Ms Time Scale Research Articles

Electromagnetic VDE and Disruption Analysis in the SMART Tokamak

The SMall aspect ratio tokamak (SMART) is a new spherical device, that is, currently being constructed at the University of Seville. The operation of SMART will cover three phases reaching a maximum plasma current ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$I_{P}$ </tex-math></inline-formula> ) of 400 kA, a toroidal magnetic field ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$B_{T}$ </tex-math></inline-formula> ) of 1 T, and a pulse length of 500 ms. Such operating conditions present notable challenges to the design and verification of SMARTs structural integrity during normal and off-normal operations. In particular, vertical displacement events (VDEs) and disruptions (Boozer, 2012) are most important as they can cause severe damage to the components directly exposed to the plasma due to the significant electromagnetic (EM) and thermal loads delivered over ms timescales. As a consequence, a detailed evaluation of the EM loads during plasma disruptions is mandatory for the correct dimensioning of the machine, in particular the vacuum vessel. The EM loads are mainly produced by: the poloidal flux variation during the thermal and current quench, halo currents (Boozer, 2013) that flow into the vacuum vessel and interacts with the toroidal magnetic field; and toroidal flux variation during the thermal and current quench. We present, here, the EM and structural analysis performed for the design of SMART. The modeling has been carried out by combining equilibrium scenarios obtained through the FIESTA code (Cunningham, 2013), estimating VDE and disruption time-scales by comparing other machines (Chen et al. 2015), (Hender et al. 2007), and (Bachmann et al. 2011) and computing EM forces through a finite element model (FEM) taking into account the effects of both eddy and halo currents (Roccella et al. 2008), (Titus et al. 2011), and (Ortwein et al. 2020). Finally, the structural assessment of the vacuum vessel is performed in order to verify its integrity during normal and off-normal events in phase 3.

EUSO-SPB2 Fluorescence Telescope trigger test within the EUSO@TurLab Project

The second generation Extreme Universe Space Observatory on a Super-Pressure Balloon (EUSO-SPB2) mission is on track to be approved by NASA for a long duration flight (up to 100 days) in 2023 from Wanaka, New Zealand. EUSO-SPB2 will monitor the night atmosphere of the Southern hemisphere from 33 km altitude to detect Ultra-High Energy Cosmic Rays (UHECRs) and search for astrophysical and cosmogenic neutrinos. EUSO-SPB2 features two telescopes, a Cherenkov (CT) and a Fluorescence (FT) Telescope. The hardware implementation and performance of the FT trigger logic were tested at the TurLab facility, hosted at the University of Turin. The tests proved the correct hardware implementation of the trigger logic and its ability to detect μs timescale transient signals.

Testing a Galactic Lensing Hypothesis with the Prompt Emission of GRB 221009A

Even at modest amplification, the optical depth to gravitational lensing through the Galaxy is < 10−5. However, the large apparent isotropic-equivalent energy of GRB 221009A coupled with a path through low Galactic latitude suggests that the conditional probability that this particular GRB was lensed is greater than the very low a priori expectation. With the extreme brightness of the prompt emission, this Galactic lensing hypothesis can be constrained by autocorrelation analysis of Fermi photons on 0.1–1000 ms timescales. In relating lensing mass, magnification, and autocorrelation timescale, I show that a lensed-induced autocorrelation signature by stellar lenses falls below the minimal variability timescale (MVT) expected from a black hole central engine. However, lensing by Galactic dark matter MACHOs (M l > 10–1000 M ⊙) could be confirmed with this approach. Regardless, at a peak γ-ray photon rate of > 30 ms−1, GRB 221009A represents a prime opportunity to measure the smallest MVTs of GRBs.

Optically induced changes in the band structure of the Weyl charge-density-wave compound

Collective modes are responsible for the emergence of novel quantum phases in topological materials. In the quasi-one dimensional (1D) Weyl semimetal , a charge density wave (CDW) opens band gaps at the Weyl points, thus turning the system into an axionic insulator. Melting the CDW would restore the Weyl phase, but 1D fluctuations extend the gapped regime far above the 3D transition temperature (T = 263 K), thus preventing the investigation of this topological phase transition with conventional spectroscopic methods.Here we use a non-equilibrium approach: we perturb the CDW phase by photoexcitation, and we monitor the dynamical evolution of the band structure by time- and angle-resolved photoelectron spectroscopy. We find that, upon optical excitation, electrons populate the linearly dispersing states at the Fermi level (E ), and fill the CDW gap. The dynamics of both the charge carrier population and the band gap renormalization (BGR) show a fast component with a characteristic time scale of a few hundreds femtoseconds. However, the BGR also exhibits a second slow component on the µs time scale. The combination of an ultrafast response and of persistent changes in the spectral weight at E , and the resulting sensitivity of the linearly dispersing states to optical excitations, may explain the high performances of as a material for broadband infrared photodetectors.

Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors.

Molecular dynamics (MD) simulations probe the conformational repertoire of macromolecular systems using Newtonian dynamic equations. The time scales of MD simulations allow the exploration of biologically relevant phenomena and can elucidate spatial and temporal properties of the building blocks of life, such as deoxyribonucleic acid (DNA) and protein, across microsecond (μs) time scales using femtosecond (fs) time steps. A principal bottleneck toward extending MD calculations to larger time scales is the long-range electrostatic force measuring component of the naive nonbonded force computation algorithm, which scales with a complexity of (N, number of atoms). In this review, we present various methods to determine electrostatic interactions in often-used open-source MD packages as well as the implementation details that facilitate acceleration of the electrostatic interaction calculation.

The Importance of Mg2+ -Free State in Nucleotide Exchange of Oncogenic K-Ras Mutants.

For efficient targeting of oncogenic K-Ras interaction sites, a mechanistic picture of the Ras-cycle is necessary. Herein, we used NMR relaxation techniques and molecular dynamics simulations to decipher the role of slow dynamics in wild-type and three oncogenic P-loop mutants of K-Ras. Our measurements reveal a dominant two-state conformational exchange on the ms timescale in both GDP- and GTP-bound K-Ras. The identified low-populated higher energy state in GDP-loaded K-Ras has a conformation reminiscent of a nucleotide-bound/Mg2+ -free state characterized by shortened β2/β3-strands and a partially released switch-I region preparing K-Ras for the interaction with the incoming nucleotide exchange factor and subsequent reactivation. By providing insight into mutation-specific differences in K-Ras structural dynamics, our systematic analysis improves our understanding of prolonged K-Ras signaling and may aid the development of allosteric inhibitors targeting nucleotide exchange in K-Ras.

Exploring the Dynamics of Shikimate Kinase through Molecular Mechanics

Shikimate kinase (SK) enzyme is a suitable target for antimicrobial drugs as it is present in pathogenic microorganisms and absent in mammals. A complete understanding of the functioning of this enzyme can unveil novel methods to inactivate it. To do this, a clear understanding of SK performance is needed. Previously, the chemical step of SK was studied in detail, but a study of longer-term scale simulations is still missing. In the present work, we performed molecular dynamics (MD) simulations in the μs time scale that allowed us to explore further regions of the SK energy landscape than previously. Simulations were conducted on the wild-type (WT) enzyme and the R116A and R116K mutants. We analyzed the dynamics of the enzymes through standard MD tools, and we found that the global motions in the mutants were perturbed. These motions can be linked to the observed undetectable binding affinity of the WT enzyme and the R116A and R116K mutants.

Initial nucleation of metastable γ-Ga2O3 during sub-millisecond thermal anneals of amorphous Ga2O3

Beta-phase gallium oxide (β-Ga2O3) is a promising semiconductor for high frequency, high temperature, and high voltage applications. In addition to the β-phase, numerous other polymorphs exist and understanding the competition between phases is critical to control practical devices. The phase formation sequence of Ga2O3, starting from amorphous thin films, was determined using lateral-gradient laser spike annealing at peak temperatures of 500–1400 °C on 400 μs to 10 ms timescales, with transformations characterized by optical microscopy, x-ray diffraction, and transmission electron microscopy (TEM). The resulting phase processing map showed the γ-phase, a defect-spinel structure, first nucleating under all annealing times for temperatures from 650 to 800 °C. The cross-sectional TEM at the onset of the γ-phase formation showed nucleation near the film center with no evidence of heterogeneous nucleation at the interfaces. For temperatures above 850 °C, the thermodynamically stable β-phase was observed. For anneals of 1–4 ms and temperatures below 1200 °C, small randomly oriented grains were observed. Large grains were observed for anneals below 1 ms and above 1200 °C, with anneals above 4 ms and 1200 °C resulting in textured films. The formation of the γ-phase prior to β-phase, coupled with the observed grain structure, suggests that the γ-phase is kinetically preferred during thermal annealing of amorphous films, with β-phase subsequently forming by nucleation at higher temperatures. The low surface energy of the γ-phase implied by these results suggests an explanation for the widely observed γ-phase inclusions in β-phase Ga2O3 films grown by a variety of synthesis methods.

Approaching Protein Aggregation and Structural Dynamics by Equilibrium and Nonequilibrium Paramagnetic Perturbation.

PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation) is the presented nuclear magnetic resonance (NMR) approach to identify at once the location of proteins' exposed surface, hindered accessibility, and exchange processes occurring on a μs-ms time scale. In addition to mapping the protein surface accessibility, the application of this method under specific conditions makes it possible to distinguish conformational mobility and chemical exchange processes, thereby providing an alternative to characterization by more demanding techniques (transverse relaxation dispersion, saturation transfer, and high-pressure NMR). Moreover, its high sensitivity enables studying samples at low, physiologically more relevant concentrations. Association, dynamics, and oligomerization are addressed by PENELOP for a component of SARS-CoV-2 replication transcription complex and an amyloidogenic protein.

Quantification of Sub-Pixel Dynamics in High-Speed Neutron Imaging.

The high penetration depth of neutrons through many metals and other common materials makes neutron imaging an attractive method for non-destructively probing the internal structure and dynamics of objects or systems that may not be accessible by conventional means, such as X-ray or optical imaging. While neutron imaging has been demonstrated to achieve a spatial resolution below 10 μm and temporal resolution below 10 μs, the relatively low flux of neutron sources and the limitations of existing neutron detectors have, until now, dictated that these cannot be achieved simultaneously, which substantially restricts the applicability of neutron imaging to many fields of research that could otherwise benefit from its unique capabilities. In this work, we present an attenuation modeling approach to the quantification of sub-pixel dynamics in cyclic ensemble neutron image sequences of an automotive gasoline direct injector at a 5 μs time scale with a spatial noise floor in the order of 5 μm.

CP-MAS and Solution NMR Studies of Allosteric Communication in CA-assemblies of HIV-1

Solution and solid-state NMR spectroscopy are highly complementary techniques for studying structure and dynamics in very high molecular weight systems. Here we have analysed the dynamics of HIV-1 capsid (CA) assemblies in presence of the cofactors IP6 and ATPγS and the host-factor CPSF6 using a combination of solution state and cross polarisation magic angle spinning (CP-MAS) solid-state NMR. In particular, dynamical effects on ns to µs and µs to ms timescales are observed revealing diverse motions in assembled CA.Using CP-MAS NMR, we exploited the sensitivity of the amide/Cα-Cβ backbone chemical shifts in DARR and NCA spectra to observe the plasticity of the HIV-1 CA tubular assemblies and also map the binding of cofactors and the dynamics of cofactor-CA complexes. In solution, we measured how the addition of host- and co-factors to CA -hexamers perturbed the chemical shifts and relaxation properties of CA-Ile and -Met methyl groups using transverse-relaxation-optimized NMR spectroscopy to exploit the sensitivity of methyl groups as probes in high-molecular weight proteins. These data show how dynamics of the CA protein assembly over a range of spatial and temporal scales play a critical role in CA function. Moreover, we show that binding of IP6, ATPγS and CPSF6 results in local chemical shift as well as dynamic changes for a significant, contiguous portion of CA, highlighting how allosteric pathways communicate ligand interactions between adjacent CA protomers.

Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability.

Thermostability is the key to maintain the structural integrity and catalytic activity of enzymes in industrial biotechnological processes, such as terpene cyclase-mediated generation of medicines, chiral synthons, and fine chemicals. However, affording a large increase in the thermostability of enzymes through site-directed protein engineering techniques can constitute a challenge. In this paper, we used ancestral sequence reconstruction to create a hyperstable variant of the ent-copalyl diphosphate synthase PtmT2, a terpene cyclase involved in the assembly of antibiotics. Molecular dynamics simulations on the μs timescale were performed to shed light on possible molecular mechanisms contributing to activity at an elevated temperature and the large 40 °C increase in melting temperature observed for an ancestral variant of PtmT2. In silico analysis revealed key differences in the flexibility of a loop capping the active site, between extant and ancestral proteins. For the modern enzyme, the loop collapses into the active site at elevated temperatures, thus preventing biocatalysis, whereas the loop remains in a productive conformation both at ambient and high temperatures in the ancestral variant. Restoring a Pro loop residue introduced in the ancestral variant to the corresponding Gly observed in the extant protein led to reduced catalytic activity at high temperatures, with only moderate effects on the melting temperature, supporting the importance of the flexibility of the capping loop in thermoadaptation. Conversely, the inverse Gly to Pro loop mutation in the modern enzyme resulted in a 3-fold increase in the catalytic rate. Despite an overall decrease in maximal activity of ancestor compared to wild type, its increased thermostability provides a robust backbone amenable for further enzyme engineering. Our work cements the importance of loops in enzyme catalysis and provides a molecular mechanism contributing to thermoadaptation in an ancestral enzyme.

Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication

Human hepatitis B virus (HBV) replication is initiated by the binding of the viral polymerase (P) to epsilon (ε), an ≈85-nucleotide (nt) cis-acting regulatory stem-loop RNA located at the 5′-end of the pre-genomic RNA (pgRNA). This interaction triggers P and pgRNA packaging and protein-primed reverse transcription and is therefore an attractive therapeutic target. Our recent nuclear magnetic resonance (NMR) structure of ε provides a useful starting point toward a detailed understanding of HBV replication, and hints at the functional importance of ε dynamics. Here, we present a detailed description of ε motions on the ps to ns and μs to ms time scales by NMR spin relaxation and relaxation dispersion, respectively. We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. These data outline a series of complex motions on multiple time scales within ε. Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, P-pgRNA packaging, protein-priming, and DNA synthesis. Taken together, our work implicates RNA dynamics as an integral feature that governs HBV replication.

Observation of breakdown wave mechanism in avalanche ionization produced atmospheric plasma generated by a picosecond CO2 laser

Understanding the formation and long-timescale evolution of atmospheric plasmas produced by ultrashort, long-wavelength infrared (LWIR) pulses is an important but partially understood problem. Of particular interest are plasmas produced in air with a peak laser intensity ∼1012 W/cm2, the so-called clamping intensity observed in LWIR atmospheric guiding experiments where tunneling and multi-photon ionization operative at near-IR or shorter wavelengths are inoperative. We find that avalanche breakdown on the surface of aerosol (dust) particles can act to seed the breakdown of air observed above the 200 GW/cm2 threshold when a train of 3 ps 10.6 μm laser pulses separated by 18 ps is used. The breakdown first appears at the best focus but propagates backward toward the focusing optic as the plasma density approaches critical density and makes forward propagation impossible. The velocity of the backward propagating breakdown can be as high as 109 cm/s, an order of magnitude greater than measured with ns pulse-produced breakdown, and can be explained rather well by the so-called breakdown wave mechanism. Transverse plasma expansion with a similar velocity is assisted by UV photoionization and is observed as a secondary longitudinal breakdown mechanism in roughly 10% of the shots. When a cm-size, TW power beam is propagated, interception of aerosol particles is guaranteed and several (40 cm−3) breakdown sites appear, each initially producing a near-critical density plasma. On a 10 ns–1 μs timescale, shockwaves from each site expand radially and coalesce to produce a large hot gas channel. The radial velocity of the expansion agrees well with the prediction of the blast wave theory developed for ultrafast atmospheric detonations.

Unique structural and dynamic properties of the HNH nuclease in mesophilic and thermophilic Cas9 revealed by NMR

CRISPR‐Cas9 is a widely utilized biochemical tool with applications in biotechnology and in medicine. Target DNA recognition and nuclease sites of Cas9 are spatially separated yet functionally coupled, indicative of an allosteric crosstalk throughout the enzyme. There are structural and dynamic changes occuring throughout Cas9 that are critical for this signal propagation. However, an understanding of the molecular motions guiding Cas9 and how this influences its mechanism are unknown. In this study we report on the structural and dynamic properties of the HNH domain between the extensively studied SpCas9 from Streptococcus pyogenes, and a recently discovered thermostable Cas9 homolog from a thermophilic bacterium Geobacillus stearothermophilus(GeoCas9). Here we show that despite sequential and structural conservation, SpHNH and GeoHNH have different dynamic profiles. We found the intrinsic dynamics of SpHNH to be on the slow (ms) timescale, while GeoHNH is highly influenced by fast (ps‐ns) timescale dynamics. Furthermore, we found that when the residue with the highest flexibility on the ps‐ns timescale is mutated in GeoHNH, its protein solubility, thermal stability, and dynamic profile are all drastically distorted. Our results demonstrate how there are mechanistic differences between the HNH domain of mesophilic and thermophilic Cas9 species. Our results also highlight how these fast timescale motions that regulate GeoHNH play a role in giving GeoCas9 its thermophilic characteristic.

Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields.

Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical models of deoxynucleosides, even at a high level of theory, are not optimal structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.

Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis.

Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational changes in enzyme catalysis; however, such studies have focused on tremendously proficient enzymes such as triosephosphate isomerase and orotidine 5′-monophosphate decarboxylase, where the rapid (μs timescale) motion of a single loop dominates the transition between catalytically inactive and active conformations. In contrast, the (βα)8-barrels of tryptophan and histidine biosynthesis, such as the specialist isomerase enzymes HisA and TrpF, and the bifunctional isomerase PriA, are decorated by multiple long loops that undergo conformational transitions on the ms (or slower) timescale. Studying the interdependent motions of multiple slow loops, and their role in catalysis, poses a significant computational challenge. This work combines conventional and enhanced molecular dynamics simulations with empirical valence bond simulations to provide rich details of the conformational behavior of the catalytic loops in HisA, PriA, and TrpF, and the role of their plasticity in facilitating bifunctionality in PriA and evolved HisA variants. In addition, we demonstrate that, similar to other enzymes activated by ligand-gated conformational changes, loops 3 and 4 of HisA and PriA act as gripper loops, facilitating the isomerization of the large bulky substrate ProFAR, albeit now on much slower timescales. This hints at convergent evolution on these different (βα)8-barrel scaffolds. Finally, our work reemphasizes the potential of engineering loop dynamics as a tool to artificially manipulate the catalytic repertoire of TIM-barrel proteins.

Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field.

We developed force field parameters for fluorinated, aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the implicitly polarized charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs time scale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling the structure and dynamics of fluorine-containing proteins at the atomic level.

Three-dimensional complex architectures observed in shock processed amino acid mixtures

Abstract Asteroid and cometary impacts have been considered one of the possible routes for exogenous delivery of organics to the early Earth. It is well established that amino acids can be synthesized due to impact-driven shock processesing of simple molecules and that amino acids can survive the extreme conditions of impact events. In the present study, we simulate impact-induced shock conditions utilizing a shock tube that can maintain a reflected shock temperature of about 5,500 K for 2 ms time scale. We have performed shock processing of various combinations of amino acids with subsequent morphological analysis carried out using Scanning Electron Microscope (SEM), revealing that the shock processed amino acids demonstrate an extensive range of complex structures. These results provide evidence for the further evolution of amino acids in impact-induced shock environments leading to the formation of complex structures and thus providing a pathway for the origin of life.

Towards sub-millisecond cryo-EM grid preparation.

Sample preparation is still a significant problem for many single particle cryo-EM workflows and our understanding and developments in the area lag behind that of image processing and microscope design. Over the last few years there has been growing evidence that many of the problems which occur during sample preparation are during the time the sample resides within the thin film created during the conventional blotting process. In parallel, faster grid preparation approaches have been developed for time-resolved cryo-EM experiments allowing for non-equilibrium intermediates to be captured on the ms timescale. Therefore, an important question is how fast can we prepare suitable grids for imaging by cryo-EM and how much does this mitigate the problems observed in sample preparation? Here we use a novel approach which has been developed for time-resolved studies to produce grids on an estimated sub-1 ms timescale. While the method comes with its own challenges, a 3.8 Å reconstruction of apoferritin prepared with the ultrafast method shows that good resolutions can be achieved. Although several orders of magnitude faster than conventional approaches we show using a ribosome sample, that interactions with the air-water interface cannot be avoided with preferred orientations still present. Therefore, the work shows that faster reactions can be captured but poses the question whether speed is the answer to problems with sample preparation.