Enforcing Local DNA Kinks by Sequence-Selective Trisintercalating Oligopeptides of a Tricationic Porphyrin: A Polarizable Molecular Dynamics Study.

Bisacridinyl-bisarginyl porphyrin (BABAP) is a trisintercalating derivative of a tricationic porphyrin, formerly designed and synthesized in order to selectively target and photosensitize the ten-base pair palindromic sequence d(CGGGCGCCCG)2 . We resorted to the previously derived (Far et al., 2004) lowest energy-minimized (EM) structure of the BABAP complex with this sequence as a starting point. We performed polarizable molecular dynamics (MD) on this complex. It showed, over a 150 ns duration, the persistent binding of the Arg side-chain on each BABAP arm to the two G bases upstream from the central porphyrin intercalation site. We subsequently performed progressive shortenings of the connector chain linking the Arg-Gly backbone to the acridine, from n=6 methylenes to 4, followed by removal of the Gly backbone and further connector shortenings, from n=4 to n=1. These resulted into progressive deformations ('kinks') of the DNA backbone. In its most accented kinked structure, the DNA backbone was found to have a close overlap with that of DNA bound to Cre recombinase, with, at the level of one acridine intercalation site, negative roll and positive tilt values consistent with those experimentally found for this DNA at its own kinked dinucleotide sequence. Thus, in addition to their photosensitizing properties, some BABAP derivatives could induce sequence-selective, controlled DNA deformations, which are targets for cleavage by endonucleases or for repair enzymes.

Solitary-like and modulated wavepackets in the Couette-Taylor flow with a radial temperature gradient.

We have performed numerical and experimental studies of the flow in a large aspect ratio Couette-Taylor system with a rotating inner cylinder and a fixed radial temperature gradient. The base flow state is a superposition of an azimuthal flow induced by rotation and an axial large convective cell induced by the temperature gradient. For a relatively large temperature gradient, the rotation rate of the inner cylinder destabilizes the convective cell to give rise to travelling wave pattern through a subcritical bifurcation. This wave pattern is associated with a temperature mode and it consists of helical vortices travelling in the annulus. In a small range of the rotation rate, helical vortices have longitudinal meandering leading to the formation of kinks randomly distributed, leading to spatio-temporal disordered patterns. The flow becomes regular for a large interval of rotation rate. The friction, the momentum and the heat transfer coefficients are computed and found to be independent of the heating direction. This article is part of the theme issue 'Taylor-Couette and related flows on the centennial of Taylor's seminal Philosophical Transactions paper (part 1)'.

Defect Facilitated Phonon Transport through Kinks in Boron Carbide Nanowires.

Nanowires of complex morphologies, such as kinked wires, have been recently synthesized and demonstrated for novel devices and applications. However, the effects of these morphologies on thermal transport have not been well studied. Through systematic experimental measurements, we show that single-crystalline, defect-free kinks in boron carbide nanowires can pose a thermal resistance up to ∼30 times larger than that of a straight wire segment of equivalent length. Analysis suggests that this pronounced resistance can be attributed to the combined effects of backscattering of highly focused phonons and required mode conversion at the kink. Interestingly, it is also found that instead of posing resistance, structural defects in the kink can actually assist phonon transport through the kink and reduce its resistance. Given the common kink-like wire morphology in nanoelectronic devices and required low thermal conductivity for thermoelectric devices, these findings have important implications in precise thermal management of electronic devices and thermoelectrics.

Structures of yeast mitochondrial ADP/ATP carriers support a domain-based alternating-access transport mechanism.

The mitochondrial ADP/ATP carrier imports ADP from the cytosol and exports ATP from the mitochondrial matrix. The carrier cycles by an unresolved mechanism between the cytoplasmic state, in which the carrier accepts ADP from the cytoplasm, and the matrix state, in which it accepts ATP from the mitochondrial matrix. Here we present the structures of the yeast ADP/ATP carriers Aac2p and Aac3p in the cytoplasmic state. The carriers have three domains and are closed at the matrix side by three interdomain salt-bridge interactions, one of which is braced by a glutamine residue. Glutamine braces are conserved in mitochondrial carriers and contribute to an energy barrier, preventing the conversion to the matrix state unless substrate binding occurs. At the cytoplasmic side a second salt-bridge network forms during the transport cycle, as demonstrated by functional analysis of mutants with charge-reversed networks. Analyses of the domain structures and properties of the interdomain interfaces indicate that interconversion between states involves movement of the even-numbered α-helices across the surfaces of the odd-numbered α-helices by rotation of the domains. The odd-numbered α-helices have an L-shape, with proline or serine residues at the kinks, which functions as a lever-arm, coupling the substrate-induced disruption of the matrix network to the formation of the cytoplasmic network. The simultaneous movement of three domains around a central translocation pathway constitutes a unique mechanism among transport proteins. These findings provide a structural description of transport by mitochondrial carrier proteins, consistent with an alternating-access mechanism.

Functional role of water in membranes updated: A tribute to Träuble.

The classical view of a cell membrane is as a hydrophobic slab in which only nonpolar solutes can dissolve and permeate. However, water-soluble non-electrolytes such as glycerol, erythritol, urea and others can permeate lipid membranes in the liquid crystalline state. Moreover, recently polar amino acid's penetration has been explained by means of molecular dynamics in which appearance of water pockets is postulated. According to Träuble (1971), water diffuses across the lipid membranes by occupying holes formed in the lipid matrix due to fluctuations of the acyl chain trans-gauche isomers. These holes, named "kinks" have the molecular dimension of CH2 vacancies. The condensation of kinks may form aqueous spaces into which molecular species of the size of low molecular weight can dissolve. This molecular view can explain permeability properties considering that water may be distributed along the hydrocarbon chains in the lipid matrix. The purpose of this review is to consolidate the mechanism anticipated by Träuble by discussing recent data in literature that directly correlates the molecular state of methylene groups of the lipids with the state of water in each of them. In addition, the structural properties of water near the lipid residues can be related with the water activity triggering kink formation by changes in the head group conformation that induces the propagation along the acyl chains and hence to the diffusion of water.

Orientation-dependent growth mechanisms of graphene islands on Ir(111).

Using low-energy electron microscopy, we find that the mechanisms of graphene growth on Ir(111) depend sensitively on island orientation with respect to Ir. In the temperature range of 750-900 °C, we observe that growing rotated islands are more faceted than islands aligned with the substrate. Further, the growth velocity of rotated islands depends not only on the C adatom supersaturation but also on the geometry of the island edge. We deduce that the growth of rotated islands is kink-nucleation-limited, whereas aligned islands are kink-advancement-limited. These different growth mechanisms are attributed to differences in the graphene edge binding strength to the substrate.

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.

Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D-shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti-Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.

Mobile Kink Solitons in a Van der Waals Charge-Density-Wave Layer.

Kinks, point-like geometrical defects along dislocations, domain walls, and DNA, are stable and mobile, as solutions of a sine-Gordon wave equation. While they are widely investigated for crystal deformations and domain wall motions, electronic properties of individual kinks have received little attention. In this work, electronically and topologically distinct kinks are discovered along electronic domain walls in a correlated van der Waals insulator of 1T-TaS2 . Mobile kinks and antikinks are identified as trapped by pinning defects and imaged in scanning tunneling microscopy. Their atomic structures and in-gap electronic states are unveiled, which are mapped approximately into Su-Schrieffer-Heeger solitons. The twelvefold degeneracy of the domain walls in the present system guarantees an extraordinarily large number of distinct kinks and antikinks to emerge. Such large degeneracy together with the robust geometrical nature may be useful for handling multilevel information in van der Waals materials architectures.

Complete internal carotid artery coil after huge carotid body tumor resection.

In this brief article, we present an 82-year-old female who came to our care due to a carotid body tumor of the right side of the neck. After an uneventful removal of the tumor, we discovered a 360-degree coil in the internal carotid artery which was not observed in the preoperative imaging. After resection, we believe that the free space left by the large tumor and prior mass effect of the tumor on the internal carotid artery have led to carotid coiling.

Plastic Deformation of High Density Polyethylene with Extended-Chain Crystal Morphology.

Samples of polyethylene with extended-chain crystal morphology, obtained by crystallization under high pressure, were subjected to uniaxial compression to various strains. Accompanying structural changes were analyzed using scanning electron microscopy. At the true strain of e = 0.2−0.3 the microbuckling instability was observed in longitudinally loaded lamellae, resulting in the formation of angular kinks. This induced a rapid reorientation of the lamellae, facilitating their further deformation by crystallographic slip. Microbuckling instability was found to occur earlier than in samples with folded-chain crystal morphology (e = 0.3−0.4) due to a smaller ratio of the amorphous to crystalline layer thickness. SEM observations demonstrated that the microbuckling instability begins with small undulation in long lamellae. Sharp angular lamellar kinks develop from the initial undulation through intense plastic deformation by crystallographic slip along the chain direction. The same slip system was found to operate throughout the kink, including the tip region as well as both limbs. In contrast to thin folded-chain lamellae that often undergo fragmentation during deformation, the thick extended-chain lamellae deform stably by chain slip and retain their continuity up to high strains, e > 1.6. This stability of deformation is related to the large thickness of extended-chain lamellae.

Microscopic Deformation Modes and Impact of Network Anisotropy on the Mechanical and Electrical Performance of Five-fold Twinned Silver Nanowire Electrodes.

Silver nanowire (AgNW) networks show excellent optical, electrical, and mechanical properties, which make them ideal candidates for transparent electrodes in flexible and stretchable devices. Various coating strategies and testing setups have been developed to further improve their stretchability and to evaluate their performance. Still, a comprehensive microscopic understanding of the relationship between mechanical and electrical failure is missing. In this work, the fundamental deformation modes of five-fold twinned AgNWs in anisotropic networks are studied by large-scale SEM straining tests that are directly correlated with corresponding changes in the resistance. A pronounced effect of the network anisotropy on the electrical performance is observed, which manifests itself in a one order of magnitude lower increase in resistance for networks strained perpendicular to the preferred wire orientation. Using a scale-bridging microscopy approach spanning from NW networks to single NWs to atomic-scale defects, we were able to identify three fundamental deformation modes of NWs, which together can explain this behavior: (i) correlated tensile fracture of NWs, (ii) kink formation due to compression of NWs in transverse direction, and (iii) NW bending caused by the interaction of NWs in the strained network. A key observation is the extreme deformability of AgNWs in compression. Considering HRTEM and MD simulations, this behavior can be attributed to specific defect processes in the five-fold twinned NW structure leading to the formation of NW kinks with grain boundaries combined with V-shaped surface reconstructions, both counteracting NW fracture. The detailed insights from this microscopic study can further improve fabrication and design strategies for transparent NW network electrodes.

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations.

HIGHLIGHTS: DNA kinking is inevitable for the highly anisotropic 1D-1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D-> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

Ultrathin 2D Fe-Nanosheets Stabilized by 2D Mesoporous Silica: Synthesis and Application in Ammonia Synthesis.

Developing high-performance Fe-based ammonia catalysts through simple and cost-efficient methods has received an increased level of attention. Herein, we report for the first time, the synthesis of two-dimensional (2D) FeOOH nanoflakes encapsulated by mesoporous SiO2 (mSiO2) via a simple solution-based method for ammonia synthesis. Due to the sticking of the mSiO2 coating layers and the limited spaces in between, the Fe after reduction retains the 2D morphology, showing high resistance against the sintering in the harsh Haber-Bosch process. Compared to supported Fe particles dispersed on mSiO2 spheres, the coated catalyst shows a significantly improved catalytic activity by 50% at 425 °C. Thermal desorption spectroscopy (TDS) reveals the existence of a higher density of reactive sites for N2 activation in the 2D Fe catalyst, which is possibly coupled to a larger density of surface defect sites (kinks, steps, point defects) that are generally considered as active centers in ammonia synthesis. Besides the structural impact of the coating on the 2D Fe, the electronic one is elucidated by partially substituting Si with Al in the coating, confirmed by 29Si and 27Al magic-angle spinning nuclear magnetic resonance (MAS NMR). An increased apparent activation energy (Ea) of the Al-containing catalyst evidences an influence on the nature of the active site. The herein-developed stable 2D Fe nanostructures can serve as an example of a 2D material applied in catalysis, offering the chance of a rational catalyst design based on a stepwise introduction of various promoters, in the coating and on the metal, maintaining the spatial control of the active centers.

Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics.

The review is devoted to a new and rapidly developing area related to the application of ideas and methods of nonlinear mathematics and theoretical physics to study the internal dynamics of DNA and, in particular, the behavior of the open states of DNA. There are two main competing approaches to this research. The first approach is based on the molecular dynamics method, which takes into account the motions of all structural elements of the DNA molecule and all interactions between them. The second approach is based on prior selection of the main (dominant) motions and their mathematical description using a small number of model equations. This review describes the results of the study of the open states of DNA performed within the framework of the second approach using the McLaughlin-Scott equation. We present the results obtained both in the case of homogeneous sequences: poly (A), poly (T), poly (G) and poly (C), and in the inhomogeneous case when the McLaughlin-Scott equation has been used for studying the dynamics of open states activated in the promoters A1, A2 and A3 of the bacteriophage T7 genome, in the genes IFNA17, ADRB2, NOS1 and IL-5, in the pBR322 and pTTQ18 plasmids. Particular attention is paid to the results concerning the effect of various external fields on the behavior of open states. In the concluding part of the review, new possibilities and prospects for the development of the considered approach and especially of the McLaughlin-Scott equation are discussed. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12551-021-00801-0.

Microbuckling Instability and the Second Yield during the Deformation of Semicrystalline Polyethylene.

Deformation instabilities, such as microbuckling or lamellar fragmentation due to slip localization, play a very important role in the deformation of semicrystalline polymers, although it still not well explored. Such instabilities often appear necessary to modify the deformation path and facilitate strain accommodation in an energy-minimizing manner. In this work, microbuckling instability was investigated using partially oriented, injection-molded (IM) samples of high-density polyethylene, deformed by a plane-strain compression. Deformed samples were probed by SEM, X-ray (small- and wide-angle X-ray scattering: SAXS, WAXS), and differential scanning calorimetry (DSC). It was found that microbuckling instability, followed quickly by the formation of lamellar kinks, occurred in high-density polyethylene (HDPE) at a true strain of about e = 0.3-0.4, mainly in those lamellar stacks which were initially oriented parallel to the compression direction. This phenomenon was observed with scanning electron microscopy, especially in the oriented skin layers of IM specimens, where a chevron morphology resulting from lamellae microbuckling/kinking was evidenced. Macroscopically, this instability manifested as the so-called "second macroscopic yield" in the form of a hump in the true stress-true strain curve. Microbuckling instability can have a profound effect on the subsequent stages of the deformation process, as well as the resulting structure. This is particularly important in deforming well-oriented lamellar structures-e.g., in drawing pre-oriented films of a semicrystalline polymer, a process commonly used in many technologies.

Investigating the effect of charged amino acids on DNA conformation in EcoRI-DNA complex: a molecular dynamics simulation study.

Sequence-specific binding of proteins to DNA is essential for almost all the cellular processes like transcription, translation, replication, etc. One among the various mechanisms that has been identified so far that contributes to the specificity in protein-DNA interaction is the DNA conformational change. Electrostatic neutralization of the phosphate groups by the positively charged amino acid residues in proteins is thought to bring about such conformational changes in DNA. Here, we employ molecular dynamics simulations to examine the effect of charge on amino acids Lys113, Arg145, and Asp91 which are attached to the scissile phosphate on the conformation of DNA in EcoRI-DNA complex. The results indicate that the charge of these amino acids is essential for maintaining the local conformation of DNA in the EcoRI-bound form. Interestingly, we observe that the positively charged amino acids Lys113 and Arg145 have a long-range influence on the DNA conformation, whereas the negatively charged amino acid Asp91 has only a localized effect on the DNA conformation. The charge on the amino acids also alters the collective dynamics of EcoRI. Collectively, the results shed light on the diversity of the effect of charges on DNA conformation as well as on protein dynamics.

Optic cup segmentation: type-II fuzzy thresholding approach and blood vessel extraction.

We introduce here a new technique for segmenting optic cup using two-dimensional fundus images. Cup segmentation is the most challenging part of image processing of the optic nerve head due to the complexity of its structure. Using the blood vessels to segment the cup is important. Here, we report on blood vessel extraction using first a top-hat transform and Otsu's segmentation function to detect the curves in the blood vessels (kinks) which indicate the cup boundary. This was followed by an interval type-II fuzzy entropy procedure. Finally, the Hough transform was applied to approximate the cup boundary. The algorithm was evaluated on 550 fundus images from a large dataset, which contained three different sets of images, where the cup was manually marked by six ophthalmologists. On one side, the accuracy of the algorithm was tested on the three image sets independently. The final cup detection accuracy in terms of area and centroid was calculated to be 78.2% of 441 images. Finally, we compared the algorithm performance with manual markings done by the six ophthalmologists. The agreement was determined between the ophthalmologists as well as the algorithm. The best agreement was between ophthalmologists one, two and five in 398 of 550 images, while the algorithm agreed with them in 356 images.

Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.

It has been shown experimentally that the action of the RSC chromatin remodeler leads to the formation of an irregular, partially remodeled nucleosome, termed a remosome. The remosome contains an extra 30-40 base pairs of DNA compared to a canonical nucleosome. Large-scale molecular simulations have provided information on the probable structure of remosomes and have explained why they remain stable in the absence of RSC. Here we explain how these simulations were carried out and what the resulting remosome models imply in terms of the mechanism of action of RSC. We notably show that local kinks within DNA are key in explaining how extra DNA can be in added to nucleosomes without unduly disturbing DNA-histone binding.

Formation mechanisms for the dominant kinks with different angles in InP nanowires.

The morphologies and microstructures of kinked InP nanowires (NWs) prepared by solid-source chemical vapor deposition method were examined using scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM). Statistical analysis and structural characterization reveal that four different kinds of kinks are dominant in the grown InP NWs with a bending angle of approximately 70°, 90°, 110°, and 170°, respectively. The formation mechanisms of these kinks are discussed. Specifically, the existence of kinks with bending angles of approximately 70° and 110° are mainly attributed to the occurrence of stacking faults and nanotwins in the NWs, which could easily form by the glide of {111} planes, while approximately 90° kinks result from the local amorphorization of InP NWs. Also, approximately 170° kinks are mainly caused by small-angle boundaries, where the insertion of extra atomic planes could make the NWs slightly bent. In addition, multiple kinks with various angles are also observed. Importantly, all these results are beneficial to understand the formation mechanisms of kinks in compound semiconductor NWs, which could guide the design of nanostructured materials, morphologies, microstructures, and/or enhanced mechanical properties.