Nanosecond Time Scale Research Articles

Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations

Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.

Oxygen-evolving photosystem II structures during S1–S2–S3 transitions

Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1–3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4–7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O–O bond formation.

Slowing Hot Electron Cooling in CdSe Quantum Dots Using Electron‐Rich Exciton‐Delocalizing Ligands

AbstractUnderstanding hot carrier dynamics in semiconductor nanocrystals is an important research focus due to their applications in photonics and photovoltaic devices. In this report, we investigated the effects of surface‐bound exciton‐delocalizing ligands (EDLs) on the lifetimes of hot electrons in CdSe quantum dots (QDs). After treatment of CdSe with two different phenylithiocarbamates (PTCs), a class of EDLs, the depletion times of the band‐edge exciton bleach were roughly equivalent as observed through ultrafast transient absorption spectroscopy. However, following the initial ultrafast depletion, the PTC‐treated samples continued to deplete while the untreated CdSe began recovering. Inspection of other transient features – such as the 3rd exciton and hot biexciton – reveal a general trend in which the PTC‐treated samples relax more slowly at short times (<10 ps) when compared with the untreated CdSe. At longer delay times, in the range of nanoseconds, the CdSe+CF3OPTC loses nearly 80 % of its excited state populations, while the CdSe+MeOPTC loses only 20–40 %. We discuss the role that exciton delocalization plays in determining these observed rates as well as how they compare to previous studies. Kinetic differences between the two ligands are attributed to their electron donating/withdrawing abilities and coupling to the CdSe QD. Coherent vibrational wavepacket analysis supports this line of reasoning, showing increased coupling between the exciton and the longitudinal optical (LO) phonon due to increased Coulombic field strength around the hole and electron‐donating MeOPTC. These results indicate that electron‐rich PTCs are especially good candidates for use in QD devices that would make use of hot carriers.

Ultrafast optical properties of stoichiometric and non-stoichiometric refractory metal nitrides TiNx, ZrNx, and HfNx.

Refractory metal nitrides have recently gained attention in various fields of modern photonics due to their cheap and robust production technology, silicon-technology compatibility, high thermal and mechanical resistance, and competitive optical characteristics in comparison to typical plasmonic materials like gold and silver. In this work, we demonstrate that by varying the stoichiometry of sputtered nitride films, both static and ultrafast optical responses of refractory metal nitrides can efficiently be controlled. We further prove that the spectral changes in ultrafast transient response are directly related to the position of the epsilon-near-zero region. At the same time, the analysis of the temporal dynamics allows us to identify three time components: the "fast" femtosecond one, the "moderate" picosecond one, and the "slow" at the nanosecond time scale. We also find out that the non-stoichiometry does not significantly decrease the recovery time of the reflectance value. Our results show the strong electron-phonon coupling and reveal the importance of both the electron and lattice temperature-induced changes in the permittivity near the ENZ region and the thermal origin of the long tail in the transient optical response of refractory nitrides.

Electronic Structure of Isolated Graphene Nanoribbons in Solution Revealed by Two-Dimensional Electronic Spectroscopy.

Structurally well-defined graphene nanoribbons (GNRs) are nanostructures with unique optoelectronic properties. In the liquid phase, strong aggregation typically hampers the assessment of their intrinsic properties. Recently we reported a novel type of GNRs, decorated with aliphatic side chains, yielding dispersions consisting mostly of isolated GNRs. Here we employ two-dimensional electronic spectroscopy to unravel the optical properties of isolated GNRs and disentangle the transitions underlying their broad and rather featureless absorption band. We observe that vibronic coupling, typically neglected in modeling, plays a dominant role in the optical properties of GNRs. Moreover, a strong environmental effect is revealed by a large inhomogeneous broadening of the electronic transitions. Finally, we also show that the photoexcited bright state decays, on the 150 fs time scale, to a dark state which is in thermal equilibrium with the bright state, that remains responsible for the emission on nanosecond time scales.

Exciton Bimolecular Annihilation Dynamics in Push-Pull Semiconductor Polymers.

Exciton-exciton annihilation is a ubiquitous nonlinear dynamic phenomenon in materials hosting Frenkel excitons. In this work, we investigate the nonlinear exciton dynamics of an electron push-pull conjugated polymer by fluence-dependent transient absorption and excitation-correlation photoluminescence spectroscopy, where we can quantitatively show the latter to be a more selective probe of the nonlinear dynamics. Simulations based on a time-independent exciton annihilation model show a decreasing trend for the extracted annihilation rates with excitation fluence. Further investigation of the fluence-dependent transients suggests that the exciton-exciton annihilation bimolecular rates are not constant in time, displaying a t-1/2 time dependence, which we rationalize as reflective of one-dimensional exciton diffusion, with a diffusion length estimated to be 9 ± 2 nm. In addition, exciton annihilation gives rise to a long-lived species that recombines on a nanosecond time scale. Our conclusions shed broad light onto nonlinear exciton dynamics in push-pull conjugated polymers.

Generation of skyrmions by combining thermal and spin-orbit torque: breaking half skyrmions into skyrmions.

Skyrmions, swirling spin textures with topologically protected stability and low critical driven-current density, can be generated from the stripe domain with current pulses, bringing them closer to practical applications in racetrack memory. However, the mechanism of this topological transition from the stripe domain to the skyrmion remains unclear because the transition process occurs at a nanosecond timescale, giving rise to difficulties in observing this process using imaging tools. In this study, we controlled the domain wall - skyrmion transition by combining Joule heating with spin-orbit torque (SOT) and experimentally observed the details of this process, by which we confirmed the mechanism: the spatial variation of the topological charge density induces half skyrmions branching from the stripe domains, and these half skyrmions overcome the surface tension and break away from the stripe domain, resulting in the generation of skyrmions. The details were observed by employing Joule heating to overcome the pinning effect and manipulating the strength of the SOT to induce the branching and breaking of half skyrmions. These findings offer new insights into skyrmion generation and serve as an important step towards the development of highly efficient devices for processing and computing based on skyrmionics.

The dynamic nature of electrostatic disorder in organic mixed ionic and electronic conductors.

Charge dynamics in disordered media is described invariably assuming that the energy landscape for hopping site energy is stationary. Within the same framework, the correlation between low electronic disorder and high charge mobility is considered extremely robust, despite the emergence of materials with mixed ionic and electronic conductivity (OMIECs) that display high mobility coexisting with large disorder. We show in this work that the disorder of OMIEC polymers is highly dynamical, i.e. the on-site energy for charge transport fluctuates with a characteristic time comparable with that of electron transport. Under these conditions, the disorder of the "frozen" system is not relevant for the charge carrier, whose dynamics are instead controlled by the underlying dynamics of the material. Deep traps exist but have a finite lifetime. The combination of classical simulations and quantum chemical calculations on the nanosecond timescale seems ideal to disclose and characterise the phenomenon.

BODIPY dyes for optical limiting applications on the nanosecond timescale.

Since 2017, the Institute for Nanotechnology Innovation at Rhodes University has studied the optical limiting properties of boron dipyrromethene (BODIPY) dyes with respect to high-intensity nanosecond timescale laser pulses. Concerns over the irresponsible use of laser pointers in the context of aviation safety have provided a need for materials that can readily transmit light under ambient conditions while rapidly attenuating intense incident laser pulses. The structural flexibility of the BODIPY chromophore facilitates the red shift of the main BODIPY spectral band that typically lies at ca. 500 nm to the red end of the visible and the near-infrared through the introduction of vinylene groups at the 3,5-positions or an aza-nitrogen atom. Research carried out in this context is described, and possible future directions are discussed.

Truth and (Mis)Information in the High-Tech Empires: Case Study: Cosmopolis: a novel, by Don DeLillo

Our contemporary time is marked by an endless flow of data that is exchanged between nations, companies, and individuals at a nanosecond timescale. All this data flow, which Katherine Hales calls “information overload”, is facilitated by the spread of computer software and digital devices that have colonized every corner on the globe. Today no secret is hidden; information is available and access to it is getting liberated from the confines of the enclosed files. Entrepreneurs, decision-makers, politicians, researchers and even common people, to mention just a few categories, each has built some kind of a digital fortress that secures its data and transmits only the information that suits its interests to the (digital) world. Yet, high-tech empires are no more than a double-edged weapon that (mis)informs not only consumers and adversaries but also the high-tech owners themselves. While high-technologies have been viewed as a sign of extreme knowledge, power and wealth, they have in fact deprived humans of their natural ‘humanity’ one way or another. More than that, instead of providing absolute knowledge as they are supposed to do, they hide the dark truth and what they really provide is no more than a mere illusion. Taking the example of Don DeLillo’s Cosmopolis: a novel, this novel envisages the influence of high-technologies on the contemporary Man and exposes the double facets of the computer and wireless networks. Through the protagonist Eric Packer, DeLillo portrays the digital world from different perspectives and lays bare the inconveniences of high-technologies as they eventually turn out to hide the ‘truth’ instead of revealing it to their owner. Indeed, the protagonist’s blind trust in his high-tech empire was caused by misinformation rather than by objective recognition of the concrete world that surrounds him. In Cosmopolis: a novel the author warns his readers that it is wiser to keep a certain amount of doubt and criticism while dealing with Artificial Intelligence and Virtual Reality.

Compositional transferability of deep potential in molten LiF-BeF2 and LaF3 mixtures: prediction of density, viscosity, and local structure.

The accumulation of lanthanide fission products carries the risk of altering the structure and properties of the nuclear fuel carrier salt LiF-BeF2 (Flibe), thereby downgrading the operating efficiency and safety of the molten salt reactor. However, the condition-limited experimental measurements, spatiotemporal-limited first-principles calculations, and accuracy-limited classical dynamic simulations are unable to capture the precise local structure and reliable thermophysical properties of heterogeneous molten salts. Therefore, the deep potential (DP) of LaF3 and Flibe molten mixtures is developed here, and DP molecular dynamics simulations are performed to systemically study the densities, diffusion coefficients, viscosities, radial distribution functions and coordination numbers of multiple molten Flibe + xLaF3, the quantitative relationships between these properties and LaF3 concentration are investigated, and the potential structure-property relationships are analyzed. Eventually, the transferability of DP on molten Flibe + LaF3 with different formulations as well as the predictability of structures and properties are achieved at the nanometer spatial scale and the nanosecond timescale.

Photocatalytic activity of dual defect modified graphitic carbon nitride is robust to tautomerism: machine learning assisted ab initio quantum dynamics.

Two-dimensional graphitic carbon nitride (GCN) is a popular metal-free polymer for sustainable energy applications due to its unique structure and semiconductor properties. Dopants and defects are used to tune GCN, and dual defect modified GCN exhibits superior properties and enhanced photocatalytic efficiency in comparison to pristine or single defect GCN. We employ a multistep approach combining time-dependent density functional theory and nonadiabatic molecular dynamics (NAMD) with machine learning (ML) to investigate coupled structural and electronic dynamics in GCN over a nanosecond timescale, comparable to and exceeding the lifetimes of photo-generated charge carriers and photocatalytic events. Although frequent hydrogen hopping transitions occur among four tautomeric structures, the electron-hole separation and recombination processes are only weakly sensitive to the tautomerism. The charge separated state survives for about 10 ps, sufficiently long to enable photocatalysis. The employed ML-NAMD methodology provides insights into rare events that can influence excited state dynamics in the condensed phase and nanoscale materials and extends NAMD simulations from pico- to nanoseconds. The ab initio quantum dynamics simulation provides a detailed atomistic mechanism of photoinduced evolution of charge carriers in GCN and rationalizes how GCN remains photo-catalytically active despite its multiple isomeric and tautomeric forms.

Ultrafast electron dynamics in excited states of conjugated thiophene-fluorene organic polymer (pF8T2) thin films.

The electronic states of poly(9,9-dioctylfluorenyl-alt-bithiophene) pF8T2 on H/Si(100) substrates, prototypical for organic photovoltaics, were investigated by ultrafast photoelectron spectroscopy and by time-resolved fluorescence studies. Occupied and unoccupied electronic states were analysed by ultraviolet photoelectron spectroscopy (UPS), static and dynamic femtosecond two-photon photoemission (2PPE), and time-correlated single photon counting (TCSPC). Time-resolved measurements allow assessment of population lifetimes of intermediate states. The combination of time-resolved photoelectron spectroscopy and fluorescence excitation allows following the electronic dynamics in excited states from the femtosecond to the nanosecond time scale. For this prototypical material the electron kinetic energy resolved lifetimes range from about a few tens of femtoseconds up to hundreds of picoseconds. After annealing these types of organic thin films the efficiency of organic solar cells usually increases. We show that annealing does not influence the initial ultrafast charge generation processes, but the long-lived states. However, the nanosecond scale fluorescence lifetimes measured by TCSPC are prolonged after annealing, which therefore is identified as the cause of a greater exciton diffusion range and thus is beneficial for charge carrier extraction.

Harnessing conformational dynamics in enzyme catalysis to achieve nature-like catalytic efficiencies: the shortest path map tool for computational enzyme redesign.

Enzymes exhibit diverse conformations, as represented in the free energy landscape (FEL). Such conformational diversity provides enzymes with the ability to evolve towards novel functions. The challenge lies in identifying mutations that enhance specific conformational changes, especially if located in distal sites from the active site cavity. The shortest path map (SPM) method, which we developed to address this challenge, constructs a graph based on the distances and correlated motions of residues observed in nanosecond timescale molecular dynamics (MD) simulations. We recently introduced a template based AlphaFold2 (tAF2) approach coupled with 10 nanosecond MD simulations to quickly estimate the conformational landscape of enzymes and assess how the FEL is shifted after mutation. In this study, we evaluate the potential of SPM when coupled with tAF2-MD in estimating conformational heterogeneity and identifying key conformationally-relevant positions. The selected model system is the beta subunit of tryptophan synthase (TrpB). We compare how the SPM pathways differ when integrating tAF2 with different MD simulation lengths from as short as 10 ns until 50 ns and considering two distinct Amber forcefield and water models (ff14SB/TIP3P versus ff19SB/OPC). The new methodology can more effectively capture the distal mutations found in laboratory evolution, thus showcasing the efficacy of tAF2-MD-SPM in rapidly estimating enzyme dynamics and identifying the key conformationally relevant hotspots for computational enzyme engineering.

Effect of π-extension and halogenation on the optical limiting properties of meso-pyrenylBODIPYdyes

The lack of suitable optical limiters that cover the entire UV-visible-NIR region has motivated research to identify novel efficient and stable optical limiting materials. There has been a strong focus on attenuating the second harmonic of Nd:YAG pulsed lasers at 532 nm on the nanosecond timescale. The photophysicochemical processes of a series of mono- and di-(4-dimethylamino)styryl-meso-pyrenylBODIPY and mono- and di-(4-dimethylamino)buta-1,3-dienyl-meso-pyrenylBODIPY dyes were studied by UV-visible absorption and fluorescence emission spectroscopy, and by determining the fluorescence and triplet state lifetimes. Z-scan measurements were carried out at a fixed concentration of 10 [Formula: see text]M so that the effective nonlinear coefficients, third-order susceptibilities, second-order hyperpolarizabilities and limiting fluences of the dyes can be compared and trends in the structure-property relationships for these optical limiting parameters can be identified.

Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms.

Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm+) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm+ from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm+. We studied the binding of Gdm+ to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm+ binding. We show that Gdm+ binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm+ binding propensity, making the Gdm+ binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.

Probing the Dissociation Pathway of a Kinetically Labile Transthyretin Mutant.

Aggregation of transthyretin (TTR) is associated with devastating amyloid diseases. Amyloidosis begins with the dissociation of the native homotetramer (a dimer of dimers) to form a monomeric intermediate that assembles into pathogenic aggregates. This process is accelerated in vitro at low pH, but the process by which TTR dissociates and reassembles at neutral pH remains poorly characterized due to the low population of intermediates. Here, we use 19F-nuclear magnetic resonance (NMR) and a highly sensitive trifluoromethyl probe to determine the relative populations of the species formed by the dissociation of a destabilized variant, A25T. The A25T mutation perturbs both the strong dimer and weak dimer-dimer interfaces. A tetramer ⇌ dimer ⇌ monomer (TDM) equilibrium model is proposed to account for concentration- and temperature-dependent population changes. Thermodynamic and kinetic parameters and activation energetics for dissociation of the native A25T tetramer, as well as a destabilized alternative tetramer (T*) with a mispacked F87 side chain, were extracted by van't Hoff and 19F-NMR line shape analysis, saturation transfer, and transition state theory. Chemical shifts for the dimer and T* species are degenerate for 19F and methyl probes close to the strong dimer interface, implicating interfacial perturbation as a common structural feature of these destabilized species. All-atom molecular dynamics simulations further suggest more frequent F87 ring flipping on the nanosecond time scale in the A25T dimer than in the native A25T tetramer. Our integrated approach offers quantitative insights into the energy landscape of the dissociation pathway of TTR at neutral pH.

Single-shot optical imaging with spectrum circuit bridging timescales in high-speed photography.

Single-shot optical imaging based on ultrashort lasers has revealed nonrepetitive processes in subnanosecond timescales beyond the recording range of conventional high-speed cameras. However, nanosecond photography without sacrificing short exposure time and image quality is still missing because of the gap in recordable timescales between ultrafast optical imaging and high-speed electronic cameras. Here, we demonstrate nanosecond photography and ultrawide time-range high-speed photography using a spectrum circuit that produces interval-tunable pulse trains while keeping short pulse durations. We capture a shock wave propagating through a biological cell with a 1.5-ns frame interval and 44-ps exposure time while suppressing image blur. Furthermore, we observe femtosecond laser processing over multiple timescales (25-ps, 2.0-ns, and 1-ms frame intervals), showing that the plasma generated at the picosecond timescale affects subsequent shock wave formation at the nanosecond timescale. Our technique contributes to accumulating data of various fast processes for analysis and to analyzing multi-timescale phenomena as a series of physical processes.

Space-temporal structure of the thunderstorm ground enhancements (TGEs)

We analyzed the structure of the Thunderstorm Ground Enhancement (TGE) using a particle detector network on Aragats. We performed a statistical analysis of the particle arrival time series on a nanosecond time scale using the largest TGE event on record, which occurred on May 23, 2023. Our findings confirm that the TGE is a mixture of multiple runaway electron avalanches that arrive independently and provide stable particle flux. The electron accelerator, operated by the dipole that emerges in the lower part of the thundercloud, sends copious electrons and gamma rays toward the Earth's surface that sustains for minutes. The experimental results are supported by simulations of electron multiplication and acceleration in strong atmospheric electric fields. We compare TGEs and Terrestrial Gamma Flashes (TGFs), which are brief bursts observed by gamma-ray detectors in orbit and are thought to be associated with atmospheric discharges.

Binary Coding by Microwave Pulses on the Transverse Magnetization of the Tetracyanoethylene Radical

The possibility of coding the response of the electron–nuclear system of the tetracyanoethylene radical under microwave pulse irradiation in combination with a pulsed magnetic field gradient in the nanosecond timescale by a binary code is demonstrated. To this end, the tetracyanoethylene radical, which has a well-resolved equidistant electron paramagnetic resonance spectrum due to the interaction of the electron with equivalent magnetic nuclei, is used. The aim is to demonstrate the possibility of implementing this procedure physically rather than to encode the longest possible sequence.