Backbone Axis Research Articles

An automatic measurement method for ankle key angles based on point cloud segmentation network

AbstractIn clinical practice, anterior distal tibialangle (ADTA) and lateral distal tibialangle (LDTA) are important evaluation indexes, which can reflect the degree of deformity and determine the type of deformity to a certain extent. The measurement process of these parameters involves the localization of multiple key regions. To simplify the process of measuring ADTA and LDTA, an automatic measurement method is proposed. First, this study constructs an ankle 3D point cloud dataset by 3D reconstruction of ankle electron computed tomography (CT) data, and then, an ankle point cloud segmentation network with a Self‐Attention mechanism and kernel point convolution combined with each other is constructed, and the ankle point cloud data with labels are input to this network to predict the ankle bone feature points. Finally, the segmented feature points are fitted, and the tibial backbone axis and distal tibial articular surface can be drawn, and based on the fitting results, ADTA and LDTA are obtained. Compared with manual measurements by physicians, the proposed method in this study achieved an average error of 0.46° with a passing rate of 97.7% for ADTA measurement. For LDTA measurement, the average error was 0.69° with a passing rate of 98%. The ankle joint key angle measurement system developed in this study meets the accuracy requirements of orthopedics and significantly reduces the workload for doctors.

Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.

Age-related changes in molecular organization of type I collagen in tendon as probed by polarized SHG and Raman microspectroscopy

Type I Collagen is one of the most abundant proteins of the extracellular matrix of the most organs. During chronological aging or in diseases, type I collagen undergoes biochemical and structural changes which can impact biomechanical and physiological properties of organs. In this study, we have investigated the age-related changes in the molecular organization of type I collagen in rat tails tendon using polarized Raman spectroscopy. Our results show that Amide I, amide III as well as the bands related to proline and hydroxyproline are highly sensitive to polarization and age-related. On the other hand, 1453 and 1270 cm−1 do not show any preferential orientation. Depolarization and anisotropic ratios were used to provide information about the changes in orientation of collagen fibers with aging. The anisotropy degree of Raman bands increase from adult to old collagen, indicating a higher collagen fibers alignment to the fascicle backbone axis in old tendons, and consequently a higher straightness of collagen fibers. These data were correlated to those obtained using polarized second harmonic generation technique. Polarized Raman mapping showed a more homogeneous spatial distribution of collagen fibers alignment to the fascicle axis in old tendon. This confirms a higher straightness of collagen fiber with aging.

Structural, electronic, and linear optical properties of organic photovoltaic PBTTT-C14 crystal

Poly(2,5-bis(3-tetradecylthiophen-2yl)thieno(3,2-b)thiophene) (PBTTT-C14) is an important electro-optical polymer, whose three-dimensional crystal structure is somewhat ambiguous and the fundamental electronic and linear optical properties are not well known. We carried out first-principles calculations to model the crystal structure and to study the effect of side-chains on the physical structure and electronic properties. Our calculations suggest that the patterns of side-chain has little direct effect on the valence band maximum and conduction band minimum but they do have impact on the bandgap through changing the π-π stacking distance. By examining the band structure and wave functions, we conclude that the fundamental bandgap of the PBTTT-C14 crystal is determined by the conduction band energy at the Q point. The calculations indicate that the bandgap of PBTTT-C14 crystal may be tunable by introducing different side-chains. The significant peak in the imaginary part of the dielectric function arises from transitions along the polymer backbone axis, as determined by the critical-point analysis and the large optical transition matrix elements in the direction of the backbone.

Highly anisotropic thermal expansion in molecular films of dicarboxylic fatty acids

Angstrom-resolution x-ray measurements reveal the existence of two-dimensional (2D) crystalline order in molecularly thin films of surface-parallel-oriented fatty diacid molecules supported on a liquid mercury surface. The thermal expansion coefficients along the two unit cell vectors are found to differ 17-fold. The high anisotropy of the 2D thermal expansion and the crystalline coherence length are traced to the different bonding in the two directions: van der Waals normal to, and covalent plus hydrogen bonding along the molecular backbone axis. Similarities with, and differences from, negative thermal expansion materials are discussed.

Structure and X‐ray spectrum of crystalline poly(3‐hexylthiophene) from DFT‐van der Waals calculations

AbstractThe minimum‐energy geometrical structure of the regioregular head‐to‐tail poly(3‐hexylthiophene) (rr‐HT‐P3HT) polymer has been addressed by means of density functional theory (DFT) calculations which include long‐range (van der Waals) interactions. The problem of the P3HT structure has been debated in the literature in the last decades mainly for what concerns the arrangement of the alkyl side chains of the polymer and the type and content of the crystalline primitive cell. The main result of our calculations is that the energetically favored structure of the crystalline polymer at T = 0 K corresponds to polythiophene chains with slightly (∼16°) non co‐planar rings and a fishbone arrangement of tilted alkyl side chains with complex internal structure. The alkyl side chains are negligibly interdigitated with those of the adjacent polymer layers; moreover the five terminal carbon atoms of each alkyl side chain are co‐planar in all‐trans staggered conformation. The optimized geometrical structure obtained for the rr‐HT‐P3HT polymer is in agreement with measured X‐ray spectra of high molecular weight P3HT crystalline samples, and confirms that two non‐equivalent polymer chains, mutually shifted along the backbone axis, are contained in an orthorhombic primitive cell.

Investigations of the polymer alignment, the nonradiative resonant energy transfer, and the photovoltaic response of poly(3-hexylthiophene)/TiO2 hybrid solar cells

We report the effects of annealing on the performance of hybrid photovoltaic (PV) cells containing poly(3-hexylthiophene) (P3HT) coated onto TiO2/Sn doped In2O3 (ITO) and ITO substrates. In the optimized device, which exhibits a higher efficiency, the backbone axes of the P3HT chains were found to lie within the substrate plane, their conjugated planes are slightly tilted, and their side chains are substantially tilted. The carboxylate group is attached via bidentate or bridging coordination to the TiO2 surface and enables photoinduced charge transfer between TiO2 and P3HT. The observed large quenching (with excitation at 488 nm) and enhanced emission (with excitation at 325 nm) indicates that efficient Förster resonance energy transfer occurs between TiO2 and P3HT. Thus, the main influences on the high efficiency of the hybrid PV cells are the photon-mediated electronic transition and the photoinduced charge transfer.

Mechanochemistry of a Viral DNA Packaging Motor

The pentameric ATPase motor gp16 packages double-stranded DNA into the bacteriophage ϕ29 virus capsid. On the basis of the results of single-molecule experimental studies, we propose a push and roll mechanism to explain how the packaging motor translocates the DNA in bursts of four 2.5 bp power strokes, while rotating the DNA. In this mechanism, each power stroke accompanies P i release after ATP hydrolysis. Since the high-resolution structure of the gp16 motor is not available, we borrowed characterized features from the P4 RNA packaging motor in bacteriophage ϕ12. For each power stroke, a lumenal lever from a single subunit is electrostatically steered to the DNA backbone. The lever then pushes sterically, orthogonal to the backbone axis, such that the right-handed DNA helix is translocated and rotated in a left-handed direction. The electrostatic association allows tight coupling between the lever and the DNA and prevents DNA from slipping back. The lever affinity for DNA decreases towards the end of the power stroke and the DNA rolls to the lever on the next subunit. Each power stroke facilitates ATP hydrolysis in the next catalytic site by inserting an Arg -finger into the site, as captured in ϕ12-P4. At the end of every four power strokes, ADP release happens slowly, so the cycle pauses constituting a dwell phase during which four ATPs are loaded into the catalytic sites. The next burst phase of four power strokes starts once spontaneous ATP hydrolysis takes place in the fifth site without insertion of an Arg finger. The push and roll model provides a new perspective on how a multimeric ATPase transports DNA, and it might apply to other ring motors as well.

Solvent Effects on the Self-Assembly of 1-Bromoeicosane on Graphite. Part I. Scanning Tunneling Microscopy

Self-assembled monolayers of 1-bromoeicosane (BrC20H41) have been investigated at the vacuum−graphite and liquid−graphite interfaces using scanning tunneling microscopy (STM) (Part I) and theory (Part II). Under ultrahigh vacuum conditions at 80 K, STM images show 1-bromoeicosane in a lamellar assembly structure where individual molecules are predominantly arranged with their bromine groups pointed head-to-head with a 66 ± 3° angle between the lamella direction and the molecular backbone axis. A significant degree of disorder is observed under vacuum conditions, in which head-to-tail defects are interspersed throughout the film. When 1-bromoeicosane monolayers are formed and imaged in equilibrium with solution at ∼290 K, the molecules again pack with their bromines oriented head-to-head but shift to form a nearly rectangular array. Subtle changes are observed depending on the solvent utilized, with the lamella−backbone angle varying between 81 ± 3° and 90 ± 2°, and the corresponding intermolecular spacing...

Backbone Dynamics of the Nafion Ionomer Studied by 19F‐13C Solid‐State NMR

AbstractThe chain dynamics of a perfluorinated ionomer, Nafion®, have been studied by 19F and 19F‐13C solid‐state NMR at 295 K. The backbone of Nafion is essentially poly(tetrafluoroethylene) (PTFE), which was investigated for reference. Fast uniaxial rotations of the helical backbone were confirmed in PTFE and detected similarly in Nafion, though with a distribution of amplitudes. The rotations produce motionally averaged 19F‐13C dipolar couplings and chemical shift anisotropies (CSAs) that are linearly correlated. Additional narrowing of the CSAs indicated that the backbone axis in hydrated Nafion moves with an amplitude >15°. Motional amplitudes of various backbone and side‐branch sites were inferred from motionally averaged 19F CSA parameters measured with CSA recoupling. They increase with the distance from the branch point, e.g., to >25° in the center of the side branch. Implications for the chain and supramolecular structure of Nafion are discussed.magnified image

Ultra-high vacuum scanning tunneling microscopy and theoretical studies of 1-halohexane monolayers on graphite

A simple model system for the 2D self-assembly of functionalized organic molecules on surfaces was examined in a concerted experimental and theoretical effort. Monolayers of 1-halohexanes were formed through vapor deposition onto graphite surfaces in ultrahigh vacuum. Low-temperature scanning tunneling microscopy allowed the molecular conformation, orientation, and monolayer crystallographic parameters to be determined. Essentially identical noncommensurate monolayer structures were found for all 1-halohexanes, with differences in image contrast ascribed mainly to electronic factors. Energy minimizations and molecular dynamics simulations reproduced structural parameters of 1-bromohexane monolayers quantitatively. An analysis of interactions driving the self-assembly process revealed the crucial role played by small but anisotropic electrostatic forces associated with the halogen substituent. While alkyl chain dispersion interactions drive the formation of a close-packed adsorbate monolayer, electrostatic headgroup forces are found to compete successfully in the control of both the angle between lamella and backbone axes and the angle between surface and backbone planes. This competition is consistent with energetic tradeoffs apparent in adsorption energies measured in earlier temperature-programmed desorption studies. In accordance with the higher degree of disorder observed in scanning tunneling microscopy images of 1-fluorohexane, theoretical simulations show that electrostatic forces associated with the fluorine substituent are sufficiently strong to upset the delicate balance of interactions required for the formation of an ordered monolayer. The detailed dissection of the driving forces for self-assembly of these simple model systems is expected to aid in the understanding of the more complex self-assembly processes taking place in the presence of solvent.

Electronic Signature of DNA Nucleotides via Transverse Transport

We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries a unique signature due to the different electronic and chemical structure of the four bases. This signature is independent of the nearest-neighbor nucleotides. Furthermore, except for the nucleotides with guanine and cytosine bases, we find that the difference in conductance of the nucleotides is large for most orientations of the bases with respect to the electrodes. By exploiting these differences it may be possible to sequence single-stranded DNA by scanning its length with conducting probes.

Phase behaviour of ultrathin crystalline n-heptane films on graphite: An atomistic simulation study

The thermal behaviour of n-heptane films adsorbed on the basal plane of graphite has been investigated using atomistic molecular dynamics simulations performed under constant temperature conditions. An uniaxially commensurate monolayer (UCM), an uniaxially commensurate bilayer (UCB) and a fully commensurate bilayer (FCB) of n-heptane have been studied in order to distinguish the contributions from coverage and in-plane density to the melting process. These ordered adlayers containing molecules whose zig-zag planes were parallel to the substrate, were stabilized at low temperatures. The calculated intermolecular energy per molecule shows that the FCB structure is more stable than the UCB structure, consistent with X-ray and neutron scattering experiments. In all of these systems, disordering processes in the solid state involves a fraction of molecules rotating about their backbone axes, in agreement with scanning tunneling microscopy studies. The molecules present in uniaxially commensurate structures (UCM and UCB) are facile to rotate about their long axes which causes these adlayers to melt at lower temperatures compared to the fully commensurate structure. The spatial correlation functions between such rotated molecules show interesting temperature dependence that indicates a loss of long-range and short-range correlations in these overlayers with increasing temperature. The importance of conformational defects for the melting of these quasi-two-dimensional systems has also been explored. Axial rotations of molecules present in the first adsorbed layer of FCB are facile between bulk and monolayer melting temperatures. This process leads to the observation of an average angle of rotation of around 40 degrees in excellent agreement with X-ray and neutron scattering experiments.

Mechanical properties of single motor molecules studied by three-dimensional thermal force probing in optical tweezers.

A new method combining three-dimensional (3D) force measurements in an optical trap with the analysis of thermally induced (Brownian) position fluctuations of a trapped probe was used to investigate the mechanical properties of a single molecule, the molecular motor kinesin. One kinesin molecule attached to the probe was bound in a rigorlike state to one microtubule. The optical trap was kept weak to measure the thermal forces acting on the probe, which were mainly counterbalanced by the kinesin tether. The stiffness of kinesin during stretching and compression with respect to its backbone axis were measured. Our results indicate that a section of kinesin close to the motor domain is the dominating element in the flexibility of the motor structure. The experiments demonstrate the power of 3D thermal fluctuation analysis to characterize mechanical properties of individual motor proteins and indicate its usefulness to study single molecule in general

A novel fingerprint for the characterization of protein folds.

A novel fingerprint, defined without the use of distances, is introduced to characterize protein folds. It is of the form of binary matrices whose elements are defined by angles between the C=O direction, the backbone axis and the line connecting the alpha-carbons of the various residues. It is shown that matches in the fingerprint matrices correspond to low r.m.s.d.

Synthesis and crystal structure of a new isomer of the μ-oxo-bis[dichlorooxobis(pyridine)rhenium(V)] complex {OReCl 2py 2} 2O

Refluxing the oxo-alkoxo complexes ReO(OR)Cl 2py 2 (where RCH 3 and C 2H 5) in toluene yielded an oxo-bridged dinuclear compound {OReCl 2py 2} 2O, in which a transtrans arrangement of pyridien and chloride ligands around rhenium was determined by an X-ray diffraction study. This compound contains the same linear OReReO backbone as the cis,cis isomer first prepared by Wlikinson's group, and the two ReCl 2N 2 planes are rotated with respect to each other by 27° about the backbone axis. Both stereoisomers are green, they exhibit very similar infrared and 13C NMR spectra, but they can be distinguished from their 1H NMR chemical shifts. An X-ray diffraction study on ReO(OCH 3)Cl 2py 2 showed the presence of a trans,trans octahedral geometry around the metal and a bent ReOCh 3 group (156°).

Pyranosyl‐RNA (‘p‐RNA’): Base‐pairing selectivity and potential to replicate. Preliminary communication

AbstractBase pairing in p‐RNA (β‐D‐ribopyranosyl‐(4′ → 2′)‐oligonucleotides) is not only stronger than in DNA and RNA, but also more selective in the sense that it is strictly confined to the Watson‐Crick mode. Homopurine sequences (tested up to decamers) exist as single strands under conditions where they undergo reverse‐Hoogsteen self‐pairing in homo‐DNA or Hoogsteen self‐pairing in DNA. This exceptional pairing selectivity is rationalized as hinging on two structural features of p‐RNA: the large inclination between backbone axis and base‐pair axes in p‐RNA duplexes, and the higher rigidity of the p‐RNA backbone compared with RNA, DNA, and homo‐DNA. The most important consequence of the pairing selectivity refers to the potential of p‐RNA to replicate. Replicative copying of sequence information by nonenzymatic template‐controlled ligation is not hampered by self‐pairing of guanine‐rich templates, as it is known to be the case in the RNA series. We have demonstrated two replicative cycles in which G‐rich p‐RNA‐octamer templates induce sequence‐selective ligation of tetramer‐2′‐phosphate derivatives to complementary C‐rich octamer sequences, and in which the latter, with comparable efficiency, induce corresponding ligation reactions back to the original G‐rich octamers. Ligation is most satisfactorily achieved after pre‐activation of the 2′‐phosphate groups as 2′,3′‐cyclophosphate derivatives; in this version, the process does not proceed as oligocondensation, but as a genuine oligomerization. This is of considerable promise for the search for potentially natural conditions under which homochiral p‐RNA strands might self‐assemble and self‐replicate.

Texture and Strength Evolution inDeformed Polypropylene

Semicrystalline polypropylene samples with high concentrations of crystallinity (≳62%) are deformed in uniaxial compression at different temperatures and different strain rates. The orientation changes of the crystalline part of the material are analyzed using X‐ray diffraction methods. Pole figure evaluation is used to obtain information about the crystal structure, the geometry of slip, and its correlation with the characteristic of strength evolution in polymers. The contribution of the crystalline part of the material to plastic flow is estimated and the textures are related to the characteristic effects in plastic and visco‐elastic response of the material during deformation and subsequent stress relaxation. The observed texture effects can be explained by the rotation of crystallographic c‐axis (backbone axis) normal to the compression direction at high temperatures in a planar slip mode. The stress/strain and relaxation behavior of the material is interpreted as a combination of viscoelastic flow of amorphous volume and irreversible plastic flow of the crystalline part which contributes to an orientation dependence of deformation and stress relaxation.

Paramagnetic organometallic liquid crystal polymers

We have synthesized a paramagnetic organometallic liquid crystal polymer containing a tetradentate Schiff base complex of copper II. The main chain liquid crystal polymer forms when the functionalized complex is combined at 220°C with the melt of a low molecular weight terpolymer. The terpolymer is a nematic liquid crystal at this temperature and contains oxybenzoate, dioxyphenyl, and pimeloate structural units. The organometallic material melts reversibly into a liquid crystalline fluid at a slightly lower temperature than the terpolymer. In external magnetic fields the tendency is for the backbone axis of the organometallic fluid to rotate away from the field direction. This observation suggests that strong interactions between the field and the paramagnetic units dictate the orientation of diamagnetic chemical sequences which normally align parallel to the magnetic field.