Investigation and Characterization of Single Hot Spot Laser-Plasma Interactions

Prof. Abraham Bers, Professor of Electrical Engineering and Computer Science Dr. Juan C. Fernández, Deputy Group Leader of P-24, LANL (Co-Supervisor)Control of parametric laser-plasma interactions (LPI) is essential to the success of inertial confinement fusion (ICF). Through a research collaboration with the Los Alamos National Laboratory (LANL), we have had the opportunity to participate in world-class laser-plasma experiments. The goal of these experiments was to gain a fundamental understanding of LPI by studying the interaction of a single laser hot spot, or speckle, with a preformed, quasi-homogeneous, long scale-length plasma. Recent single hot spot experiments resulted in a wealth of data and the first definitive observation of two LPIs. Namely, the Langmuir decay instability (LDI) cascade and stimulated scattering off of an acoustic-like electron mode below the usual electron plasma wave frequency. The LDI is the result of the electron plasma wave (EPW) generated by stimulated Raman scattering (SRS) growing to a sufficient amplitude such that it exceeds a threshold (proportional to the damping of the LDI daughter waves) and undergoes parametric decay into another counter-propagating EPW and a co-propagating ion acoustic wave (IAW). Subsequent EPW decays due to LDI are possible and collectively more than one EPW generated by LDI is called LDI cascade. The LDI cascade can play a role in the saturation of SRS since wave energy from the SRS EPW couples into secondary waves that are nonresonant with the SRS process. Stimulated scattering from an electrostatic wave at a frequency and phase velocity ( ω ≈0.4 ωpe, v φ≈1.4ve) between that of an EPW and IAW was also observed. In this thesis, a Vlasov-Maxwell code is used to numerically predict the time evolution of the electron distribution function for the experimental parameters. The resultant distribution function is then modeled as a bi-Maxwellian (one background and one beaming) to show that it exhibits linear modes that include the observed electron acoustic wave. A quasimode analysis of laser scattering off of this linear mode is presented as one possible explanation of the experimental observation.LAN

Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh

Crystal structures of the Ffh NG GTPase domain at < 1.24 Å resolution reveal multiple overlapping nucleotide binding modes

On airborne tire wear particles along roads with different traffic characteristics using passive sampling and optical microscopy, single particle SEM/EDX, and µ-ATR-FTIR analyses

Tire wear particles (TWPs) are a major category of microplastic pollution produced by friction between tires and road surfaces. This non-exhaust particulate matter (PM) is transported through the air and with runoff leading to environmental pollution and health concerns. Here, we collected airborne PM along paved roads with different traffic volumes and speeds using Sigma-2 passive samplers. Particles entering the samplers deposit onto substrates for analysis, or, as we modified it, directly into small (60 ml) separatory funnels, which is particularly useful with high particle loads, where a density separation aids in isolating the microplastics. We quantified putative TWPs (∼10–80 µm) deposited on the substrates (primarily adhesive tape on glass slides) and in the funnels using stereomicroscopy. Putative TWP deposition rates (particles/cm2/day ± SD) at 5 m from the road were highest near a busy highway (324 ± 129), followed by a boulevard with moderate traffic (184 ± 93), and a slow traffic avenue (29 ± 7). We observed that deposition rates increased within proximity to the highway: 99 ± 54, 180 ± 88, and 340 ± 145 at 30, 15, and 5 m, respectively. We show that TWP abundances (i.e., deposition and mass concentration) increase with vehicle braking (driving behavior). We observed no differences (p \u3e 0.05) between the separatory funnel and adhesive tape collection methods. In addition, we were able to obtain FTIR spectra of TWPs (\u3e10 µm) using µ-ATR-FTIR. Both deserve further scrutiny as novel sampling and analytical approaches. In a separate sampling campaign, we differentiated 1438 particles (∼1–80 µm) deposited on boron substrates into TWP, metal, mineral, and biogenic/organic classes with single particle SEM/EDX analysis based on morpho-textural-chemical classification and machine learning. The results revealed similar concentration trends with traffic (high \u3e moderate \u3e low), with the distribution of particle sources alike for the highway and the moderate road: TWPs (∼38–39%) \u3e biogenic (∼34–35%) \u3e minerals (∼23–26%), and metallic particles (∼2–3%). The low traffic road yielded a much different distribution: biogenic (65%) \u3e minerals (27%) \u3e TWPs (7%) \u3e metallic particles (1%). Overall, this work provides much-needed empirical data on airborne TWPs along different types of roads

Direct visualization reveals dynamics of a transient intermediate during protein assembly

Interactions between proteins underlie numerous biological functions. Theoretical work suggests that protein interactions initiate with formation of transient intermediates that subsequently relax to specific, stable complexes. However, the nature and roles of these transient intermediates have remained elusive. Here, we characterized the global structure, dynamics, and stability of a transient, on-pathway intermediate during complex assembly between the Signal Recognition Particle (SRP) and its receptor. We show that this intermediate has overlapping but distinct interaction interfaces from that of the final complex, and it is stabilized by long-range electrostatic interactions. A wide distribution of conformations is explored by the intermediate; this distribution becomes more restricted in the final complex and is further regulated by the cargo of SRP. These results suggest a funnel-shaped energy landscape for protein interactions, and they provide a framework for understanding the role of transient intermediates in protein assembly and biological regulation

X-ray Structures of the Signal Recognition Particle Receptor Reveal Targeting Cycle Intermediates

The signal recognition particle (SRP) and its conjugate receptor (SR) mediate cotranslational targeting of a subclass of proteins destined for secretion to the endoplasmic reticulum membrane in eukaryotes or to the plasma membrane in prokaryotes. Conserved active site residues in the GTPase domains of both SRP and SR mediate discrete conformational changes during formation and dissociation of the SRP·SR complex. Here, we describe structures of the prokaryotic SR, FtsY, as an apo protein and in two different complexes with a non-hydrolysable GTP analog (GMPPNP). These structures reveal intermediate conformations of FtsY containing GMPPNP and explain how the conserved active site residues position the nucleotide into a non-catalytic conformation. The basis for the lower specificity of binding of nucleotide in FtsY prior to heterodimerization with the SRP conjugate Ffh is also shown. We propose that these structural changes represent discrete conformational states assumed by FtsY during targeting complex formation and dissociation

Structures of SRP54 and SRP19, the Two Proteins that Organize the Ribonucleic Core of the Signal Recognition Particle from Pyrococcus furiosus

In all organisms the Signal Recognition Particle (SRP), binds to signal sequences of proteins destined for secretion or membrane insertion as they emerge from translating ribosomes. In Archaea and Eucarya, the conserved ribonucleoproteic core is composed of two proteins, the accessory protein SRP19, the essential GTPase SRP54, and an evolutionarily conserved and essential SRP RNA. Through the GTP-dependent interaction between the SRP and its cognate receptor SR, ribosomes harboring nascent polypeptidic chains destined for secretion are dynamically transferred to the protein translocation apparatus at the membrane. We present here high-resolution X-ray structures of SRP54 and SRP19, the two RNA binding components forming the core of the signal recognition particle from the hyper-thermophilic archaeon Pyrococcus furiosus (Pfu). The 2.5 Å resolution structure of free Pfu-SRP54 is the first showing the complete domain organization of a GDP bound full-length SRP54 subunit. In its ras-like GTPase domain, GDP is found tightly associated with the protein. The flexible linker that separates the GTPase core from the hydrophobic signal sequence binding M domain, adopts a purely α-helical structure and acts as an articulated arm allowing the M domain to explore multiple regions as it scans for signal peptides as they emerge from the ribosomal tunnel. This linker is structurally coupled to the GTPase catalytic site and likely to propagate conformational changes occurring in the M domain through the SRP RNA upon signal sequence binding. Two different 1.8 Å resolution crystal structures of free Pfu-SRP19 reveal a compact, rigid and well-folded protein even in absence of its obligate SRP RNA partner. Comparison with other SRP19•SRP RNA structures suggests the rearrangement of a disordered loop upon binding with the RNA through a reciprocal induced-fit mechanism and supports the idea that SRP19 acts as a molecular scaffold and a chaperone, assisting the SRP RNA in adopting the conformation required for its optimal interaction with the essential subunit SRP54, and proper assembly of a functional SRP

Structures of the Signal Recognition Particle Receptor from the Archaeon Pyrococcus furiosus: Implications for the Targeting Step at the Membrane

In all organisms, a ribonucleoprotein called the signal recognition particle (SRP) and its receptor (SR) target nascent proteins from the ribosome to the translocon for secretion or membrane insertion. We present the first X-ray structures of an archeal FtsY, the receptor from the hyper-thermophile Pyrococcus furiosus (Pfu), in its free and GDP•magnesium-bound forms. The highly charged N-terminal domain of Pfu-FtsY is distinguished by a long N-terminal helix. The basic charges on the surface of this helix are likely to regulate interactions at the membrane. A peripheral GDP bound near a regulatory motif could indicate a site of interaction between the receptor and ribosomal or SRP RNAs. Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution. Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP•SR targeting complexes