Alkoxy Chain Effect on the Viscosity of a Quaternary Ammonium Ionic Liquid: Molecular Dynamics Simulations

The viscosity of ionic liquids based on quaternary ammonium cations is reduced when one of the alkyl chains is replaced by an alkoxy chain (Zhou et al. Chem. Eur. J. 2005, 11, 752.). A microscopic picture of the role played by the ether function in decreasing the viscosity of quaternary ammonium ionic liquids is provided here by molecular dynamics (MD) simulations. A model for the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM(2)E TFSI, is compared to the tetraalky-lammonium counterpart. The alkoxy derivative has lower viscosity, higher ionic diffusion coefficients, and higher conductivity than the tetraalkyl system at the same density and temperature. A clear signature of the ether function on the liquid structure is observed in cation-cation correlations, but not in anion-anion or anion-cation correlations. In both the alkyl and the alkoxy ionic liquids, there is aggregation of long chains of neighboring cations within micelle-like structures. The MD simulations indicate that the less effective assembly between the more flexible alkoxy chains, in comparison to alkyl chains, is the structural reason for higher ionic mobility in MOENM(2)E TFSI.

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Isomery of SU3 states in the strictly restricted dynamics model

Employing the general principles of classification of SU3 states, we have found 285 quantum number isomers (QNI), i.e. nuclei for which there are two possible SU3 quantum number sets, characterized by the maximal eigenvalue of the SU3 group Casimir operator, at the minimal value N-0(min) for the quantum number N-0 of the group U3(A-1) symmetric representation, allowed by the Pauli principle. 41 of these QNI can be attributed to the nun-excited, ground SU3 configurations of realistic nuclei. Two examples of QNI: Si-28 and Zn-60, have been studied in detail in the framework of the strictly restricted dynamics model (SRDM).

Quantum tunneling fragmentation model

A nonthermal quantum mechanical statistical fragmentation model based on tunneling of particles through potential barriers is studied in compact two- and three-dimensional systems. It is shown that this fragmentation dynamics gives origin to several static and dynamic scaling relations. The critical exponents are found and compared with those obtained in classical statistical models of fragmentation of general interest, in particular with thermal fragmentation involving classical processes over potential barriers. Besides its general theoretical interest, the fragmentation dynamics discussed here is complementary to classical fragmentation dynamics of interest in chemical kinetics and can be useful in the study of a number of other dynamic processes such as nuclear fragmentation. ©2000 The American Physical Society.

Molecular Dynamics simulations of track formation at different ensembles

A series of Molecular Dynamics simulations of thermal spikes has been run in zircon. For two different ensembles: microcanonical one and a combination of microcanonical one acting on the simulation core with Langevin one on the side walls of simulation. Depending on the used ensemble, different track-formation threshold energies were found. When the combined ensemble is carried out, the total energy of the simulations varies with the temperature which can influence how annealing fission-track models should deal with the lattice recovery. A fission-track annealing model is tested with the simulation results. © 2012 Elsevier Ltd. All rights reserved.

On the unzipping mechanisms of carbon nanotubes: Insights from reactive molecular dynamics simulations

Unzipping carbon nanotubes (CNTs) is considered one of the most promising approaches for the controlled and large-scale production of graphene nanoribbons (GNR). These structures are considered of great importance for the development of nanoelectronics because of its dimensions and intrinsic nonzero band gap value. Despite many years of investigations some details on the dynamics of the CNT fracture/unzipping processes remain unclear. In this work we have investigated some of these process through molecular dynamics simulations using reactive force fields (ReaxFF), as implemented in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. We considered multi-walled CNTs of different dimensions and chiralities and under induced mechanical stretching. Our preliminary results show that the unzipping mechanisms are highly dependent on CNT chirality. Well-defined and distinct fracture patterns were observed for the different chiralities. Armchair CNTs favor the creation of GNRs with well-defined armchair edges, while zigzag and chiral ones produce GNRs with less defined and defective edges. © 2012 Materials Research Society.

Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (k cat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. © 2013 Elsevier B.V. All rights reserved.

A new probabilistic canopy dynamics model (SLCD) that is suitable for evergreen and deciduous forest ecosystems

There are strong uncertainties regarding LAI dynamics in forest ecosystems in response to climate change. While empirical growth & yield models (G&YMs) provide good estimations of tree growth at the stand level on a yearly to decennial scale, process-based models (PBMs) use LAI dynamics as a key variable for enabling the accurate prediction of tree growth over short time scales. Bridging the gap between PBMs and G&YMs could improve the prediction of forest growth and, therefore, carbon, water and nutrient fluxes by combining modeling approaches at the stand level.Our study aimed to estimate monthly changes of leaf area in response to climate variations from sparse measurements of foliage area and biomass. A leaf population probabilistic model (SLCD) was designed to simulate foliage renewal. The leaf population was distributed in monthly cohorts, and the total population size was limited depending on forest age and productivity. Foliage dynamics were driven by a foliation function and the probabilities ruling leaf aging or fall. Their formulation depends on the forest environment.The model was applied to three tree species growing under contrasting climates and soil types. In tropical Brazilian evergreen broadleaf eucalypt plantations, the phenology was described using 8 parameters. A multi-objective evolutionary algorithm method (MOEA) was used to fit the model parameters on litterfall and LAI data over an entire stand rotation. Field measurements from a second eucalypt stand were used to validate the model. Seasonal LAI changes were accurately rendered for both sites (R-2 = 0.898 adjustment, R-2 = 0.698 validation). Litterfall production was correctly simulated (R-2 = 0.562, R-2 = 0.4018 validation) and may be improved by using additional validation data in future work. In two French temperate deciduous forests (beech and oak), we adapted phenological sub-modules of the CASTANEA model to simulate canopy dynamics, and SLCD was validated using LAI measurements. The phenological patterns were simulated with good accuracy in the two cases studied. However, IA/max was not accurately simulated in the beech forest, and further improvement is required.Our probabilistic approach is expected to contribute to improving predictions of LAI dynamics. The model formalism is general and suitable to broadleaf forests for a large range of ecological conditions. (C) 2014 Elsevier B.V. All rights reserved.

Structural and functional insights into the conductive pili of Geobacter sulfurreducens revealed in molecular dynamics simulations

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Surgical Performance During Laparoscopic Radical Nephrectomy Is Improved With Training in a Porcine Model

Background and Purpose: Becoming proficient in laparoscopic surgery is dependent on the acquisition of specialized skills that can only be obtained from specific training. This training could be achieved in various ways using inanimate models, animal models, or live patient surgery-each with its own pros and cons. Currently, there are substantial data that support the benefits of animal model training in the initial learning of laparoscopy. Nevertheless, whether these benefits extent themselves to moderately experienced surgeons is uncertain. The purpose of this study was to determine if training using a porcine model results in a quantifiable gain in laparoscopic skills for moderately experienced laparoscopic surgeons. Materials and Methods: Six urologists with some laparoscopic experience were asked to perform a radical nephrectomy weekly for 10 weeks in a porcine model. The procedures were recorded, and surgical performance was assessed by two experienced laparoscopic surgeons using a previously published surgical performance assessment tool. The obtained data were then submitted to statistical analysis. Results: With training, blood loss was reduced approximately 45% when comparing the averages of the first and last surgical procedures (P = 0.006). Depth perception showed an improvement close to 35% (P = 0.041), and dexterity showed an improvement close to 25% (P = 0.011). Total operative time showed trends of improvement, although it was not significant (P = 0.158). Autonomy, efficiency, and tissue handling were the only aspects that did not show any noteworthy change (P = 0.202, P = 0.677, and P = 0.456, respectively). Conclusions: These findings suggest that there are quantifiable gains in laparoscopic skills obtained from training in an animal model. Our results suggest that these benefits also extend to more advanced stages of the learning curve, but it is unclear how far along the learning curve training with animal models provides a clear benefit for the performance of laparoscopic procedures. Future studies are necessary to confirm these findings and better understand the impact of this learning tool on surgical practice.

Effective carrying capacity and analytical solution of a particular case of the Richards-like two-species population dynamics model

We consider a generalized two-species population dynamic model and analytically solve it for the amensalism and commensalism ecological interactions. These two-species models can be simplified to a one-species model with a time dependent extrinsic growth factor. With a one-species model with an effective carrying capacity one is able to retrieve the steady state solutions of the previous one-species model. The equivalence obtained between the effective carrying capacity and the extrinsic growth factor is complete only for a particular case, the Gompertz model. Here we unveil important aspects of sigmoid growth curves, which are relevant to growth processes and population dynamics. (C) 2011 Elsevier B.V. All rights reserved.

Molecular Dynamics Investigations of PRODAN in a DLPC Bilayer

Molecular dynamics computer simulations have been performed to identify preferred positions of the fluorescent probe PRODAN in a fully hydrated DLPC bilayer in the fluid phase. In addition to the intramolecular charge-transfer first vertical excited state, we considered different charge distributions for the electronic ground state of the PRODAN molecule by distinct atomic charge models corresponding to the probe molecule in vacuum as well as polarized in a weak and a strong dielectric solvent (cyclohexane and water). Independent on the charge distribution model of PRODAN, we observed a preferential orientation of this molecule in the bilayer with the dimethylamino group pointing toward the membrane's center and the carbonyl oxygen toward the membrane's interface. However, changing the charge distribution model of PRODAN, independent of its initial position in the equilibrated DLPC membrane, we observed different preferential positions. For the ground state representation without polarization and the in-cyclohexane polarization, the probe maintains its position close to the membrane's center. Considering the in-water polarization model, the probe approaches more of the polar headgroup region of the bilayer, with a strong structural correlation with the choline group, exposing its oxygen atom to water molecules. PRODAN's representation of the first vertical excited state with the in-water polarization also approaches the polar region of the membrane with the oxygen atom exposed to the bilayer's hydration shell. However, this model presents a stronger structural correlation with the phosphate groups than the ground state. Therefore, we conclude that the orientation of the PRODAN molecule inside the DLPC membrane is well-defined, but its position is very sensitive to the effect of the medium polarization included here by different models for the atomic charge distribution of the probe.

Characterization of suramin binding sites on the human group IIA secreted phospholipase A(2) by site-directed mutagenesis and molecular dynamics simulation

Suramin is a polysulphonated naphthylurea with inhibitory activity against the human secreted group IIA phospholipase A(2) (hsPLA2GIIA), and we have investigated suramin binding to recombinant hsPLA2GIIA using site-directed mutagenesis and molecular dynamics (MD) simulations. The changes in suramin binding affinity of 13 cationic residue mutants of the hsPLA2GIIA was strongly correlated with alterations in the inhibition of membrane damaging activity of the protein. Suramin binding to hsPLA2GIIA was also studied by MD simulations, which demonstrated that altered intermolecular potential energy of the suramin/mutant complexes was a reliable indicator of affinity change. Although residues in the C-terminal region play a major role in the stabilization of the hsPLA2GIIA/suramin complex, attractive and repulsive hydrophobic and electrostatic interactions with residues throughout the protein together with the adoption of a bent suramin conformation, all contribute to the stability of the complex. Analysis of the h5PLA2GIIA/suramin interactions allows the prediction of the properties of suramin analogues with improved binding and higher affinities which may be candidates for novel phospholipase A(2) inhibitors. (C) 2012 Elsevier Inc. All rights reserved.

Spectroscopic properties from hybrid QM, MM molecular dynamics simulation

The central aim of this thesis work is the application and further development of a hybrid quantum mechanical/molecular mechanics (QM/MM) based approach to compute spectroscopic properties of molecules in complex chemical environments from electronic structure theory. In the framework of this thesis, an existing density functional theory implementation of the QM/MM approach is first used to calculate the nuclear magnetic resonance (NMR) solvent shifts of an adenine molecule in aqueous solution. The findings show that the aqueous solvation with its strongly fluctuating hydrogen bond network leads to specific changes in the NMR resonance lines. Besides the absolute values, also the ordering of the NMR lines changes under the influence of the solvating water molecules. Without the QM/MM scheme, a quantum chemical calculation could have led to an incorrect assignment of these lines. The second part of this thesis describes a methodological improvement of the QM/MM method that is designed for cases in which a covalent chemical bond crosses the QM/MM boundary. The development consists in an automatized protocol to optimize a so-called capping potential that saturates the electronic subsystem in the QM region. The optimization scheme is capable of tuning the parameters in such a way that the deviations of the electronic orbitals between the regular and the truncated (and "capped") molecule are minimized. This in turn results in a considerable improvement of the structural and spectroscopic parameters when computed with the new optimized capping potential within the QM/MM technique. This optimization scheme is applied and benchmarked on the example of truncated carbon-carbon bonds in a set of small test molecules. It turns out that the optimized capping potentials yield an excellent agreement of NMR chemical shifts and protonation energies with respect to the corresponding full molecules. These results are very promising, so that the application to larger biological complexes will significantly improve the reliability of the prediction of the related spectroscopic properties.

Molecular dynamics simulations of sheared brush-like systems

Mit Hilfe von Molekulardynamik-Simulationen untersuchen wir bürstenartige Systeme unter guten Lösungsmittelbedingungen. Diese Systeme sind, dank ihren vielfältigen Beschaffenheiten, die von Molekularparametern und äußeren Bedingungen abhängig sind, wichtig für viele industrielle Anwendungen. Man vermutet, dass die Polymerbürsten eine entscheidende Rolle in der Natur wegen ihrer einzigartigen Gleiteigenschaften spielen. Ein vergröbertes Modell wird verwendet, um die strukturellen und dynamischen Eigenschaften zweier hochkomprimierter Polymerbürsten, die eine niedrige Reibung aufweisen, zu untersuchen. Allerdings sind die Lubrikationseigenschaften dieser Systeme, die in vielen biologischen Systemen vorhanden sind, beeinflußt. Wir untersuchen so-genannte "weiche Kolloide", die zwischen den beiden Polymerbürsten eingebettet sind, und wie diese Makroobjekte auf die Polymerbürsten wirken.rnrnNicht-Gleichgewichts-Molekulardynamik-Simulationen werden durchgeführt, in denen die hydrodynamischen Wechselwirkungen durch die Anwendung des DPD-Thermostaten mit expliziten Lösungsmittelmolekülen berücksichtigt werden. Wir zeigen, dass die Kenntnis der Gleichgewichtseigenschaften des Systems erlaubt, dynamische Nichtgleichgewichtsigenschaften der Doppelschicht vorherzusagen.rnrnWir untersuchen, wie die effektive Wechselwirkung zwischen kolloidalen Einschlüßen durch die Anwesenheit der Bürsten (in Abhängigkeit der Weichheit der Kolloide und der Pfropfdichte der Bürsten) beeinflußt wird. Als nächsten Schritt untersuchen wir die rheologische Antwort von solchen komplexen Doppelschichten auf Scherung. Wir entwickeln eine Skalen-Theorie, die die Abhängigkeit der makroskopischen Transporteigenschaften und der lateralen Ausdehnung der verankerten Ketten von der Weissenberg Zahl oberhalb des Bereichs, in dem die lineare Antwort-Theorie gilt, voraussagt. Die Vorhersagen der Theorie stimmen gut mit unseren und früheren numerischen Ergebnissen und neuen Experimenten überein. Unsere Theorie bietet die Möglichkeit, die Relaxationszeit der Doppelschicht zu berechnen. Wenn diese Zeit mit einer charakteristischen Längenskala kombiniert wird, kann auch das ''transiente'' (nicht-stationäre) Verhalten beschrieben werden.rnrnrnWir untersuchen die Antwort des Drucktensors und die Deformation der Bürsten während der Scherinvertierung für grosse Weissenberg Zahlen. Wir entwickeln eine Vorhersage für die charakteristische Zeit, nach der das System wieder den stationären Zustand erreicht.rnrnrnElektrostatik spielt eine bedeutende Rolle in vielen biologischen Prozessen. Die Lubrikationseigenschaften der Polymerbürsten werden durch die Anwesenheit langreichweitiger Wechselwirkungen stark beeinflusst. Für unterschiedliche Stärken der elektrostatischen Wechselwirkungen untersuchen wir rheologische Eigenschaften der Doppelschicht und vergleichen mit neutralen Systemen. Wir studieren den kontinuierlichen Übergang der Systemeigenschaften von neutralen zu stark geladenen Bürsten durch Variation der Bjerrumlänge und der Ladungsdichte.