Kink Formation Research Articles

Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase

5-Methylthioribose 1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related proteins such as ribose-1,5-bisphosphate isomerase (R15Pi) and the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B). To identify the distinct structural features that lead to divergent functional obligations of M1Pi as well as to understand the mechanism of enzyme catalysis, the crystal structure of M1Pi from a hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined. A meticulous structural investigation of the dimeric M1Pi revealed the presence of an N-terminal extension and a hydrophobic patch absent in R15Pi and the regulatory α-subunit of eIF2B. Furthermore, unlike R15Pi in which a kink formation is observed in one of the helices, the domain movement of M1Pi is distinguished by a forward shift in a loop covering the active-site pocket. All these structural attributes contribute towards a hydrophobic microenvironment in the vicinity of the active site of the enzyme making it favorable for the reaction mechanism to commence. Thus, a hydrophobic active-site microenvironment in addition to the availability of optimal amino-acid residues surrounding the catalytic residues in M1Pi led us to propose its probable reaction mechanism via a cis-phosphoenolate intermediate formation.

A theoretical investigation of the glide dislocations in the sphalerite ZnS

The 90° and 30° partial glide dislocations in ZnS are investigated theoretically in the framework of the fully discrete Peierls model and first-principles calculation. It is found that there are four types of equilibrium cores for each kind of partial glide dislocation, which are named as the O-Zn-core, the B-Zn-core, the O-S-core, and the B-S-core, according to their geometrical feature and atomic ingredient at the core. For the 90° partial dislocation, the O-Zn-core (double-period core) and the B-S-core (single-period core) are stable. The Peierls barrier heights of the O-Zn-core and the B-S-core are about 0.03 eV/Å and 0.01 eV/Å, respectively. For the 30° partial dislocation, the O-Zn-core (double-period core) and the B-Zn-core (single-period core) are stable and their Peierls barrier heights are approximately the same as that of the O-Zn-core of the 90° partial dislocation. The Peierls stress related to the barrier height is about 800 MPa for the 90° partial dislocation with the B-S-core. The existence of unstable equilibrium cores enables us to introduce the concept of the partial kink. Based on the concept of the partial kink, a minimum energy path is proposed for the formation and migration of kinks. It is noticed that the step length in kink migration is doubled due to the core reconstruction.

A new reconstruction core of the 30° partial dislocation in silicon

ABSTRACTThe partial dislocation in silicon is investigated theoretically in the framework of the fully discrete Peierls–Nabarro model and first-principles calculations. A new reconstructed core composed of a periodic arrangement of one tetragon and two heptagons (477-core) is proposed. Similar to the partial dislocation, we find that there are actually two types of reconstructed cores for the partial dislocation, namely, a well-known 558-core and a new 477-core. The energy of the 477-core is 0.137 eV/Å higher than that of the 558-core. However, from the molecular dynamics simulation, we found that the 477-core may have a macroscopic lifetime for temperature below 30 K. The full kinks and the partial kinks due to the appearance of the 477-core are also studied. Remarkably, it is found that formation and migration of the global kinks deeply involve with the partial kinks, and the creation and motion of partial kinks can be attributed to the rotation of a single bond. Our results are helpful in understanding the mechanism of kink nucleation and the plasticity of silicon.

Anisotropic plastic deformation of single crystals of the MAX phase compound Ti3SiC2 investigated by micropillar compression

The anisotropic deformation behavior of single crystals of Ti3SiC2 has been investigated at room temperature as a function of loading axis orientation and specimen size by micropillar compression tests. Basal slip is found to be only the operative slip system at room temperature. The a/3[12¯10] basal dislocation responsible for basal slip dissociates into two partial dislocations of the Shockley-type and glides between Ti1 and Si atomic layers, as confirmed both experimentally and theoretically. The CRSS value for basal slip increases with the decrease in the specimen size, following an inverse power-law relationship with a very large power-law exponent of about 1.0, which is almost the upper limit of those reported for FCC metals. When the loading axis is parallel to the basal plane, kink band formation occurs only after the occurrence of basal-plane delamination and the subsequent activation of a-dislocations gliding on the basal plane. Kink bands consists of a/3[12¯10] basal edge dislocations of the same sign, each of which had glided between Ti1 and Si atomic layers. These results indicates that the kink formation can simply be interpreted by the classical dislocation-based kink-formation model.

Quantum mechanical tunnel nucleation of kink-solitons in a random potential

In connection with the development of nanotechnology, the sizes of the objects under study have approached the values at which the fundamental quantum mechanical laws of dynamics come into play. An important component of such dynamics in extended systems is the process of domain formation and propagation of their boundaries. In quasi-one-dimensional systems, these boundaries are peculiar quasiparticles—topological kink-solitons or simply kinks. Various processes such as switching states or phase transformations of a system can be described in terms of nucleation and propagation of kinks. With decreasing temperature, the thermal activation mechanism of nucleation of kinks is replaced by quantum mechanical subbarrier tunneling. The insufficient perfection of materials imposes often uncontrolled perturbations that modify the regularities of the tunnel formation of kinks. The influence of perturbations of the type of spatial ‘Gaussian noise’ is modeled in the work. The distribution of the rate of quantum mechanical tunnel nucleation of kinks over realizations of random fields is studied. It is shown that even relatively weak perturbations, as compared to the threshold of metastability, lead to a wide spectrum of kink nucleation times and a significant modification of the dependence of their typical characteristics on the driving force.

Strong deformations of DNA: Effect on the persistence length

.Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.Graphical abstract

Tunneling Nucleation of Kink Pairs on Dislocations in the Peierls Potential Relief with Random Distortions

In view of the recent increased interest in the mechanical properties of quantum crystals, the study of the low-temperature dynamics of dislocations is necessary. Tunneling through the barriers created by periodic relief of the crystal lattice, which leads to the formation of pairs of kinks, makes an important contribution to this dynamics. Incomplete perfection of crystals often imposes uncontrollable perturbations that modify the features of the process of the tunneling nucleation of kinks. This article presents the modelling of perturbation effect by the random fields of internal stresses such as spatial “Gaussian noise.” The average value of the realizations of the rate of quantum-mechanical tunnel formation of kink pairs in the random fields is calculated. It is shown that even perturbations that are relatively weak in comparison with the crystalline relief lead to a significant modification of the kink formation rate dependence on a driving force.

Thermally activated deformation of nanocrystalline and coarse grained CoCrFeNiMn high entropy alloy in the temperature range 4.2–350 K

Mechanical properties of a nanocrystalline (∼ 60 nm) and a coarse grained (grain sizes ∼ 4 µm) CoCrFeNiMn high entropy alloys were studied in uniaxial compression in the temperature range 4.2–350 K. Temperature dependences of yield strength, flow stress and strain rate sensitivity have been registered and analyzed in the framework of two thermal activation deformation models, that of thermal activation of local barrier overcoming, and that of Peierls valley double kink formation. Microscopic parameters of dislocation interaction with the barriers for thermally activated motion are estimated and low temperature deformation mechanisms are discussed.

C-terminal kink formation is required for lateral gating in BamA

In Gram-negative bacteria, the outer membrane contains primarily β-barrel transmembrane proteins and lipoproteins. The insertion and assembly of β-barrel outer-membrane proteins (OMPs) is mediated by the β-barrel assembly machinery (BAM) complex, the core component of which is the 16-stranded transmembrane β-barrel BamA. Recent studies have indicated a possible role played by the seam between the first and last β-barrel strands of BamA in the OMP insertion process through lateral gating and a destabilized membrane region. In this study, we have determined the stability and dynamics of the lateral gate through over 12.5 μs of equilibrium simulations and 4 μs of free-energy calculations. From the equilibrium simulations, we have identified a persistent kink in the C-terminal strand and observed spontaneous lateral-gate separation in a mimic of the native bacterial outer membrane. Free-energy calculations of lateral gate opening revealed a significantly lower barrier to opening in the C-terminal kinked conformation; mutagenesis experiments confirm the relevance of C-terminal kinking to BamA structure and function.

631 Comprehensive in-vivo biomechanical study of IPP function dependent on length of RTE

A comprehensive in-vivo biomechanical study of the 3 most popular inflatable penile prosthesis (IPP) brands was conducted where the effect of rear tip extenders was compared in a three cadaver in vivo study. Certified and recognized surgeons inserted the IPPs and recognized scientists and engineers conducted biomechanical testing using approaches that were correlated to standard test methods. Longitudinal compression, modified cantilever deflection, and flexural 3-point bending were used to compare the three IPPs where each were surgically inserted with 1cm, 1.5cm, or 2cm rear tips in three cadavers and inflated to 10psi and 20psi conditions. Furthermore for a corporal length IPP of 20cm made by using an 18cm + 2cm rear tip, a 20cm IPP with no rear tip was tested for comparison. Funding for this study was obtained from Coloplast Corporation. Compression, modified cantilever, and bend data were acquired for the in vivo IPPs. Analysis was assessed based on kink formation in compression, max loading in cantilever testing and 3-point bend testing. Rigidity was also used to assess rear tip effects. Testing order, sequence, and pressure level were other parameters for the assessment.

241 Comprehensive in-vivo biomechanical study of IPPs yields interesting results

Due to the inflatable penile prosthesis (IPP) we have seen a new era ushered in the management of erectile dysfunction. A growing interest in the biomechanical properties of IPP is leading to systematic studies of the ex-vivo and in-vivo evaluation of the inflated rigidity of the IPP and comparative properties of different implants. This study is a comprehensive in-vivo biomechanical study of the 3 most popular IPPs assessed by longitudinal (column compression), Horizontal (modified cantilever deflection) and flexure (3-point bending) methods. IPPs were surgically placed in three cadavers via an infrapubic approach. The biomechanical measurements were obtained in a bind testing study performed by engineers from Rice University. Two pressures for the implants were chosen and 10 implant conditions were assessed based on mechanical measurements and visual and audio recordings of the analysis. Funding for this study was obtained from Coloplast Corporation. Compression, cantilever, and bend data were acquired for the in vivo IPP. Analysis was assessed based on kink formation in compression, max loading in cantilever testing and 3-point bend testing. Rigidity was also assessed based on plotted slopes indicating stiffness, and the differences in slope change, kinking, and IPP buckling. Data was correlated to vaginal insertion strength, horizontal load strength, and prosthesis rigidity.

Biomechanical Comparison of Inflatable Penile Implants: A Cadaveric Pilot Study

BackgroundThroughout the last decade there has been a growing interest in the biomechanical differences between inflatable penile prostheses (IPPs) and their significance with regard to the patient experience. AimTo present our findings assessing the biomechanical properties of IPPs with and without rear tip extenders (RTEs). MethodsThis is a biomechanical study of the 3 most commonly used IPPs (AMS CX, AMS LGX, and Coloplast Titan) as assessed by column compression, modified cantilever deflection, and 3-point bending methods. The IPPs were surgically placed into 3 fresh cadavers via an infrapubic technique by a single large-volume implanter. A biomechanical evaluation of the properties of each IPP inside the fibroelastic tunica albuginea was assessed in blinded testing, and analyses were based on industry standard methods for assessment. OutcomesMaximum axial load; kink formation; horizontal stiffness; and resistance to 3-point flexure testing were measured. ResultsAt maximum inflation, all 3 implants had similar performance. Differences appear to be most affected by fill pressures. In fact, only the AMS LGX at less than maximum inflation (LTMI) was unable to consistently withstand the roughly 0.9 kg (2 lbs) of pressure for column load testing mimicking vaginal intromission. The Coloplast Titan showed slightly better rigidity than the AMS LGX and CX devices in horizontal load testing, and, with 3-point flexure testing, the CX showed the best rigidity in the shortest phallus (A). Overall, the Titan showed slightly better rigidity in the longest phallus (C) and the phallus with mild Peyronie's disease (B). Clinical TranslationsPenile implants with circumferential expansion had higher rigidity on biomechanical testing and should be considered in a patient's decision during selection of a penile implant. Strengths and LimitationsStrengths include blinding of the biomechanical testing and analyses, surgical procedures performed by a highly experienced surgeon, and that this is the “closest to” in vivo evaluation (inside the tunica albuginea) of penile implant function and properties to date. Weaknesses are that this study was performed in cadavers and not in live patients. It also has a small sample size, including the use of only 3 cadavers, and there was no correlation of performance to patient satisfaction. ConclusionThe results of this study support the conclusion that all devices are capable of functionally restoring erectile capacity. However, we observed that, in general, the 2 circumferentially expanding penile prosthesis showed greater resistance in biomechanical testing when compared with longitudinal and circumferential expanding devices. This should be considered as a guide during device selection for a patient undergoing penile prosthesis.Wallen JJ, Barrera EV, Ge L, et al. Biomechanical Comparison of Inflatable Penile Implants: A Cadaveric Pilot Study. J Sex Med 2018;15:1034–1040.

Quantum perspective on the localized strand separation and cyclization of DNA double helix

We apply Heisenberg model to study local strand separation and cyclization of double-stranded DNA molecule. By mapping the conformational properties of DNA onto the Heisenberg spin system, we show that denaturation can be viewed as a quench-induced quantum phase transition (QPT) at a finite non-zero temperature. These phase transitions lead to the formation of kinks in Heisenberg model that, in turn, correspond to sharp bends in helical axes of double-stranded DNA molecule. In this scenario we study the cyclization of DNA fragments of short length. Our results are in agreement with the reported observation that there is 1 open bp per circle of about 70 bp. Also we have computed the probability of the formation of kinks in circles of various sizes and have observed that beyond 100 bp it decreases sharply which is in agreement with experimental result.

Free-Energy Landscape of the Dissolution of Gibbsite at High pH.

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of direct experimental probes. In this regard, we have applied atomistic simulations to map the free-energy landscape of the dissolution of gibbsite from a step edge as a model of metal hydroxide dissolution. The overall reaction combines kink formation and kink propagation. Two individual reactions were found to be rate-limiting for kink formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, our results will enable the development of microscopic mechanistic models of metal oxide dissolution.

Probing the role of intercalating protein sidechains for kink formation in DNA.

Protein binding can induce DNA kinks, which are for example important to enhance the specificity of the interaction and to facilitate the assembly of multi protein complexes. The respective proteins frequently exhibit amino acid sidechains that intercalate between the DNA base steps at the site of the kink. However, on a molecular level there is only little information available about the role of individual sidechains for kink formation. To unravel structural principles of protein-induced DNA kinking we have performed molecular dynamics (MD) simulations of five complexes that varied in their architecture, function, and identity of intercalated residues. Simulations were performed for the DNA complexes of wildtype proteins (Sac7d, Sox-4, CcpA, TFAM, TBP) and for mutants, in which the intercalating residues were individually or combined replaced by alanine. The work revealed that for systems with multiple intercalated residues, not all of them are necessarily required for kink formation. In some complexes (Sox-4, TBP), one of the residues proved to be essential for kink formation, whereas the second residue has only a very small effect on the magnitude of the kink. In other systems (e.g. Sac7d) each of the intercalated residues proved to be individually capable of conferring a strong kink suggesting a partially redundant role of the intercalating residues. Mutation of the key residues responsible for kinking either resulted in stable complexes with reduced kink angles or caused conformational instability as evidenced by a shift of the kink to an adjacent base step. Thus, MD simulations can help to identify the role of individual inserted residues for kinking, which is not readily apparent from an inspection of the static structures. This information might be helpful for understanding protein-DNA interactions in more detail and for designing proteins with altered DNA binding properties in the future.

Indentation response of a 3D non-woven carbon-fibre composite

Abstract

A mechanism for energy absorption: Sequential micro-kinking in ceramic reinforced aluminum alloy lattices during out-of-plane compression

The current study examines the out-of-plane compressive response of ceramic/aluminum hybrid lattice materials with an anodic alumina outer shell and an aluminum alloy core. The combination of increasing truss angle and oxide coating thickness results in a six-fold increase in compressive strength, two-fold increase in densification strain, twelve-fold increase in energy absorption per volume, and twenty-fold increase in energy absorption per mass. Such improvements are caused by the change in failure mode from mid-strut buckling to a hinge kinking mode as the oxide coating thickness increases. Microscopy and analytical modelling reveal that kink formation is most likely initiated by aluminum shear band formation followed by oxide rotation and fracture (analogous to micro-kinking in fiber composites). In terms of energy absorption, the best performing lattice materials in the current study were on par with the best available cellular materials in existing literature.

Compressive response of a 3D non-woven carbon-fibre composite

The compressive response of a three-dimensional (3D) non-interlaced composite comprising three orthogonal sets of carbon fibre tows within an epoxy matrix is analysed. First, the compressive response is measured in three orthogonal directions and the deformation/failure modes analysed by a combination of X-ray tomography and optical microscopy. In contrast to traditional unidirectional and two-dimensional (2D) composites, stable and multiple kinks (some of which zig-zag) form in the tows that are aligned with the compression direction. This results in an overall composite compressive ductility of about 10% for compression in the low fibre volume fraction direction. While the stress for the formation of the first kink is well predicted by a usual micro-buckling analysis, the composite displays a subsequent hardening response associated with formation of multiple kinks. Finite element (FE) calculations are also reported to analyse the compressive response with the individual tows modelled as anisotropic continua via a Hill plasticity model. The FE calculations are in good agreement with the measurements including prediction of multiple kinks that reflect from the surfaces of the tows. The FE calculations demonstrate that the three-dimensionality of the microstructure constrains the kinks and this results in the stable compressive response. In fact, the hardening and peak strength of these composites is not set by the tows in direction of compression, but rather set by the out-of-plane compressive response of the tows perpendicular to the compression direction.

Nanoparticle Stability in Axial InAs-InP Nanowire Heterostructures with Atomically Sharp Interfaces.

The possibility to expand the range of material combinations in defect-free heterostructures is one of the main motivations for the great interest in semiconductor nanowires. However, most axial nanowire heterostructures suffer from interface compositional gradients and kink formation, as a consequence of nanoparticle-nanowire interactions during the metal-assisted growth. Understanding such interactions and how they affect the growth mode is fundamental to achieve a full control over the morphology and the properties of nanowire heterostructures for device applications. Here we demonstrate that the sole parameter affecting the growth mode (straight or kinked) of InP segments on InAs nanowire stems by the Au-assisted method is the nanoparticle composition. Indeed, straight InAs-InP nanowire heterostructures are obtained only when the In/Au ratio in the nanoparticles is low, typically smaller than 1.5. For higher In content, the InP segments tend to kink. Tailoring the In/Au ratio by the precursor fluxes at a fixed growth temperature enables us to obtain straight and radius-uniform InAs-InP nanowire heterostructures (single and double) with atomically sharp interfaces. We present a model that is capable of describing all the experimentally observed phenomena: straight growth versus kinking, the stationary nanoparticle compositions in pure InAs and InAs-InP nanowires, the crystal phase trends, and the interfacial abruptness. By taking into account different nanowire/nanoparticle interfacial configurations (forming wetting or nonwetting monolayers in vertical or tapered geometry), our generalized model provides the conditions of nanoparticle stability and abrupt heterointerfaces for a rich variety of growth scenarios. Therefore, our results provide a powerful tool for obtaining high quality InAs-InP nanowire heterostructures with well-controlled properties and can be extended to other material combinations based on the group V interchange.

Resonance phenomena in the φ8 kinks scattering

We study the scattering of the φ8 kinks with power-law asymptotics. We found two critical values of the initial velocity, and , which separate different regimes of the kink-antikink collision. At the initial velocities kinks can not collide due to repulsive force between them. At the kinks escape to spatial infinities after one collision. In the range we observed kinks capture and formation of their bound state. Besides that, at these initial velocities we found resonance phenomena — escape windows.