Influence of silicon nanocone on cell membrane self-sealing capabilities for targeted drug delivery-Computer simulation study.

Efficient and non-invasive techniques of cargo delivery to biological cells are the focus of biomedical research because of their great potential importance for targeted drug therapy. Therefore, much effort is being made to study the characteristics of using nano-based biocompatible materials as systems that can facilitate this task while ensuring appropriate self-sealing of the cell membrane. Here, we study the effects of indentation and withdrawal of nanocone on phospholipid membrane by applying steered molecular dynamics (SMD) technique. Our results show that the withdrawal process directly depends on the initial position of the nanocone. The average force and work are considerably more significant in case of the withdrawal starting from a larger depth. This result is attributed to stronger hydrophobic interactions between the nanocone and lipid tails of the membrane molecules. Furthermore, when the indenter was started from the lower initial depth, the number of lipids removed from the membrane was several times smaller than the deeper indentation. The choice of the least invasive method for nanostructure-assisted drug delivery is crucial for possible applications in medicine. Therefore, the results presented in this work might be helpful in efficient and safe drug delivery with nanomaterials.

Steered Molecular Dynamics of Lipid Membrane Indentation by Carbon and Silicon-Carbide Nanotubes-The Impact of Indenting Angle Uncertainty.

Due to the semi-liquid nature and uneven morphologies of biological membranes, indentation may occur in a range of non-ideal conditions. These conditions are relatively unstudied and may alter the physical characteristics of the process. One of the basic challenges in the construction of nanoindenters is to appropriately align the nanotube tip and approach the membrane at a perpendicular angle. To investigate the impact of deviations from this ideal, we performed non-equilibrium steered molecular dynamics simulations of the indentation of phospholipid membranes by homogeneous CNT and non-homogeneous SiCNT indenters. We used various angles, rates, and modes of indentation, and the withdrawal of the relative indenter out of the membrane in corresponding conditions was simulated.

Albumin-Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics.

The lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin is one of the major components in synovial fluid. Its electrostatic properties, including the ability to form molecular complexes, are closely related to pH, solvation, and the presence of ions. In the context of synovial fluid, it is relevant to describe the possible interactions between albumin and hyaluronate, taking into account solution composition effects. In this study, the influence of Na+, Mg2+, and Ca2+ ions on human serum albumin-hyaluronan interactions were examined using molecular dynamics tools. It was established that the presence of divalent cations, and especially Ca2+, contributes mostly to the increase of the affinity between hyaluronan and albumin, which is associated with charge compensation in negatively charged hyaluronan and albumin. Furthermore, the most probable binding sites were structurally and energetically characterized. The indicated moieties exhibit a locally positive charge which enables hyaluronate binding (direct and water mediated).

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.

Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations.

Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T=260, 285, 310, 335 and 360K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared.

Delivery of nitric oxide to the interior of mammalian cell by carbon nanotube: MD simulation.

Computer simulations have been performed to study the nanoindentation of phospholipid bilayer by the single-walled armchair carbon nanotube, filled with the nitric oxide molecules. The process has been simulated by means of molecular dynamics (MD) technique at physiological temperature T = 310 K with a constant pulling velocity of the nanotube. The force acting on the nanotube during membrane penetration has been calculated. We show that the indentation by carbon nanotube does not permanently destroy the membrane structure (self-sealing of the membrane occurs). The mobility of nitric oxide molecules during the membrane nanoindentation is discussed.

Two-dimensional phases of confined 5-cyano-biphenyl: Computer simulation study.

The properties of composites of mesogens and two-dimensional (2D) materials are of great interest due to their practical applications in flexible displays, optoelectronics, microelectronics, and novel nanodevices. The properties of such composites are very complex and strongly depend on the interactions between the host material and the mesogen filling. We have performed molecular dynamics simulations for 4-cyano-4^{'}-pentylbiphenyl embedded between graphene and hexagonal 2D boron nitride layers. The structural and dynamical properties of such systems were investigated in terms of the order parameters, density profiles, mean square displacement, and autocorrelation function of the single-molecule dipole moment. Our simulations have shown that the mesogenic molecules form highly stable ordered layered structures and that their dynamics are strongly related to the structural properties. We have investigated not only the effects of the polarization of the host material, but also the effects of the spatial repetition of such composites by using two models of mesogens embedded in 2D layers: the direct sheet and the structure formed by multiplying a single unit of the composite in the direction perpendicular to the substrate surface.

Application of Graphene as a Nanoindenter Interacting with Phospholipid Membranes-Computer Simulation Study.

Synthesis of graphene (GN) in 2004 stimulated wide interest in potential applications of 2D materials in catalysis, optoelectronics, biotechnology, and construction of sensing devices. In the presented study, interactions between GN sheets and phospholipid bilayers are examined using steered molecular dynamics simulations. GN sheets of different sizes were inserted into a bilayer and subsequently withdrawn from it at two different rates (1 and 2 m/s). In some cases, nanoindentation led to substantial damage of the phospholipid bilayer; however, an effective self-sealing process occurred even after significant degradation. The average force and work, deflection of the membrane during indentation, withdrawal processes, and structural changes caused by moving sheets are discussed. These quantities are utilized to estimate the suitability of GN sheets for targeted drug delivery or other nanomedicine tools. The results are compared with those obtained for other nanostructures such as homogeneous and heterogeneous nanotubes.

Impact of polarized nanotube surface on ultrathin mesogen film properties: Computer simulation study.

We studied properties of monolayer films of n-cyanobiphenyl (with n=5,...,8) series of mesogens anchored on the surface of single walled boron nitride nanotube. In order to assess the impact of substrate polarization on the ordering effects we compare translational and reorientational dynamics of the films with the characteristics of analogous carbon and silicon carbide nanotube based systems. We observed significant increase of the ordering degree accompanied by increased thermal stability. This ordering is less selective than those induced by the silicon carbide nanotube, which were previously reported. The antiparallel orientation of the nearest neighboring mesogens is predominant, while the system does not exhibit any long-range spatial correlations which indicates that the size of the domains is constrained to this region. These features might be of potential importance in the design of novel optoelectronic devices.

The dynamics of cholesterol molecules near the surface of protein farnesyltransferase - computer simulation.

We have made the molecular dynamics (MD) simulations for the cluster of cholesterols localized near the protein farnesyltransferase (1FT2) at the physiological temperature T=309.75K. We have observed that the cholesterol molecules form a lodgment on the surface of protein. Several physical characteristics of the deposited cholesterol cluster have been calculated among those: the mean square displacement, diffusion coefficient, linear and angular velocity autocorrelation function and their Fourier transforms.

Molecular dynamics (MD) in homocysteine nanosystems - computer simulation.

Excessive of homocysteine in the human body is recently considered as a factor increasing the risk of the cardiovascular system diseases. The nanosystem composed of finite number of homocysteine molecules (n=20, 50 and 80) have been studied by MD technique. Several physical quantities of homocysteine nanosystem have been calculated as a function of temperature and a number of molecules in homocysteine cluster. The total dipole moment autocorrelation function and dielectric loss of the cluster have been also obtained.

The influence of the carbon nanotube on the structural and dynamical properties of cholesterol cluster.

We have performed the molecular dynamics simulations for the free cholesterol cluster and the same cluster located near the carbon nanotube. We have found that the cholesterol molecules quite evenly cover the surface of single walled armchair (10, 10) carbon nanotube, forming the molecular layer. Moreover, the characteristic alignment of cholesterol molecules within the layer (along the nanotube) is observed. The comparison of the structural and dynamical observable characterizing cholesterol molecule is presented and discussed, both for the cluster with and without the presence of the nanotube.