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Alberto Hidalgo, Fabrizio Salomone, Nieves Fresno, Guillermo Orellana, Antonio Cruz, Jesus Perez-Gil
Pulmonary surfactant is a crucial system to stabilize the respiratory air-liquid interface. Furthermore, pulmonary surfactant has been proposed as an effective method for targeting drugs to the lungs. However, few studies have examined in detail the mechanisms of incorporation of drugs into surfactant, the impact of the presence of drugs on pulmonary surfactant performance at the interface under physiologically-meaningful conditions, or the ability of pulmonary surfactant to use the air-liquid interface to vehiculise drugs to long distances...
July 24, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Xiaojing Wu, Jean-Marie Teuler, Fabien Cailliez, Carine Clavaguera, Dennis R Salahub, Aurélien de la Lande
We propose a methodology for simulating attosecond electron dynamics in large molecular systems. Our approach is based on the combination of Real-Time Time-Dependent-Density-Functional-Theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol) with the point-charge-dipole model of electrostatic induction. We implemented this methodology in the software deMon2k that relies heavily on auxiliary fitted densities. In the context of RT-TDDFT/MMpol simulations, fitted densities allow the cost of the calculations to be reduced drastically on three fronts i) the Kohn-Sham potential, ii) the electric field created by the (fluctuating) electron cloud which is needed in the QM/MM interaction, and iii) the analysis of the fluctuating electron density on-the-fly...
July 24, 2017: Journal of Chemical Theory and Computation
Adrián Regos, Luis Tapia, Alberto Gil-Carrera, Jesús Domínguez
Monitoring protected areas (PAs) is essential for systematic evaluation of their effectiveness in terms of habitat protection, preservation and representativeness. This study illustrates how the use of species distribution models that combine remote sensing data and information about biodiversity surrogates can contribute to develop a systematic protocol for monitoring PAs. In particular, we assessed the effectiveness of the Natura 2000 (N2000) network, for conserving and preserving the representativeness of seven raptor species in a highly-dynamic landscape in northwest Spain between 2001 and 2014...
2017: PloS One
Jinfeng Liu, Xiao He
Accurate prediction of physicochemical properties of ionic liquids (ILs) is of great significance to understand and design novel ILs with unique properties. This study employed the electrostatically embedded generalized molecular fractionation (EE-GMF) method for accurate energy calculation of IL clusters. The accuracy and efficiency of the EE-GMF method are systematically assessed at different ab initio levels (including HF, DFT and MP2) with diverse basis sets. With the fixed charge model for the embedding field, the deviations of the EE-GMF approach from conventional full system calculations are within 2...
July 24, 2017: Physical Chemistry Chemical Physics: PCCP
Anastasia A Markina, Viktor A Ivanov, Pavel V Komarov, Alexei R Khokhlov, Shih-Huang Tung
The influence of inorganic salt on the structure of lecithin/bile salt mixtures in aqueous solution is studied by means of dissipative particle dynamics simulations. We propose a coarse-grained model of phosphatidylcholine and two types of bile salts (sodium cholate and sodium deoxycholate), and also take into account the presence of low molecular weight salt. This model allows us to study the system on rather large time and length scales (up to about ~20 µs and 50 nm) and to reveal mechanisms of experimentally observed increasing of viscosity upon increasing the low molecular weight salt concentration in this system...
July 24, 2017: Journal of Physical Chemistry. B
Ivan Popov, Andrew Weatherbee, I Alex Vitkin
A closed-form analytical expression is obtained for the spatio-temporal correlation function of the scattered radiation detected in fiber-based optical coherence tomography (OCT), assuming a clean optical system arrangement in the OCT sample arm. It is shown that the transverse flow component causes purely translational speckle motion with the predicted speckle velocity 2x higher than the velocity of the flowing particles as would be observed in the image plane under incoherent illumination. It is also shown that both speckle velocity and speckle radius do not depend on the position of the scattering volume relative to the focal plane, hence the derived correlation function is independent of the position of the scattering volume relative to the focal plane...
April 1, 2017: Biomedical Optics Express
Stefania Pallotta, Silvia Calusi, Leonardo Foggi, Riccardo Lisci, Laura Masi, Livia Marrazzo, Cinzia Talamonti, Lorenzo Livi, Gabriele Simontacchi
PURPOSE: Radiotherapy treatment of moving lesions is a challenging task in which different strategies can be used to adequately treat the tumor while sparing the surrounding tissue. The complexity of these strategies requires accurate and appropriate quality assurance tests. For this purpose, ADAM (Anthropomorphic Dynamic breAthing Model), a new phantom which simulates realistic patient breathing, was developed aiming to test the image quality and dose delivery in lung cancer treatments...
July 20, 2017: Physica Medica: PM
Laura Escorihuela, Alberto Fernández, Robert Rallo, Benjamí Martorell
The solubility of metal oxides is one of the key descriptors for the evaluation of their potential toxic effects, both in the bulk form and in nanoparticulated aggregates. Current work presents a new methodology for the in silico assessment of the solubility of metal oxides, which is demonstrated using a well-studied system, ZnO. The calculation of the solubility is based on statistical thermodynamics tools combined with Density Functional Tight Binding theory for the evaluation of the free energy exchange during the dissolution process...
July 20, 2017: Food and Chemical Toxicology
Shai Pilosof, Gili Greenbaum, Boris R Krasnov, Yuval R Zelnik
Epidemic spread in single-host systems strongly depends on the population's transmission network. However, little is known regarding the spread of epidemics across networks representing populations of multiple hosts. We explored cross-species transmission in a multilayer network where layers represent populations of two distinct hosts, and disease can spread across intralayer (within-host) and interlayer (between-host) edges. We developed an analytic framework for the SIR epidemic model to examine the effect of (i) source of infection and (ii) between-host asymmetry in infection probabilities, on disease risk...
July 21, 2017: Journal of Theoretical Biology
Ariane Scheuren, Esther Wehrle, Felicitas Flohr, Ralph Müller
Mechanically driven bone (re)modeling is a multiscale process mediated through complex interactions between multiple cell types and their microenvironments. However, the underlying mechanisms of how cells respond to mechanical signals are still unclear and are at the focus of the field of bone mechanobiology. Traditionally, this complex process has been addressed by reducing the system to single scales and cell types. It is only recently that more integrative approaches have been established to study bone mechanobiology across multiple scales in which mechanical load at the organ level is related to molecular responses at the cellular level...
July 22, 2017: Biomechanics and Modeling in Mechanobiology
Friedemann Pulvermüller
Neurocognitive and neurolinguistics theories make explicit statements relating specialized cognitive and linguistic processes to specific brain loci. These linking hypotheses are in need of neurobiological explanation. Recent mathematical models of human language mechanisms constrained by fundamental neuroscience principles and established knowledge about comparative neuroanatomy offer explanations for where, when and how language is processed in the human brain. In these models, network structure and connectivity along with action- and perception-induced correlation of neuronal activity co-determine neurocognitive mechanisms...
July 19, 2017: Progress in Neurobiology
Zdenek Futera, Niall J English
The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods...
July 21, 2017: Journal of Chemical Physics
Lucas B Newcomb, Mohammad Alaghemandi, Jason R Green
While hydrogen is a promising source of clean energy, the safety and optimization of hydrogen technologies rely on controlling ignition through explosion limits: pressure-temperature boundaries separating explosive behavior from comparatively slow burning. Here, we show that the emergent nonequilibrium chemistry of combustible mixtures can exhibit the quantitative features of a phase transition. With stochastic simulations of the chemical kinetics for a model mechanism of hydrogen combustion, we show that the boundaries marking explosive domains of kinetic behavior are nonequilibrium critical points...
July 21, 2017: Journal of Chemical Physics
Noriyuki Yoshii, Yuki Nimura, Kazushi Fujimoto, Susumu Okazaki
The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor...
July 21, 2017: Journal of Chemical Physics
R Horstmann, M Vogel
We perform molecular dynamics simulations to ascertain effects of the molecular polarity on structural and dynamical properties of water-like systems, in particular, on their glassy slowdown. To systematically vary the molecular dipole moments, we scale the partial charges of the established SPC/E and TIP4P/2005 models. In broad ranges of the molecular polarity, the studied SPC/E and TIP4P/2005 descendants show a density anomaly, which can be attributed to the removal of water molecules interstitial between the first and the second neighbor shells upon cooling...
July 21, 2017: Journal of Chemical Physics
W T Coffey, M Zarifakis, Y P Kalmykov, S V Titov, W J Dowling, A S Titov
The itinerant oscillator model describing rotation of a dipole about a fixed axis inside a cage formed by its surrounding polar molecules is revisited in the context of modeling the dielectric relaxation of a polar fluid via the Langevin equation. The dynamical properties of the model are studied by averaging the Langevin equations describing the complex orientational dynamics of two bodies (molecule-cage) over their realizations in phase space so that the problem reduces to solving a system of three index linear differential-recurrence relations for the statistical moments...
July 21, 2017: Journal of Chemical Physics
Zhijun Zhang, Xinzijian Liu, Zifei Chen, Haifeng Zheng, Kangyu Yan, Jian Liu
We show a unified second-order scheme for constructing simple, robust, and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB algorithm that has been recently investigated. We show that the scheme is also useful for other types of thermostats, such as the Andersen thermostat and Nosé-Hoover chain, regardless of whether the thermostat is deterministic or stochastic. In addition to analytical analysis, two 1-dimensional models and three typical real molecular systems that range from the gas phase, clusters, to the condensed phase are used in numerical examples for demonstration...
July 21, 2017: Journal of Chemical Physics
Yorghos Apostolopoulos, Michael K Lemke, Adam E Barry, Kristen Hassmiller Lich
BACKGROUND AND AIMS: The drinking environment is a complex system consisting of a number of heterogeneous, evolving, and interacting components, which exhibit circular causality and emergent properties. These characteristics reduce the efficacy of commonly used research approaches, which typically do not account for the underlying dynamic complexity of alcohol consumption and the interdependent nature of diverse factors influencing misuse over time. We use alcohol misuse among college students in the United States as an example for framing our argument for a complex systems paradigm...
July 22, 2017: Addiction
Mark A Phuong, Ke Bi, Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes...
July 22, 2017: Molecular Ecology
Todd Hurst, Volker Rehbock
We apply numerical optimal control methods to an existing algae growth model with the aim to determine the best performance of the model under known conditions using a variety of decision variables. We transform the system of differential algebraic equations in the existing model to a system of ordinary differential equations which introduces dynamics for average light intensity and chlorophyll. In addition we allow for variable nitrogen concentration of the inflow as well as variable initial nitrogen concentration of the raceway...
July 22, 2017: Biotechnology Progress
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