Mass distribution and skewness for passive scalar transport in pipes with polygonal and smooth cross sections

We extend our previous results characterizing the loading properties of a diffusing passive scalar advected by a laminar shear flow in ducts and channels to more general cross‐sectional shapes, including regular polygons and smoothed corner ducts originating from deformations of ellipses. For the case of the triangle and localized, cross‐wise uniform initial distributions, short‐time skewness is calculated exactly to be positive, while long‐time asymptotics shows it to be negative. Monte Carlo simulations confirm these predictions, and document the timescale for sign change. The equilateral triangle appears to be the only regular polygon with this property—all others possess positive skewness at all times. Alternatively, closed‐form flow solutions can be constructed for smooth deformations of ellipses, and illustrate how both nonzero short‐time skewness and the possibility of multiple sign switching in time is unrelated to domain corners. Exact conditions relating the median and the skewness to the mean are developed which guarantee when the sign for the skewness implies front (more mass to the right of the mean) or back (more mass to the left of the mean) “loading” properties of the evolving tracer distribution along the pipe. Short‐ and long‐time asymptotics confirm this condition, and Monte Carlo simulations verify this at all times. The simulations are also used to examine the role of corners and boundaries on the distribution for short‐time evolution of point source , as opposed to cross‐wise uniform, initial data.     

Theoretical Design of Biodegradable Phthalic Acid Ester Derivatives in Marine and Freshwater Environments

The biodegradability of phtalic acid esters in marine and freshwater environments was characterized by their binding free energy with corresponding degrading enzymes. According to comprehensive biodegradation effects weights, the binding free energy values were converted into dimensionless efficacy coefficient using ratio normalization method. Then, considering comprehensive dual biodegradation effects value and the structural parameters of PAEs in both marine and freshwater environments, a 3D-QSAR pharmacophore model was constructed, five PAE derivatives (DBP−COOH, DBP−CHO, DBP−OH, DINP−NH₂, and DINP−NO₂) were screened out based on their environmental friendliness, functionality and stability. The prediction of biodegradation effects on five PAE derivatives by biodegradation models in marine and freshwater environment increased by 15.90 %, 15.84 %, 27.21 %, 12.33 %, and 8.32 %, and 21.57 %, 15.21 %, 20.99 %, 15.10 %, and 9.74 %, respectively. By simulating the photodegradation path of the PAE derivative molecular, it was found that DBP−OH can generate ^.OH and provides free radicals for the photodegradation of microplastics in the environment.     

Studying the Electrically Driven Switching of the Planar Light Guide

Liquid crystalline materials can be used as an active media for the new generation of planar light guides. The main characteristics which governs light-guiding and switching abilities of such devices are the spatial distributions of the refraction indices (defined via the distribution of nematic director) for the liquid crystal confined within a light-guiding pore. We aim to obtain these distributions from the molecular dynamics simulation of the liquid crystalline cell with the homeotropic boundary conditions being applied. We discuss the reorientation kinetics of the homeotropic-planar transition and obtain the equilibrium director profile upon application of the planar reorienting field.     

Phonon-mediated heat dissipation in a monatomic lattice: case study on Ni

The recently introduced analytical model for the heat current autocorrelation function of a crystal with a monatomic lattice [Evteev et al., Phil. Mag. 94 (2014) p. 731 and 94 (2014) p. 3992] is employed in conjunction with the Green–Kubo formalism to investigate in detail the results of an equilibrium molecular dynamics calculations of the temperature dependence of the lattice thermal conductivity and phonon dynamics in f.c.c. Ni. Only the contribution to the lattice thermal conductivity determined by the phonon–phonon scattering processes is considered, while the contribution due to phonon–electron scattering processes is intentionally ignored. Nonetheless, during comparison of our data with experiment an estimation of the second contribution is made. Furthermore, by comparing the results obtained for f.c.c. Ni model to those for other models of elemental crystals with the f.c.c. lattice, we give an estimation of the scaling relations of the lattice thermal conductivity with other lattice properties such as the coefficient of thermal expansion and the bulk modulus. Moreover, within the framework of linear response theory and the fluctuation-dissipation theorem, we extend our analysis in this paper into the frequency domain to predict the power spectra of equilibrium fluctuations associated with the phonon-mediated heat dissipation in a monatomic lattice. The practical importance of the analytical treatment lies in the fact that it has the potential to be used in the future to efficiently decode the generic information on the lattice thermal conductivity and phonon dynamics from a power spectrum of the acoustic excitations in a monatomic crystal measured by a spectroscopic technique in the frequency range of about 1–20 THz.     

Effect of additive length and chemistry on the morphology of blends of conjugated thiophenes and fullerene derivative acceptor molecules

Small molecule additives have been shown to increase the device efficiency of conjugated polymer (donor) and fullerene derivative (acceptor) based organic solar cells by modifying the morphology of the device active layer. In this paper we conduct a systematic study of how additives affect the donor‐acceptor morphology using molecular dynamics simulations of blends of thiophene‐based oligomers, mimicking poly(3‐dodecylthiophene) (P3DDT) or poly(2,2′:5′,2”‐3,3”‐didocyl‐terthiophene) (PTTT), and fullerene derivatives with additives of varying length and chemical functionalization, mimicking experimentally used additives like methyl ester additives, diiodooctane, and alkanedithiols. We find that functionalization of additives with end groups that are attracted to acceptor molecules are necessary to induce increased donor‐acceptor macrophase separation. In blends where acceptors intercalate between oligomer alkyl side chains, functionalized additives decrease acceptor intercalation. Functionalized additives with shorter alkyl segments increase acceptor macrophase separation more than additives with same chemical functionalization but longer alkyl segments. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1046–1057     

Ionic Conductivity of β‐Cyclodextrin–Polyethylene‐Oxide/Alkali‐Metal‐Salt Complex

Highly conductive, crystalline, polymer electrolytes, β‐cyclodextrin (β‐CD)–polyethylene oxide (PEO)/LiAsF₆ and β‐CD–PEO/NaAsF₆, were prepared through supramolecular self‐assembly of PEO, β‐CD, and LiAsF₆/NaAsF₆. The assembled β‐CDs form nanochannels in which the PEO/X⁺ (X=Li, Na) complexes are confined. The nanochannels provide a pathway for directional motion of the alkali metal ions and, at the same time, separate the cations and the anions by size exclusion.     

Dynamics of water and sodium in gels under salt‐induced phase transition

Synthetic and biological gels undergo a sharp volume phase transition when subjected to a variety of environmental changes. Water and ion dynamics within swollen and compact phases are critical for understanding fundamental concepts in cellular (specifically neuronal) biophysics, for models of bound, free, or ordered water in complex environments; and for practical applications such as the design of gels for drug release, biomimetics, sensors, or actuators. In this work, we find, for the first time, basic physical parameters that shed light on the interaction of gels with water and electrolytes, across a volume phase transition. Water within a gel can be separated into bound and free populations with high exchange rate. We show that free water dynamics in compact gels are the same as those in pure water. Bound water was found to comprise a single layer around the polymers in both phases, with a correlation time three orders of magnitude higher than that of free water. Most importantly, salt‐induced phase transition was found to be different from a standard coil‐globule transition (e.g., temperature‐induced), with no rejection of bound water as the gel compacts. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1620–1628     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.