Molecular Dynamics Study of Gas–Surface Interactions in a Force-Driven Flow of Argon through a Rectangular Nanochannel

In recent times, flows through micro- and nanochannels have gained prominence due to their applicability to the fast growing fields of micro- and nanotechnology among others. Understanding gas–surface interactions in such flows is crucial, because the size of the micro/nanoscale devices is typically comparable to boundary layer thickness near a wall and the surface starts playing a significant role. An attempt is made to understand these interactions by modeling simple force-driven argon gas flow between two parallel platinum plates by the molecular dynamics method. One of the most important parameters that describes gas–surface interactions—that is, the tangential momentum accommodation coefficient, along with flow properties such as velocity and density—is calculated for a range of Knudsen numbers in the early transitional flow regime. A deeper insight into the flow physics is obtained by considering various case studies for the variation of aforesaid properties with respect to external driving forces and gas–wall interaction strengths.     

Modulating protein adsorption onto hydroxyapatite particles using different amino acid treatments

Hydroxyapatite (HA) is a material of choice for bone grafts owing to its chemical and structural similarities to the mineral phase of hard tissues. The combination of osteogenic proteins with HA materials that carry and deliver the proteins to the bone-defective areas will accelerate bone regeneration. The study investigated the treatment of HA particles with different amino acids such as serine (Ser), asparagine (Asn), aspartic acid (Asp) and arginine (Arg) to enhance the adsorption ability of HA carrier for delivering therapeutic proteins to the body. The crystallinity of HA reduced when amino acids were added during HA preparation. Depending on the types of amino acid, the specific surface area of the amino acid-functionalized HA particles varied from 105 to 149 m² g^–1. Bovine serum albumin (BSA) and lysozyme were used as model proteins for adsorption study. The protein adsorption onto the surface of amino acid-functionalized HA depended on the polarities of HA particles, whereby, compared with lysozyme, BSA demonstrated higher affinity towards positively charged Arg-HA. Alternatively, the binding affinity of lysozyme onto the negatively charged Asp-HA was higher when compared with BSA. The BSA and lysozyme adsorptions onto the amino acid-functionalized HA fitted better into the Freundlich than Langmuir model. The amino acid-functionalized HA particles that had higher protein adsorption demonstrated a lower protein-release rate.     

Synthesis of water dispersible reduced graphene oxide via supramolecular complexation with modified β-cyclodextrin

A noncovalent functionalization of the edges of reduced graphene oxide (RGO) with β-cyclodextrin-graft-hyperbranched polyglycerol (β-CD-g-HPG) was successfully performed via a host-guest interaction. The results showed that β-CD-g-HPG disperses the graphene sheets better than pure β-CD or HPG. The resulted supramolecular structure is stable in neutral water medium more than one week. However, in acidic medium the host-guest interaction is collapsed and graphene nanosheets precipitate.     

Effects of fluoridation of porcine hydroxyapatite on osteoblastic activity of human MG63 cells

Abstract

Biological hydroxyapatite, derived from animal bones, is the most widely used bone substitute in orthopedic and dental treatments. Fluorine is the trace element involved in bone remodeling and has been confirmed to promote osteogenesis when administered at the appropriate dose. To take advantage of this knowledge, fluorinated porcine hydroxyapatite (FPHA) incorporating increasing levels of fluoride was derived from cancellous porcine bone through straightforward chemical and thermal treatments. Physiochemical characteristics, including crystalline phases, functional groups and dissolution behavior, were investigated on this novel FPHA. Human osteoblast-like MG63 cells were cultured on the FPHA to examine cell attachment, cytoskeleton, proliferation and osteoblastic differentiation for in vitro cellular evaluation. Results suggest that fluoride ions released from the FPHA play a significant role in stimulating osteoblastic activity in vitro, and appropriate level of fluoridation (1.5 to 3.1 atomic percents of fluorine) for the FPHA could be selected with high potential for use as a bone substitute.     

Coiling/uncoiling behaviour of sodium polystyrenesulfonate in 2‐ethoxyethanol–water mixed solvent media as probed using viscometry

Precise measurements of the viscosities of solutions of sodium polystyrenesulfonate in water and in 2‐ethoxyethanol–water mixtures containing varying amounts of 2‐ethoxyethanol have been performed at 308.15, 313.15, 318.15 and 323.15 K. The intramolecular contributions to the reduced viscosities of the polyelectrolyte solutions were obtained through isoionic dilution maintaining the total ionic strengths of the solutions at polyelectrolyte concentrations of 0.0033, 0.0054 and 0.0080 eq L^?1 with sodium chloride. The Huggins constants were also obtained from the experimental data. The influences of the medium and the temperature on the intramolecular contributions to the reduced viscosities as well as on the Huggins constants have been interpreted from the points of view of the conformational characteristics and polyelectrolyte–solvent and polyelectrolyte–polyelectrolyte interactions prevailing in the polyelectrolyte solutions under investigation. Polyion chains were found to coil upon addition of 2‐ethoxyethanol to water or upon an increase of temperature. Thermodynamic affinities for polyelectrolyte–solvent and polyelectrolyte–polyelectrolyte interactions were found to depend greatly on the medium. © 2014 Society of Chemical Industry     

Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine

Experimental protein structures provide spatial information at the atomic level. A further dimension, time, is supplemented by molecular dynamics. Since the pioneering work on the 58-residue inhibitor of bovine pancreatic trypsin in the group of Martin Karplus in the seventies, molecular dynamics simulations have shown that the intrinsic flexibility of proteins is essential for their function. Here, we review simulation studies of bromodomains. These protein modules are involved in the recognition of acetylated lysine side chains, a post-translational modification frequently observed in histone tails. The molecular dynamics simulations have unmasked: (i) the large plasticity of the loops lining the acetyl-lysine binding site (coupled to its self-occlusion), and (ii) multiple binding modes of acetyl-lysine. These simulation results suggest that recognition of histone tails by bromodomains is modulated by their intrinsic flexibility, and further corroborate the utility of molecular dynamics in understanding (macro)molecular recognition.     

Protein-ion Interactions: Simulations of Bovine Serum Albumin in Physiological Solutions of NaCl,KCl and LiCl

Specific interactions that depend on the nature of electrolytes are observed when proteins and other molecules are studied by potentiometric, spectroscopic and theoretical methods at high salt concentrations. More recently, it became clear that such interactions may also be observed in solutions that can be described by the Debye-Hückel theory, i.e., at physiological (0.1 mol dm⁻³) and lower concentrations. We carried out molecular dynamics simulations of bovine serum albumin in physiological solutions at T=300 and 350 K. Analysis of the simulations revealed some differences between LiCl solutions and those of NaCl and KCl. The binding of Li⁺ ions to the protein was associated with a negative free energy of interaction whereas much fewer Na⁺ and K⁺ ions were associated with the protein surface. Interestingly, unlike other proteins BSA does not show a preference to Na⁺ over K⁺. Quantum chemical calculations identified a significant contribution from polarisation to the hydration of Li⁺ and (to a lesser degree) Na⁺, which may indicate that polarisable force-fields will provide more accurate results for such systems.     

GPU-based simulation of the long-range Potts model via parallel tempering

We discuss the efficiency of parallelization on graphical processing units (GPUs) for the simulation of the one-dimensional Potts model with long-range interactions via parallel tempering. We investigate the behavior of some thermodynamic properties, such as equilibrium energy and magnetization, critical temperatures as well as the separation between the first- and second-order regimes. By implementing multispin coding techniques and an efficient parallelization of the interaction energy computation among threads, the GPU-accelerated approach reached speedup factors of up to 37.