled for a number of cycles with almost the same bacterial adsorption capability.

Molecular Dynamics Simulation of Pure n-Alkanes and Their Mixtures at Elevated Temperatures Using Atomistic and Coarse-Grained Force Fields

The properties of higher n-alkanes and their mixtures is a topic of significant interest for the oil and chemical industry. However, the experimental data at high temperatures are scarce. The present study focuses on simulating n-dodecane, n-octacosane, their binary mixture at a n-dodecane mole fraction of 0.3, and a model mixture of the commercially available hydrocarbon wax SX-70 to evaluate the performance of several force fields on the reproduction of properties such as liquid densities, surface tension, and viscosities. Molecular dynamics simulations over a broad temperature range from 323.15 to 573.15 K were employed in examining a broad set of atomistic molecular models assessed for the reproduction of experimental data. The well-established united atom TraPPE (TraPPE-UA) was compared against the all atom optimized potentials for liquid simulations (OPLS) reparametrization for long n-alkanes, L-OPLS, as well as Lipid14 and MARTINI force fields. All models qualitatively reproduce the temperature dependence of the aforementioned properties, but TraPPE-UA was found to reproduce liquid densities most accurately and consistently over the entire temperature range. TraPPE-UA and MARTINI were very successful in reproducing surface tensions, and L-OPLS was found to be the most accurate in reproducing the measured viscosities as compared to the other models. Our simulations show that these widely used force fields originating from the world of biomolecular simulations are suitable candidates in the study of n-alkane properties, both in the pure and mixture states.

Interactions of Functionalized Multi-Wall Carbon Nanotubes with Giant Phospholipid Vesicles as Model Cellular Membrane System

Carbon Nanotubes (CNTs) are considered alternative materials for the design of advanced drug and gene delivery vectors. However, the mechanism responsible for the cellular membrane intake of CNTs is not well understood. In the present study, we show how multi-walled carbon nanotubes (MWCNTs) owning different surface properties, interact with giant unilamellar vesicles (GUVs), a simple model system for cellular membranes. In particular, we want to address the hydrophilic/hydrophobic interactions between MWCNTs and lipid membranes and the subsequent mechanical properties changes of the systems. In order to elucidate this interaction, we made the following chemical modifications on MWCNTs: oxidized MWCNTs (ox-MWCNTs) displaying reduced hydrophobic surface character, pristine MWCNTs (p-MWCNTs), and alkyl functionalized MWCNTs (alk-MWCNTs) exhibiting enhanced hydrophobic surface properties, were put in contact with GUVs and observed by confocal microscopy. Our observations revealed that the interaction between the CNTs and GUVs depends on the type of chemical functionalization: ox-MWCNTs remain at the membrane interacting with the polar head of the phospholipids, p-MWCNTs internalize GUVs spontaneously, and alk-MWCNTs persist inside the membrane. The mechanical properties of MWCNTs@GUVs systems were measured using the electrodeformation method, which shows an increased bending stiffness (κ) of the GUVs as MWCNTs concentration increases. High concentrations of p-MWCNTs and alk-MWCNTs induced vesicle adhesion; p-MWCNTs produced a considerable reduction in the average size of the GUVs, while alk-MWCNTs form complex stable structures inside the membrane. The statistical analyses of the experimental results are compared with available computer simulations. The picture emerging from our results is that the interaction between GUVs and MWCNTs is due mainly to hydrophobicity.

Specific Features of Structure, Electrical Conductivity and Interlayer Adhesion of the Natural Polymer Matrix from the Layers of Branched Carbon Nanotube Networks Filled with Albumin, Collagen and Chitosan

This paper considers the problem of creating a conductive matrix with a framework made of carbon nanotubes (CNTs) for cell and tissue engineering. In silico investigation of the electrical conductivity of the framework formed by T-junctions of single-walled carbon nanotubes (SWNTs) (12, 12) with a diameter of 1.5 nm has been carried out. A numerical evaluation of the contact resistance and electrical conductivity of seamless and suture T-junctions of SWCNTs is given. The effect of the type of structural defects in the contact area of the tubes on the contact resistance of the T-junction of SWCNTs was revealed. A coarse-grained model of a branched SWCNT network with different structure densities is constructed and its electrical conductivity is calculated. A new layered bioconstruction is proposed, the layers of which are formed by natural polymer matrixes: CNT-collagen, CNT-albumin and CNT-chitosan. The energy stability of the layered natural polymer matrix has been analyzed, and the adhesion of various layers to each other has been calculated. Based on the obtained results, a new approach has been developed in the formation of 3D electrically conductive bioengineering structures for the restoration of cell activity.

Crumpled Aluminum Hydroxide Nanostructures as a Microenvironment Dysregulation Agent for Cancer Treatment

Owing to their unique physicochemical properties, nanomaterials have become a focus of multidisciplinary research efforts including investigations of their interactions with tumor cells and stromal compartment of tumor microenvironment (TME) toward the development of next-generation anticancer therapies. Here, we report that agglomerates of radially assembled Al hydroxide crumpled nanosheets exhibit anticancer activity due to their selective adsorption properties and positive charge. This effect was demonstrated in vitro by decreased proliferation and viability of tumor cells, and further confirmed in two murine cancer models. Moreover, Al hydroxide nanosheets almost completely inhibited the growth of murine melanoma in vivo in combination with a minimally effective dose of doxorubicin. Our direct molecular dynamics simulation demonstrated that Al hydroxide nanosheets can cause significant ion imbalance in the living cell perimembranous space through the selective adsorption of extracellular anionic species. This approach to TME dysregulation could lay the foundation for development of novel anticancer therapy strategies.

Identification of Effective Dimeric Gramicidin-D Peptide as Antimicrobial Therapeutics over Drug Resistance: In-Silico Approach

Discovering and developing the antimicrobial peptides are recently focused on pharmaceutical firm, since they serve as complementary to antibiotics in prevailing over drug resistance by eliciting the disruption of microbial membrane. Still, there are lots of challenges to bring up the structurally stable and functionally efficient antimicrobial peptides. It is well known that gramicidin D is the prominent antimicrobial peptide that exists as g-AB, g-BC, and g-AC. This study analyzes the structural stability and the functional activity of hetero-dimeric double-stranded gramicidin-D peptides, thereby demonstrating its potent antimicrobial activity against antibiotic-resistant micro-organisms. To investigate the structural stability and functionality of gramicidin D, we performed static and dynamic analysis. Initially, we observed a maximum number of intermolecular interactions and membrane penetration in g-AB as compared to g-BC and g-AC. To substantiate further, the geometrical and thermodynamic parameters revealed the retention of maximum stability in g-AB than g-AC and g-BC. Thus, the conformational free energy and the binding free energy showed the variation among gramicidin-D peptides for the prediction of increased stability and functionality. In conclusion, g-AB peptide has definitely demonstrated adequate structural stability and functionality and this work will need to be considered in peptide-based drug discovery.

A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites

By employing coarse grained (CG) molecular dynamics (MD) simulation, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube (CNT)-dendrimer composites has been studied, to find a stable composite with high solubility in water and the capability to be used in drug delivery applications. For this purpose, composites consisting of core-shell dendrimer complexes including: [PPI{core}-PAMAM{shell}], [PAMAM{core}-polyethyleneglycol (PEG){shell}] and [PAMAM{core}-fattyacid (FTA){shell}] were constructed. A new CG model for the fatty acid (FTA) molecules as functionalized to the dendrimer was developed, which, unlike the previous models, could generate the structural conformations of the FTA properly. The obtained results indicated that the dendrimer complexes with short FTA chains can form stable composites with the CNT. Also, it was found that the pristine PAMAM and PPI-PAMAM with small PPI, and PAMAM-PEG dendrimers with short PEG chains, can distribute their chains into the water medium and interact with the CNT efficiently, to form a stable water-soluble CNT-dendrimer composite. The results demonstrated that the structural difference between the interior and exterior of a core-shell dendrimer complex can prevent the core and the interior layers of the dendrimer complex from interacting with the CNT. An overall analysis of the results manifested that the CNT-PAMAM:4-PEG:4 is the most stable composite, due to strong binding of the dendrimer with the CNT while also having high solubility in water, and its core retains its structure properly and unchanged, suitable for encapsulating drugs in the targeted delivery applications.

Understanding carbon nanotube channel formation in the lipid membrane

Carbon nanotubes (CNTs) have been considered a prominent nano-channel in cell membranes because of their prominent ion-conductance and ion-selectivity, offering agents for a biomimetic channel platform. Using a coarse-grained molecular dynamics simulation, we clarify a construction mechanism of vertical CNT nano-channels in a lipid membrane for a long period, which has been difficult to observe in previous CNT-lipid interaction simulations. The result shows that both the lipid coating density and length of CNT affect the suitable fabrication condition for a vertical and stable CNT channel. Also, simulation elucidated that a lipid coating on the surface of the CNT prevents the CNT from burrowing into the lipid membrane and the vertical channel is stabilized by the repulsion force between the lipids in the coating and membrane. Our study provides an essential understanding of how CNTs can form stable and vertical channels in the membrane, which is important for designing new types of artificial channels as biosensors for bio-fluidic studies.

Uptake of Engineered Nanoparticles by Food Crops: Characterization, Mechanisms, and Implications

With the rapidly increasing demand for and use of engineered nanoparticles (NPs) in agriculture and related sectors, concerns over the risks to agricultural systems and to crop safety have been the focus of a number of investigations. Significant evidence exists for NP accumulation in soils, including potential particle transformation in the rhizosphere and within terrestrial plants, resulting in subsequent uptake by plants that can yield physiological deficits and molecular alterations that directly undermine crop quality and food safety. In this review, we document in vitro and in vivo characterization of NPs in both growth media and biological matrices; discuss NP uptake patterns, biotransformation, and the underlying mechanisms of nanotoxicity; and summarize the environmental implications of the presence of NPs in agricultural ecosystems. A clear understanding of nano-impacts, including the advantages and disadvantages, on crop plants will help to optimize the safe and sustainable application of nanotechnology in agriculture for the purposes of enhanced yield production, disease suppression, and food quality.

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.

Receptor-Mediated Endocytosis of Nanoparticles: Roles of Shapes, Orientations, and Rotations of Nanoparticles

A complete understanding of the interactions between nanoparticles (NPs) and the cell membrane is essential for the potential biomedical applications of NPs. The rotation of the NP during the cellular wrapping process is of great biological significance and has been widely observed in experiments and simulations. However, the underlying mechanisms of the rotation and their potential influences on the wrapping behavior are far from being fully understood. Here, by coupling the rotation of the NP with the diffusion of the receptors, we set up a model to theoretically investigate the wrapping pathway and the internalization rate of the rotatable NP in the receptor-mediated endocytosis. Based on this model, it is found that the endocytosis proceeds through the symmetric-asymmetric or asymmetric-symmetric-asymmetric wrapping pathway due to the bending and membrane tension competition induced rotation of NP. In addition, we show that the wrapping rate in the direction that the wrapping proceeds can be largely accelerated by the rotation. Moreover, the time to fully wrap the NP depends not only on the size and shape of the NP but also on its rotation and initial orientation. These results reveal the roles of the shape, rotation, and initial orientation of the NP on the receptor-mediated endocytosis and may provide guidelines for the design of NP-based drug delivery systems.

Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery

The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor–acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)–phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device.

Carbon Nanotubes Mediate Fusion of Lipid Vesicles

The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets. As the CNT moves away from the symmetry axis connecting the vesicle centers, the inner leaflets merge, forming a pore that completes fusion. The distinct mechanism of CNT-mediated membrane fusion may be transferable, providing guidance in the development of fusion agents, e.g., for the targeted delivery of drugs or nucleic acids.

Effects of charge and surface defects of multi-walled carbon nanotubes on the disruption of model cell membranes

The direct contact between multi-walled carbon nanotubes (MWCNTs) and cell membranes causes membrane disruption, potentially leading to cytotoxicity. However, the role of electrostatic forces and MWCNT properties is still open to debate. In this study, the influences of charge and MWCNT surface defects on membrane disruption were investigated by microscopy and a quartz crystal microbalance with dissipation monitoring (QCM-D). Positively/negatively charged giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs) were made as model cell membranes. Negatively charged MWCNTs disrupted the GUVs containing positively charged lipids, which confirmed the electrostatically mediated interaction. However, the mass loss was detected from the negatively charged SLBs after MWCNT exposure, which suggests the extraction of phospholipids. The defect degree of MWCNTs correlated with their adhesion amount on the membranes. Both the oxygenated functional groups and unoxidized dangling carbon bonds were active sites for MWCNT-membrane interactions. The MWCNTs were observed to be engulfed inside the GUVs. The results clearly demonstrate that phospholipid extraction by MWCNTs could occur in electrostatically repulsive conditions, and MWCNT defects were active binding sites whether or not they were oxygenated. Our findings should be helpful in the design and safe applications of carbon nanomaterials.

Synthesis of nanocomposites of polypyrrole/carbon nanotubes/silver nano particles and their application in water disinfection

Contamination of drinking or irrigation water with pathogenic bacteria, such as Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), is a major global health problem.

Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study

Carbon nanotube porins (CNTPs), small segments of carbon nanotubes capable of forming defined pores in lipid membranes, are important future components for bionanoelectronic devices as they could provide a robust analog of biological membrane channels. In order to control the incorporation of these CNT channels into lipid bilayers, it is important to understand the structure of the CNTPs before and after insertion into the lipid bilayer as well as the impact of such insertion on the bilayer structure. Here we employed a noninvasive in situ probe, small-angle X-ray scattering, to study the integration of CNT porins into dioleoylphosphatidylcholine bilayers. Our results show that CNTPs in solution are stabilized by a monolayer of lipid molecules wrapped around their outer surface. We also demonstrate that insertion of CNTPs into the lipid bilayer results in decreased bilayer thickness with the magnitude of this effect increasing with the concentration of CNTPs.

Translocation of Functionalized Multi-Walled Carbon Nanotubes across Human Pulmonary Alveolar Epithelium: Dominant Role of Epithelial Type 1 Cells

Uptake and translocation of short functionalized multi-walled carbon nanotubes (short-fMWCNTs) through the pulmonary respiratory epithelial barrier depend on physicochemical property and cell type. Two monoculture models, immortalized human alveolar epithelial type 1 (TT1) cells and primary human alveolar epithelial type 2 cells (AT2), which constitute the alveolar epithelial barrier, were employed to investigate the uptake and transport of 300 and 700 nm in length, poly(4-vinylpyridine)-functionalized, multi-walled carbon nanotubes (p(4VP)-MWCNTs) using quantitative imaging and spectroscopy techniques. The p(4VP)-MWCNT exhibited no toxicity on TT1 and AT2 cells, but significantly decreased barrier integrity (*p < 0.01). Uptake of p(4VP)-MWCNTs was observed in 70% of TT1 cells, correlating with compromised barrier integrity and basolateral p(4VP)-MWCNT translocation. There was a small but significantly greater uptake of 300 nm p(4VP)-MWCNTs than 700 nm p(4VP)-MWCNTs by TT1 cells. Up to 3% of both the 300 and 700 nm p(4VP)-MWCNTs reach the basal chamber; this relatively low amount arose because the supporting transwell membrane minimized the amount of p(4VP)-MWCNT translocating to the basal chamber, seen trapped between the basolateral cell membrane and the membrane. Only 8% of AT2 cells internalized p(4VP)-MWCNT, accounting for 17% of applied p(4VP)-MWCNT), with transient effects on barrier function, which initially fell then returned to normal; there was no MWCNT basolateral translocation. The transport rate was MWCNT length modulated. The comparatively lower p(4VP)-MWCNT uptake by AT2 cells is proposed to reflect a primary barrier effect of type 2 cell secretions and the functional differences between the type 1 and type 2 alveolar epithelial cells.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems

Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers

Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.

Wrapping of nanoparticles by the cell membrane: the role of interactions between the nanoparticles

A fundamental understanding of the interactions between nanoparticles (NPs) and the cell membrane is essential to improve the performance of the NP-based biomedical applications and assess the potential toxicity of NPs. Despite the great progress in understanding the interaction between individual NP and the membrane, little is known about the interaction between multiple NPs and the membrane. In this work, we investigate the wrapping of two parallel elongated NPs by the membrane, taking the NP-NP electrostatic interaction and van der Waals (vdW) interaction into consideration. Three types of NPs, namely the rigid NPs with circular and elliptic cross-sections and the deformable NPs, are systematically investigated. The results show that the electrostatic interaction would enhance the tendency of the independent wrapping and inhibit the rotation of the elongated and equally charged NPs with elliptic cross-sections. Under the vdW interaction, the competition of the NP-NP adhesion and the membrane elastic energies with the NP-membrane adhesion energy leads the NPs to be wrapped cooperatively or independently. For the system with elongated NPs with elliptic cross-sections, the NPs are more likely to be wrapped independently as the shapes become more anisotropic and the NPs would rotate to contact each other with the flat sides in the cooperative wrapping configuration. Moreover, the soft NPs are more likely to be wrapped cooperatively compared with the stiff NPs. These results may provide guidelines to control the internalization pathway of NPs and improve the efficiency of NP-based drug delivery systems.

Cell interaction with graphene microsheets: near-orthogonal cutting versus parallel attachment

Recent experiments indicate that graphene microsheets can either undergo a near-orthogonal cutting or a parallel attachment mode of interaction with cell membranes. Here we perform a theoretical analysis to characterize the deformed membrane microstructure and investigate how these two interaction modes are influenced by the splay, tilt, compression, tension, bending and adhesion energies of the membrane. Our analysis indicates that, driven by the membrane splay and tension energies, a two-dimensional microsheet such as graphene would adopt a near-perpendicular configuration with respect to the membrane in the transmembrane penetration mode, whereas the membrane bending and tension energies would lead to parallel attachment in the absence of cross membrane penetration. These interaction modes may have broad implications in applications involving drug delivery, cell encapsulation and protection, and the measurement of the dynamic cell response.

Molecular modeling of interaction between lipid monolayer and graphene nanosheets: implications for pulmonary nanotoxicity and pulmonary drug delivery

Understanding how nanoparticles interact with the pulmonary surfactant monolayer (PSM) is of great importance for safe applications in biomedicine and for evaluation of both health and environment impacts.

Strong electronic polarization of the C60 fullerene by imidazolium-based ionic liquids: accurate insights from Born–Oppenheimer molecular dynamic simulations

Fullerenes are known to be polarizable due to their strained carbon–carbon bonds and high surface curvature.

The importance of membrane defects-lessons from simulations

The defects and pores within lipid membranes are scientifically interesting and have a number of biological applications. Although lipid bilayers are extremely thin hydrophobic barriers, just ∼3 nm thick, they include diverse chemistry and have complex structures. Bilayers are soft and dynamic, and as a result, they can bend and deform in response to different stimuli by means of structural changes in their component lipids. Though defects occur within these structures, their transience and small size have made it difficult to characterize them. However, with recent advances in computer power and computational modeling techniques, researchers can now use simulations as a powerful tool to probe the mechanism and energies of defect and pore formation in a number of situations. In this Account, we present results from our detailed molecular dynamics computer simulations of hydrophilic pores and related defects in lipid bilayers at an atomistic level. Electroporation can be used to increase the permeability of cellular membranes, with potential therapeutic applications. Atomistic simulations of electroporation have illustrated the molecular details of this process, including the importance of water dipole interactions at the water-membrane interface. Characterization of the lipid-protein interactions provides an important tool for understanding transmembrane protein structure and thermodynamic stability. Atomistic simulations give a detailed picture of the free energies of model peptides and side chains in lipid membranes; the energetic cost of defect formation strongly influences the energies of interactions between lipids and polar and charged residues. Many antimicrobial peptides form hydrophilic pores in lipid membranes, killing bacteria or cancer cells. On the basis of simulation data, at least some of these peptides form defects and pores near the center of the bilayer, with a common disordered structure where hydrated headgroups form an approximately toroidal shape. The localization and trafficking of lipids supports general membrane structure and a number of important signaling cascades, such as those involving ceramide, diacylglycerol, and cholesterol. Atomistic simulations have determined the rates and free energies of lipid flip-flop. During the flip-flop of most phosphatidylcholine lipids, a hydrophilic pore forms when the headgroup moves near the center of the bilayer. Simulations have provided novel insight into many features of defects and pores in lipid membranes. Simulation data from very different systems and models show how water penetration and defect formation can determine the free energies of many membrane processes. Bilayers can deform and allow transient defects and pores when exposed to a diverse range of stimuli. Future work will explore many aspects of membrane defects with increased resolution and scope, including the study of more complex lipid mixtures, membrane domains, and large-scale membrane remodeling. Such studies will examine processes including vesicle budding and fusion, non-bilayer lipid phases, and interactions between lipid bilayers and other biomolecules. Simulations provide information that complements experimental studies, allowing microscopic insight into experimental observations and suggesting novel hypotheses and experiments. These studies should enable a deeper understanding of the role of lipid bilayers in cellular biology and support the development of future lipid-based biotechnology.

Large scale molecular simulations of nanotoxicity

The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells.