A finite difference method for studying thermal deformation in three-dimensional thin films exposed to ultrashort pulsed lasers

Thermal analysis related to ultrashort-pulsed lasers has been intensely studied in science and engineering communities in recent years, because the pulse duration of ultrashort-pulsed lasers is only the order of sub-picoseconds to femtoseconds, and the lasers have exclusive capabilities in limiting the undesirable spread of the thermal process zone in the heated sample. Studying the thermal deformation induced by ultrashort-pulsed lasers is essential for preventing thermal damage. For the ultrashort-pulsed laser, the thermal damage is different from that caused by the long pulsed lasers and cracks occur after heating. This dissertation presents a new finite difference method for studying thermal deformation in 3D thin films exposed to ultrashort-pulsed lasers. The method is obtained based on the parabolic two-step model and implicit finite difference schemes on a staggered grid. It accounts for the coupling effect between lattice temperature and strain rate, as well as for the hot electron-blast effect in momentum transfer. In particular, a fourth-order compact scheme is developed for evaluating those stress derivatives in the dynamic equations of motion. The method allows us to avoid non-physical oscillation in the solution. To test the applicability of the developed numerical scheme, we investigated the temperature rise and thermal deformation in two physical cases: (1) a 3D single-layered thin film; and (2) a 3D double-layered thin film, where the central part of the top surface was irradiated by ultrashort-pulsed lasers. Results show no non-physical oscillations in the solution. Numerical results also show the displacement and stress alterations from negative value to positive value at the center along the z-direction, and along x and y-directions, indicating that the central part of the thin film expands during heating

Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C.

The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency

A NIMA-related kinase suppresses the flagellar instability associated with the loss of multiple axonemal structures

CCDC39 and CCDC40 were first identified as causative mutations in primary ciliary dyskinesia patients; cilia from patients show disorganized microtubules, and they are missing both N-DRC and inner dynein arms proteins. In Chlamydomonas, we used immunoblots and microtubule sliding assays to show that mutants in CCDC40 (PF7) and CCDC39 (PF8) fail to assemble N-DRC, several inner dynein arms, tektin, and CCDC39. Enrichment screens for suppression of pf7; pf8 cells led to the isolation of five independent extragenic suppressors defined by four different mutations in a NIMA-related kinase, CNK11. These alleles partially rescue the flagellar length defect, but not the motility defect. The suppressor does not restore the missing N-DRC and inner dynein arm proteins. In addition, the cnk11 mutations partially suppress the short flagella phenotype of N-DRC and axonemal dynein mutants, but do not suppress the motility defects. The tpg1 mutation in TTLL9, a tubulin polyglutamylase, partially suppresses the length phenotype in the same axonemal dynein mutants. In contrast to cnk11, tpg1 does not suppress the short flagella phenotype of pf7. The polyglutamylated tubulin in the proximal region that remains in the tpg1 mutant is reduced further in the pf7; tpg1 double mutant by immunofluorescence. CCDC40, which is needed for docking multiple other axonemal complexes, is needed for tubulin polyglutamylation in the proximal end of the flagella. The CCDC39 and CCDC40 proteins are likely to be involved in recruiting another tubulin glutamylase(s) to the flagella. Another difference between cnk11-1 and tpg1 mutants is that cnk11-1 cells show a faster turnover rate of tubulin at the flagellar tip than in wild-type flagella and tpg1 flagella show a slower rate. The double mutant shows a turnover rate similar to tpg1, which suggests the faster turnover rate in cnk11-1 flagella requires polyglutamylation. Thus, we hypothesize that many short flagella mutants in Chlamydomonas have increased instability of axonemal microtubules. Both CNK11 and tubulin polyglutamylation play roles in regulating the stability of axonemal microtubules

Effect of Multiple Layered Vegetation on the Velocity Distribution of Flow in an Open Channel

Vegetation of various heights widely co-exists in natural rivers and wetlands, where the ecological environment and flow process are affected by the riparian vegetation, which has drawn great attention in river engineering and aquatic environmental management. Majority of studies in the past have been mainly focused on the understanding of flow through vegetation of single-layered vegetation. However, in natural riverine environments, mixing vegetation with different heights often occurs in natural rivers, which have a different effect on the flow than the single-layered vegetation does. In a flow condition under multiple layered vegetation, it is limited known about the impact of such vegetation on the flow velocity of channel, which is pre-requisite for many problems in river engineering and environmental management. In this paper, a novel experiment was designed to study the flow characteristics in an open-channel with vegetation of three different heights that exists on the channel bed, with a focus on the effect of the vegetation on the velocity distribution. Experiments were conducted in both partially submerged and fully submerged conditions. Three heights of dowels, 10, 15 and 20 cm, were used to mimic rigid vegetation in a staggered pattern for each type of dowel. Velocities at various locations across a section of channel were measured by Acoustic Doppler Velocimetry (ADV) and propeller velocimetry. Experimental results showed that the vertical velocity distribution is affected by vegetation heights. The results also revealed that the vegetation height have significant impact on the vertical distribution of velocity between and behind the vegetation. The vertical change of velocity behind TP (tall vegetation) and MP (medium vegetation) increases slowly beneath medium vegetation’s height (15cm) and then rapidly increases to the water surface. While the vertical change of velocity behind SP (short vegetation) and BP (blank space between vegetation) decreases a short amount beneath water height 5cm and increases rapidly to the water surface. Generally, the steamwise velocities at short vegetation zone and blank space are larger than tall vegetation zone and medium vegetation zone. These findings on the flow with multiple layered vegetation would be helpful for riparian management practices to maintain healthy ecological and habitat zones

Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. Using X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core, together with cross-linking coupled to mass spectrometry, we were able to use IMP to position and orient all eIF3 components on the 40S•eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. For more information about how to reproduce this modeling, see https://salilab.org/40S-eIF1-eIF3 or the README file

IκBβ acts to inhibit and activate gene expression during the inflammatory response

The activation of pro-inflammatory gene programs by nuclear factor-κB (NF-κB) is primarily regulated through cytoplasmic sequestration of NF-κB by the inhibitor of κB (IκB) family of proteins1. IκBβ, a major isoform of IκB, can sequester NF-κB in the cytoplasm2, although its biological role remains unclear. Although cells lacking IκBβ have been reported3, 4, in vivo studies have been limited and suggested redundancy between IκBα and IκBβ5. Like IκBα, IκBβ is also inducibly degraded; however, upon stimulation by lipopolysaccharide (LPS), it is degraded slowly and re-synthesized as a hypophosphorylated form that can be detected in the nucleus6, 7, 8, 9, 10, 11. The crystal structure of IκBβ bound to p65 suggested this complex might bind DNA12. In vitro, hypophosphorylated IκBβ can bind DNA with p65 and c-Rel, and the DNA-bound NF-κB:IκBβ complexes are resistant to IκBα, suggesting hypophosphorylated, nuclear IκBβ may prolong the expression of certain genes9, 10, 11. Here we report that in vivo IκBβ serves both to inhibit and facilitate the inflammatory response. IκBβ degradation releases NF-κB dimers which upregulate pro-inflammatory target genes such as tumour necrosis factor-α (TNF-α). Surprisingly, absence of IκBβ results in a dramatic reduction of TNF-α in response to LPS even though activation of NF-κB is normal. The inhibition of TNF-α messenger RNA (mRNA) expression correlates with the absence of nuclear, hypophosphorylated-IκBβ bound to p65:c-Rel heterodimers at a specific κB site on the TNF-α promoter. Therefore IκBβ acts through p65:c-Rel dimers to maintain prolonged expression of TNF-α. As a result, IκBβ^(−/−) mice are resistant to LPS-induced septic shock and collagen-induced arthritis. Blocking IκBβ might be a promising new strategy for selectively inhibiting the chronic phase of TNF-α production during the inflammatory response