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Scalableand low-cost methods to align and orient block copolymer(BCP) films and membranes are critical for their adaptation for nonlithographicapplications. Cold zone annealing (CZA) can align BCP microdomainsand is scalable via roll-to-roll (R2R) manufacturing. However, theefficacy of orientation by CZA is strongly dependent on the thermalzone velocity (Vcza). Optimization ofthis rate can be time-consuming and tedious. To address this shortcoming,we report rotational or radial CZA (RCZA) that provides a combinatorialapproach to efficiently determine how linear Vczarate impacts microdomain orientation. RCZA rapidly identifiesthe optimal CZA velocities for perpendicular orientation of cylindersin polystyrene-block-poly(methyl methacrylate) filmsthat previously required tens of measurements [Macromolecules2012, 45, 7107], demonstratedhere with much finer velocity resolution using three overlapping radialregimes. Notably, the efficacy of CZA for perpendicular alignmentrapidly decays for Vcza> 10 μm/s.To overcome this limitation, the addition of 2 wt % 1-ethyl-3-methylimidazoliumbis(trifluoromethylsulfonyl)imide sufficiently altersthe surface tension and segmental relaxations via reduced viscosityto increase the processing window for perpendicular cylinders, approximately75% at Vcza≈ 330 μm/s, approachingR2R speeds. Further increasing ionic liquid content to 5 wt % leadsto mostly parallel orientation due to surface wetting. Ionic liquidscan dramatically increase BCP processing speeds for applications,such as membranes, and RCZA can efficiently map out the optimal processingparameters. [ABSTRACT FROM AUTHOR]

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNAmodels are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNAmodel with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model which prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states. [ABSTRACT FROM AUTHOR]

We present an event-driven molecular dynamics study of glass formation in two-dimensional binary mixtures composed of hard disks and hard ellipses, where both types of particles have the same area. We demonstrate that characteristic glass-formation behavior appears upon compression under appropriate conditions in such systems. In particular, while a rotational glass transition occurs only for the ellipses, both types of particles undergo a kinetic arrest in the translational degrees of freedom at a single density. The translational dynamics for the ellipses is found to be faster than that for the disks within the same system, indicating that shape anisotropy promotes the translational motion of particles. We further examine the influence of mixture's composition and aspect ratio on the glass formation. For the mixtures with an ellipse aspect ratio of k = 2, both translational and rotational glass transition densities decrease with increasing the disk concentration at a similar rate, and hence, the two glass transitions remain close to each other at all concentrations investigated. By elevating k, however, the rotational glass transition density diminishes at a faster rate than the translational one, leading to the formation of an orientational glass for the ellipses between the two transitions. Our simulations imply that mixtures of particles with different shapes emerge as a promising model for probing the role of particle shape in determining the properties of glass-forming liquids. Furthermore, our work illustrates the potential of using knowledge concerning the dependence of glass-formation properties on mixture's composition and particle shape to assist in the rational design of amorphous materials. [ABSTRACT FROM AUTHOR]

We study the point-to-set length scales and dynamics in three-dimensional Kob-Andersen glass-forming liquids with amorphous boundary conditions by using molecular dynamics simulation, where a set of particles in an equilibrium configuration are pinned while other particles move as before. We consider three different geometries, i.e., spherical cavity, cubic cavity, and walls, for the pinning set of particles. We present the growing static and dynamic point-to-set correlation length scales in the temperature range higher than the ideal mode-coupling theory transition temperature of the bulk. Our results reveal that the two-point static spatial correlations are almost the same for these three geometries at the same temperature, which implies weak geometry dependence on the structure of such glass-forming liquids. By analyzing z (the distance from the wall) dependent point-to-set overlaps, we find that the particles in the layers near the pinning wall relax slower than those far away from the wall. Associated with the dynamical slowdown, the static length scale increases modestly while the dynamic length scale increases dramatically as the temperature is lowered. Compared with the two cavities, the "Walls" system relaxes faster at the same temperature and the same distance from the wall and has smaller length scales. Moreover, the relation between time scale and static length scales depends on the degree of supercooling and the type of geometries. We did not see any clear evidence for the one-to-one correspondence between static and dynamic point-to-set length scales, and also for the one-to-one correspondence between static length scales and relaxation time in the deep supercooled regime. Our results provide clues for the existence of multi-relaxation modes in the supercooled regime in three-dimensional Kob-Andersen glass-forming liquids. [ABSTRACT FROM AUTHOR]

We study the influence of shape of Janus particles on their orientation and surface activity at fluidfluid interfaces via molecular dynamics simulations. The Janus particles are characterized by two regions with different wettability divided along their major axes. Three types of Janus particles are considered: Janus spheres, Janus rods, and Janus disks. We find that Janus spheres and Janus rods prefer one orientation at the interface, regardless of the surface property. In contrast, Janus disks can adopt one of two orientations when adhered to a fluid-fluid interface: one orientation corresponds to the equilibrium state and the other is a kinetically trapped metastable state. The orientation of Janus disks strongly depends on the disk characteristics, such as their size, aspect ratio, and surface property. Furthermore, we find that changes in the shape of Janus particles strongly influence the interfacial tension at the fluid-fluid interface. According to the time evolution of the interfacial tension, the adsorption of Janus particles is characterized by three adsorption stages based on different surface activities and adsorption kinetics depending on the particle shape. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are adopted to calculate the equation of state characteristic parameters P, , and Tof isotactic polypropylene (iPP) and poly(ethylene-co-octene) (PEOC), which can be further used in the Sanchez−Lacombe lattice fluid theory (SLLFT) to describe the respective physical properties. The calculated Tis a function of the temperature, which was also found in the literature. To solve this problem, we propose a Boltzmann fitting of the data and obtain Tat the high-temperature limit. With these characteristic parameters, the pressure−volume−temperature (PVT) data of iPP and PEOC are predicted by the SLLFT equation of state. To justify the correctness of our results, we also obtain the PVT data for iPP and PEOC by experiments. Good agreement is found between the two sets of data. By integrating the Euler−Lagrange equation and the Cahn−Hilliard relation, we predict the density profiles and the surface tensions for iPP and PEOC, respectively. Furthermore, a recursive method is proposed to obtain the characteristic interaction energy parameter between iPP and PEOC. This method, which does not require fitting to the experimental phase equilibrium data, suggests an alternative way to predict the phase diagrams that are not easily obtained in experiments. As an example, in the framework of SLLFT, the spinodal curve for the iPP/PEOC blend is predicted at the low molecular weights that are used in the simulations. [ABSTRACT FROM AUTHOR]

The particle-transfer molecular-dynamics technique is adopted to construct the Lennard-Jones fluid gas-liquid phase diagram. Detailed study of the dependence of the simulation results on the system size and the cutoff distance is performed to test the validity of the simulation technique. Both the traditional cutoff plus long-range correction (CPC) and Ewald summation methods are used in the simulations to calculate the interactions. In the intermediate range of temperatures, the results with the Ewald summation method are almost the same as those with the CPC method. However, in the range close to the critical point, the results with the CPC method deviate from those with the Ewald summation. Compared with the results obtained via the Ewald summation in a smaller system, simply increasing the system size in the CPC scheme may not give better results. [ABSTRACT FROM AUTHOR]

Accumulation and aggregation of amyloid β-protein (Aβ) play an important role in the pathogenesis of Alzheimer's disease. There has been increased interest in finding new anti-amyloidogenic compounds to inhibit Aβ aggregation. Herein, thioflavin T fluorescent assay and transmission electron microscopy results showed that hematoxylin, a natural organic molecule extracted from Caesalpinia sappan, was a powerful inhibitor of Aβ42 fibrillogenesis. Circular dichroism studies revealed hematoxylin reduced the β-sheet content of Aβ42 and made it assemble into antiparallel arrangement, which induced Aβ42 to form off-pathway aggregates. As a result, hematoxylin greatly alleviated Aβ42-induced cytotoxicity. Molecular dynamics simulations revealed the detailed interactions between hematoxylin and Aβ42. Four binding sites of hematoxylin on Aβ42 hexamer were identified, including the N-terminal region, S8GY10 region, turn region, and C-terminal region. Notably, abundant hydroxyl groups made hematoxylin prefer to interact with Aβ42 via hydrogen bonds. This also contributed to the formation of π-π stacking and hydrophobic interactions. Taken together, the research proved that hematoxylin was a potential agent against Aβ fibrillogenesis and cytotoxicity. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been performed to investigate the structures of Lennard—Jones (LJ) nanowires (NWs) encapsulated in carbon nanotubes (CNTs). We find that the structures of NWs in a small CNT only adopt multi-shell motifs, while the structures of NWs in a larger CNT tend to adopt various motifs. Among these structures, three of them have not been reported previously. The phase boundaries among these structures are obtained regarding filling fractions, as well as the interaction between NWs and CNTs. [ABSTRACT FROM AUTHOR]

Combined docking and molecular dynamics (MD) simulations are carried out for the rational design of affinity peptide ligand of tissue-type plasminogen activator (t-PA). Ten amino acids that have high affinity to three different regions of t-PA are identified by the amino acids location method on the basis of candidate pocket structure of t-PA. Then, 14 tetrapeptides are built and docked into the candidate pocket of t-PA. The absolute value of the Dscore calculated from the docking simulation is used to assess the affinity of a peptide for t-PA. Consequently, six tetrapeptides that have high Dscore values are selected and linked to a spacer arm of [ᅳNH(CH2)6NH2] that is present on EAH Sepharose gel. The linked compounds are further evaluated by docking into the candidate pocket of t-PA. As a result, the tetrapeptide QDES with the highest Dscore value is selected. Molecular surface analysis with the MOLCAD program reveals that electrostatic interactions and hydrogen bonds (H-bonds) contribute to the affinity interactions between the tetrapeptide and t-PA. MD simulations indicate that QDES-t-PA complex keeps stable, and the distances between the carboxyl groups of Asp189, Gln192 and Asp194 and the charged amino group of glutamine change little. Moreover, all the nine H-bonds found in the docking simulation are confirmed by the MD simulations. It is also found that three water molecules act as bridges between the ligand and the protein pocket by hydrogen bonding. Finally, high binding affinity and specificity of the peptide ligand are confirmed by the purification of t-PA from crude porcine heart extract using the immobilized-ligand column for affinity chromatography. [Copyright &y& Elsevier]