The interlayer swelling and molecular packing in organoclays

Understanding the interlayer swelling and molecular packing in organoclays is important to the formation and design of polymer nanocomposites. This paper presents recent experimental and molecular simulation studies on a variety of organoclays that show a linear relationship between the increase of d-spacing and the mass ratio between organic and clay. A denser molecular packing is observed in organoclays containing surfactants with hydroxyl-ethyl units. Moreover, our simulation results show that the head (nitrogen) groups are essentially tethered to the clay surface while the long hydrocarbon chains tend to adopt a layering structure with disordered conformation, which contrasts with the previous assumptions of either the chains lying parallel to the clay surface or being tilted at rather precise angles. (c) 2005 Elsevier Inc. All rights reserved.

Transport of simple fluids in nanopores: Theory and simulation

A theory is discussed of single-component transport in nanopores, recently developed by Bhatia and coworkers. The theory considers the oscillatory motion of molecules between diffuse wall collisions, arising from the fluid-wall interaction, along with superimposed viscous flow due to fluid-fluid interaction. The theory is tested against molecular dynamics simulations for hydrogen, methane, and carbon tetrafluoride flow in cylindrical nanopores in silica. Although exact at low densities, the theory performs well even at high densities, with the density dependency of the transport coefficient arising from viscous effects. Such viscous effects are reduced at high densities because of the large increase in viscosity, which explains the maximum in the transport coefficient with increase in density. Further, it is seen that in narrow pore sizes of less than two molecular diameters, where a complete monolayer cannot form on the surface, the mutual interference of molecules on opposite sides of the cross section can reduce the transport coefficient, and lead to a maximum in the transport coefficient with increasing density. The theory is also tested for the case of partially diffuse reflection and shows the viscous contribution to be negligible when the reflection is nearly specular. (c) 2005 American Institute of Chemical Engineers AIChE J, 52: 29-38, 2006.

Dynamical frustration of protein's environment at the nanoseconds time scale

A 21-residue peptide in explicit water has been simulated using classical molecular dynamics. The system's trajectory has been analysed with a novel approach that quantifies the process of how atom's environment trajectories are explored. The approach is based on the measure of Statistical Complexity that extracts complete dynamical information from the signal. The introduced characteristic quantifies the system's dynamics at the nanoseconds time scale. It has been found that the peptide exhibits nanoseconds long periods that significantly differ in the rates of the exploration of the dynamically allowed configurations of the environment. During these periods the rates remain the same but different from other periods and from the rate for water. Periods of dynamical frustration are detected when only limited routes in the space of possible trajectories of the surrounding atoms are realised.

Computational mechanics of molecular systems:quantifying high-dimensional dynamics by distribution of Poincaré recurrence times

A framework that connects computational mechanics and molecular dynamics has been developed and described. As the key parts of the framework, the problem of symbolising molecular trajectory and the associated interrelation between microscopic phase space variables and macroscopic observables of the molecular system are considered. Following Shalizi and Moore, it is shown that causal states, the constituent parts of the main construct of computational mechanics, the e-machine, define areas of the phase space that are optimal in the sense of transferring information from the micro-variables to the macro-observables. We have demonstrated that, based on the decay of their Poincare´ return times, these areas can be divided into two classes that characterise the separation of the phase space into resonant and chaotic areas. The first class is characterised by predominantly short time returns, typical to quasi-periodic or periodic trajectories. This class includes a countable number of areas corresponding to resonances. The second class includes trajectories with chaotic behaviour characterised by the exponential decay of return times in accordance with the Poincare´ theorem.

Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water-Na+ system

The computational mechanics approach has been applied to the orientational behavior of water molecules in a molecular dynamics simulated water–Na + system. The distinctively different statistical complexity of water molecules in the bulk and in the first solvation shell of the ion is demonstrated. It is shown that the molecules undergo more complex orientational motion when surrounded by other water molecules compared to those constrained by the electric field of the ion. However the spatial coordinates of the oxygen atom shows the opposite complexity behavior in that complexity is higher for the solvation shell molecules. New information about the dynamics of water molecules in the solvation shell is provided that is additional to that given by traditional methods of analysis.

Molecular mechanisms of salt effects on carbon nanotube dispersions in an organic solvent (N-methyl-2-pyrrolidone)

We consider the effects of salt (sodium iodide) on pristine carbon nanotube (CNT) dispersions in an organic solvent, N-methyl-2-pyrrolidone (NMP). We investigate the molecular-scale mechanisms of ion interactions with the nanotube surface and we show how the microscopic ion-surface interactions affect the stability of CNT dispersions in NMP. In our study we use a combination of fully atomistic Molecular Dynamics simulations of sodium and iodide ions at the CNT-NMP interface with direct experiments on the CNT dispersions. In the experiments we analyze the effects of salt on the stability of the dispersions by photoluminescence (PL) and optical absorption spectroscopy of the samples as well as by visual inspection. By fully atomistic Molecular Dynamics simulations we investigate the molecular-scale mechanisms of sodium and iodide ion interactions with the nanotube surface. Our simulations reveal that both ions are depleted from the CNT surface in the CNT-NMP dispersions mainly due to the two reasons: (1) there is a high energy penalty for the ion partial desolvation at the CNT surface; (2) NMP molecules form a dense solvation layer at the CNT surface that prevents ions to come close to the CNT surface. As a result, an increase of the salt concentration increases the "osmotic" stress in the CNT-NMP system and, thus, decreases the stability of the CNT dispersions in NMP. Direct experiments confirm the simulation results: addition of NaI salt into the NMP dispersions of pristine CNTs leads to precipitation of CNTs (bundle formation) even at very small salt concentration (∼10 -3 mol L -1). In line with the simulation predictions, the effect increases with the increase of the salt concentration. Overall, our results show that dissolved salt ions have strong effects on the stability of CNT dispersions. Therefore, it is possible to stimulate the bundle formation in the CNT-NMP dispersions and regulate the overall concentration of nanotubes in the dispersions by changing the NaI concentration in the solvent. © 2012 The Royal Society of Chemistry.

Multiscale modelling:approaches and challenges

Multiscale systems that are characterized by a great range of spatial–temporal scales arise widely in many scientific domains. These range from the study of protein conformational dynamics to multiphase processes in, for example, granular media or haemodynamics, and from nuclear reactor physics to astrophysics. Despite the diversity in subject areas and terminology, there are many common challenges in multiscale modelling, including validation and design of tools for programming and executing multiscale simulations. This Theme Issue seeks to establish common frameworks for theoretical modelling, computing and validation, and to help practical applications to benefit from the modelling results. This Theme Issue has been inspired by discussions held during two recent workshops in 2013: ‘Multiscale modelling and simulation’ at the Lorentz Center, Leiden (http://www.lorentzcenter.nl/lc/web/2013/569/info.php3?wsid=569&venue=Snellius), and ‘Multiscale systems: linking quantum chemistry, molecular dynamics and microfluidic hydrodynamics’ at the Royal Society Kavli Centre. The objective of both meetings was to identify common approaches for dealing with multiscale problems across different applications in fluid and soft matter systems. This was achieved by bringing together experts from several diverse communities.

Avaliação funcional e estrutural de um novo peptídeo antimicrobiano do escorpião Tityus stigmurus

In Brazil, there is a high incidence of venomous animals. Among them, scorpions are highlighted by their medical importance, and for being their venom a source of several molecules with biological and pharmacological activity not yet fully understood, including several bioactive peptides. Antimicrobial peptides (AMPs) are components of the immune system in prokaryotes and eukaryotes, used in the first line of defense against microorganisms. In the present study, we characterized the first PAM previously identified through transcriptome of the venom gland of the scorpion Tityus stigmurus, named Stigmurin. The characteristics of Stigmurin were investigated by computational modeling and construction of dendrogram. In vitro tests investigated the antibacterial, antifungal, haemolytic and cytotoxic effects of crude venom and Stigmurin. In addition, the structural characteristics of Stigmurin were investigated by circular dochroism in water, 2, 2 , 2- trifluoethanol (TFE) and sodium dodecyl sulfate (SDS) and the models were refined by molecular dynamics simulations. The results showed that the selected sequence encodes a mature protein of 17 amino acid residues and the dendrogram reveals a case of convergent evolution. The crude venom showed no antimicrobial activity, however, Stigmurin exhibited a broad spectrum of antibacterial activity, with minimal inhibitory concentrations (MIC) ranging from 31.25 and 250 µg/mL for different strains, while the hemolytic activity at these concentrations was low. In cytotoxicity studies, the crude venom was unable to reduce cell viability in VERO E6 cells; in contrast, its activity in SiHa cells was significantly higher, corresponding to IC50 of 3.6 µg/mL. For Stigmurin the concentration sable to decrease cell viability of Vero E6 and SiHa cells in 50% were 275.67 µg/mL and 212.54 µg/mL, respectively. The dichroism spectra revealed the conformational flexibility, with predominating extended and β–sheet structures, as well as a remark able renaturation ability. The results suggest that Stigmurin could be considered as a potential antiinfective drug

Modelagem molecular voltada para a construção de um nanobiossensor para detecção do herbicida Imazaquin

In this study, our goal was develop and describe a molecular model of the enzyme-inhibiting interaction which can be used for an optimized projection of a Microscope Force Atomic nanobiosensor to detect pesticides molecules, used in agriculture, to evaluate its accordance with limit levels stipulated in valid legislation for its use. The studied herbicide (imazaquin) is a typical member of imidazolinone family and is an inhibitor of the enzymatic activity of Acetohydroxiacid Synthase (AHAS) enzyme that is responsible for the first step of pathway for the synthesis of side-chains in amino acids. The analysis of this enzyme property in the presence of its cofactors was made to obtain structural information and charge distribution of the molecular surface to evaluate its capacity of became immobilized on the Microscopy Atomic Force tip. The computational simulation of the system, using Molecular Dynamics, was possible with the force-field parameters for the cofactor and the herbicides obtained by the online tool SwissParam and it was implemented in force-field CHARMM27, used by software GROMACS; then appropriated simulations were made to validate the new parameters. The molecular orientation of the AHAS was defined based on electrostatic map and the availability of the herbicide in the active site. Steered Molecular Dynamics (SMD) Simulations, followed by quantum mechanics calculations for more representative frames, according to the sequential QM/MM methodology, in a specific direction of extraction of the herbicide from the active site. Therefore, external harmonic forces were applied with similar force constants of AFM cantilever for to simulate herbicide detection experiments by the proposed nanobiosensor. Force value of 1391 pN and binding energy of -14048.52 kJ mol-1 were calculated.

A study of electrochemical transport and diffuse charge dynamics using a Langevin equation

This thesis aims to develop new numerical and computational tools to study electrochemical transport and diffuse charge dynamics at small scales. Previous efforts at modeling electrokinetic phenomena at scales where the noncontinuum effects become significant have included continuum models based on the Poisson-Nernst-Planck equations and atomic simulations using molecular dynamics algorithms. Neither of them is easy to use or conducive to electrokinetic transport modeling in strong confinement or over long time scales. This work introduces a new approach based on a Langevin equation for diffuse charge dynamics in nanofluidic devices, which incorporates features from both continuum and atomistic methods. The model is then extended to include steric effects resulting from finite ion size, and applied to the phenomenon of double layer charging in a symmetric binary electrolyte between parallel-plate blocking electrodes, between which a voltage is applied. Finally, the results of this approach are compared to those of the continuum model based on the Poisson-Nernst-Planck equations.

Probing the biophysical interaction between Neocarzinostatin toxin and EpCAM RNA aptamer

Neocarzinostatin (NCS) a potent DNA-damaging, anti-tumor toxin extracted from Streptomyces carzinostaticus that recognizes double-stranded DNA bulge and induces DNA damage. 2 Fluoro (2F) Modified EpCAM RNA aptamer is a 23-mer that targets EpCAM protein, expressed on the surface of epithelial tumor cells. Understanding the interaction between NCS and the ligand is important for carrying out the targeted tumor therapy. In this study, we have investigated the biophysical interactions between NCS and 2-fluro Modified EpCAM RNA aptamer using Circular Dichroism (CD) and Infra-Red (IR) spectroscopy. The aromatic amino acid residues spanning the β sheets of NCS are found to participate in intermolecular interactions with 2 F Modified EpCAM RNA aptamer. In-silico modeling and simulation studies corroborate with CD spectra data. Furthermore, it reinforces the involvement of C and D1 strand of NCS in intermolecular interactions with EpCAM RNA aptamer. This the first report on interactions involved in the stabilization of NCS-EpCAM aptamer complex and will aid in the development of therapeutic modalities towards targeted cancer therapy.

Liquid Mixtures Involving Hydrogenated and Fluorinated Alcohols: Thermodynamics, Spectroscopy, and Simulation

This article reports a combined thermodynamic, spectroscopic, and computational study on the interactions and structure of binary mixtures of hydrogenated and fluorinated substances that simultaneously interact through strong hydrogen bonding. Four binary mixtures of hydrogenated and fluorinated alcohols have been studied, namely, (ethanol + 2,2,2-trifluoroethanol (TFE)), (ethanol + 2,2,3,3,4,4,4-heptafluoro-1-butanol), (1-butanol (BuOH) + TFE), and (BuOH + 2,2,3,3,4,4,4-heptafluoro-1-butanol). Excess molar volumes and vibrational spectra of all four binary mixtures have been measured as a function of composition at 298 K, and molecular dynamics simulations have been performed. The systems display a complex behavior when compared with mixtures of hydrogenated alcohols and mixtures of alkanes and perfluoroalkanes. The combined analysis of the results from different approaches indicates that this results from a balance between preferential hydrogen bonding between the hydrogenated and fluorinated alcohols and the unfavorable dispersion forces between the hydrogenated and fluorinated chains. As the chain length increases, the contribution of dispersion increases and overcomes the contribution of H-bonds. In terms of the liquid structure, the simulations suggest the possibility of segregation between the hydrogenated and fluorinated segments, a hypothesis corroborated by the spectroscopic results. Furthermore, a quantitative analysis of the infrared spectra reveals that the presence of fluorinated groups induces conformational changes in the hydrogenated chains from the usually preferred all-trans to more globular arrangements involving gauche conformations. Conformational rearrangements at the CCOH dihedral angle upon mixing are also disclosed by the spectra.

Vapor pressure and liquid density of fluorinated alcohols:Experimental, simulation and GC-SAFT-VR predictions

The vapor pressure of four liquid 1H,1H-perfluoroalcohols (CF3(CF2)n(CH2)OH, n ¼ 1, 2, 3, 4), often called odd-fluorotelomer alcohols, was measured as a function of temperature between 278 K and 328 K. Liquid densities were also measured for a temperature range between 278 K and 353 K. Molar enthalpies of vaporization were calculated from the experimental data. The results are compared with data from the literature for other perfluoroalcohols as well as with the equivalent hydrogenated alcohols. The results were modeled and interpreted using molecular dynamics simulations and the GC-SAFT-VR equation of state.

Comparing charge transport predictions for a ternary electrolyte using the Maxwell–Stefan and Nernst–Planck equations

In this work, we investigate and compare the Maxwell–Stefan and Nernst–Planck equations for modeling multicomponent charge transport in liquid electrolytes. Specifically, we consider charge transport in the Li+/I−/I3−/ACN ternary electrolyte originally found in dye-sensitized solar cells. We employ molecular dynamics simulations to obtain the Maxwell–Stefan diffusivities for this electrolyte. These simulated diffusion coefficients are used in a multicomponent charge transport model based on the Maxwell– Stefan equations, and this is compared to a Nernst–Planck based model which employs binary diffusion coefficients sourced from the literature. We show that significant differences between the electrolyte concentrations at electrode interfaces, as predicted by the Maxwell–Stefan and Nernst–Planck models, can occur. We find that these differences are driven by a pressure term that appears in the Maxwell–Stefan equations. We also investigate what effects the Maxwell–Stefan diffusivities have on the simulated charge transport. By incorporating binary diffusivities found in the literature into the Maxwell–Stefan framework, we show that the simulated transient concentration profiles depend on the diffusivities; however, the simulated equilibrium profiles remain unaffected.

Atomistic numerical investigation of single-crystal copper nanowire with surface defects

Based on the embedded atom method (EAM), a molecular dynamics (MD) simulation is performed to study the single-crystal copper nanowire with surface defects through tension. The tension simulations for nanowire without defect are first carried out under different temperatures, strain rates and time steps and then surface defect effects for nanowire are investigated. The stress-strain curves obtained by the MD simulations of various strain rates show a rate below 1 x 10(9) s-1 will exert less effect on the yield strength and yield point, and the Young's modulus is independent of strain rate. a time step below 5 fs is recommend for the atomic model during the MD simulation. It is observed that high temperature leads to low Young's modulus, as well as the yield strength. The surface defects on nanowires are systematically studied in considering different defect orientations. It is found that the surface defect serves as a dislocation source, and the yield strength shows 34.20% decresse with 45 degree surface defect. Both yield strength and yield point are significantly influenced by the surface defects, except the Young's modulus.