Structural Dynamics Research Articles

The Balancing Act: Ownership Structure and Market Dynamism in Entrepreneurial Family Firms

The Balancing Act: Ownership Structure and Market Dynamism in Entrepreneurial Family Firms

Exploring the Use of Cold Atmospheric Plasma for Sound and Vibration Generation.

In this study, we investigate the potential of cold atmospheric plasma (CAP) as a non-contact excitation device, comparing its performance with an ultrasound transmitter. Utilizing a scanning Laser Doppler Vibrometer (LDV), we visualize the acoustic wavefront generated by a CAP probe and an ultrasound sensor within a designated 50 mm × 50 mm area in front of each probe. Our focus lies in assessing the applicability of a CAP probe for exciting a small polymethyl methacrylate (PMMA) sample. By adjusting the dimensions of the sample to resonate at the excitation frequency of the probe, we can achieve high vibrational velocities, enabling further mechanical analysis. In contrast with traditional vibration excitation techniques such as electrodynamical shakers and hammer impact excitation, a plasma probe can offer distinct advantages without altering the structure's dynamics since it is contactless. Furthermore, in comparison with laser excitation, plasma excitation provides a higher power level. Additionally, while pressurized air systems are applicable for limited low frequencies, plasma probes can perform at higher frequencies. Our findings in this study suggest that CAP is comparable with acoustic excitation, indicating its potential as an effective mechanical excitation method.

Experimental and Computational Study Toward Identifying Active Sites of Supported SnOx Nanoparticles for Electrochemical CO2 Reduction Using Machine-Learned Interatomic Potentials.

SnOx has received great attention as an electrocatalyst for CO2 reduction reaction (CO2RR), however; it still suffers from low activity. Moreover, the atomic-level SnOx structure and the nature of the active sites are still ambiguous due to the dynamism of surface structure and difficulty in structure characterization under electrochemical conditions. Herein, CO2RR performance is enhanced by supporting SnO2 nanoparticles on two common supports, vulcan carbon and TiO2. Then, electrolysis of CO2 at various temperatures in a neutral electrolyte reveals that the application window for this catalyst is between 12 and 30°C. Furthermore, this study introduces a machine learning interatomic potential method for the atomistic simulation to investigate SnO2 reduction and establish a correlation between SnOx structures and their CO2RR performance. In addition, selectivity is analyzed computationally with density functional theory simulations to identify the key differences between the binding energies of *H and *CO2 -, where both are correlated with the presence of oxygen on the nanoparticle surface. This study offers in-depth insights into the rational design and application of SnOx-based electrocatalysts for CO2RR.

A method of network attack-defense game and collaborative defense decision-making based on hierarchical multi-agent reinforcement learning

Faced with the challenges of security strategy design brought about by the complexity of attack behavior and the dynamism of network structure, dynamic hierarchical intelligent defense methods have shown their effectiveness. However, in complex network environments, their application requires a higher level of coordination mechanisms. Therefore, this paper proposes a hierarchical multi-agent reinforcement learning network attack and defense game and cooperative defense decision-making method, which autonomously and efficiently completes the formulation of defense strategies and defense behavior responses. Firstly, we construct a Stackelberg hypergame model of cyberspace conflicts, and under the condition of information loss, characterize the multi-layer dynamic defense coordination response mechanism. Secondly, By utilizing a hierarchical multi-agent reinforcement learning method as the driving force for game evolution, we sequentially solve the Nash equilibrium of the game, and form a dynamic autonomous defense strategy. Finally, we construct a hierarchical multi-agent reinforcement learning framework, which decouples the defense decision problem, reduces the dimension of the defense action space and the exploration difficulty of the strategy space, and learns coordinated defense strategies more efficiently. We used the CybORG (Cyber Operations Research Gym) environment for simulation. We compared and analyzed the autonomously generated cyber defense strategies with other related works, verifying the superior coordination performance of our method in defense strategy generation and control.

Application of high-speed atomic force microscopy in visualizing the dynamics of synthetic polymers

Abstract High-speed atomic force microscopy (HS-AFM) is a technique that enables real-time imaging of nanoscale phenomena in solution. It was originally developed to visualize biomolecules, whose dynamics in solution significantly affect the manifestation of their functions, and has contributed to the understanding of molecular mechanisms based on the observation of single-molecule dynamics of proteins. In recent years, its application has broadened to include not only biomolecules, but also the structural dynamics of supramolecular assemblies that associate and dissociate in solution, as well as the evaluation of synthetic molecules such as polymer gels that swell in solution. In this paper, we review some of our recent studies on the application of HS-AFM to supramolecular polymers and hydrogel particles.

Time-Resolved Ultraviolet Photodissociation Mass Spectrometry Probes the Mutation-Induced Alterations in Protein Stability and Unfolding Dynamics.

How mutations impact protein stability and structure dynamics is crucial for understanding the pathological process and rational drug design. Herein, we establish a time-resolved native mass spectrometry (TR-nMS) platform via a rapid-mixing capillary apparatus for monitoring the acid-initiated protein unfolding process. The molecular details in protein structure unfolding are further profiled by a 193 nm ultraviolet photodissociation (UVPD) analysis of the structure-informative photofragments. Compared with the wild-type dihydrofolate reductase (WT-DHFR), the M42T/H114R mutant (MT-DHFR) exhibits a significant stability decrease in TR-nMS characterization. UVPD comparisons of the unfolding intermediates and original DHFR forms indicate the special stabilization effect of cofactor NADPH on DHFR structure, and the M42T/H114R mutations lead to a significant decrease in NADPH-DHFR interactions, thus promoting the structure unfolding. Our study paves the way for probing the mutation-induced subtle changes in the stability and structure dynamics of drug targets.

Structural dynamics of the active HER4 and HER2/HER4 complexes is finely tuned by different growth factors and glycosylation

Human Epidermal growth factor Receptor 4 (HER4 or ERBB4) carries out essential functions in the development and maintenance of the cardiovascular and nervous systems. HER4 activation is regulated by a diverse group of extracellular ligands including the neuregulin (NRG) family and betacellulin (BTC), which promote HER4 homodimerization or heterodimerization with other HER receptors. Important cardiovascular functions of HER4 are exerted via heterodimerization with its close homolog and orphan receptor, HER2. To date structural insights into ligand-mediated HER4 activation have been limited to crystallographic studies of HER4 ectodomain homodimers in complex with NRG1β. Here, we report cryo-EM structures of near full-length HER2/HER4 heterodimers and full-length HER4 homodimers bound to NRG1β and BTC. We show that the structures of the heterodimers bound to either ligand are nearly identical and that in both cases the HER2/HER4 heterodimer interface is less dynamic than those observed in structures of HER2/EGFR and HER2/HER3 heterodimers. In contrast, structures of full-length HER4 homodimers bound to NRG1β and BTC display more large-scale dynamics mirroring states previously reported for EGFR homodimers. Our structures also reveal the presence of multiple glycan modifications within HER4 ectodomains, modeled for the first time in HER receptors, that distinctively contribute to the stabilization of HER4 homodimer interfaces over those of HER2/HER4 heterodimers.

Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics.

Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values-indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus.

Semirational Design Based on Consensus Sequences to Balance the Enzyme Activity-Stability Trade-Off.

In this study, the phenomenon of the stability-activity trade-off, which is increasingly recognized in enzyme engineering, was explored. Typically, enhanced stability in enzymes correlates with diminished activity. Utilizing Rosa roxburghii copper-zinc superoxide dismutase (RrCuZnSOD) as a model, single-site mutations were introduced based on a semirational design derived from consensus sequences. The initial set of mutants was selected based on activity, followed by combinatorial mutation. This approach yielded two double-site mutants, D25/A115T (18,688 ± 206 U/mg) and A115T/S135P (18,095 ± 1556 U/mg), exhibiting superior enzymatic properties due to additive and synergistic effects. These mutants demonstrated increased half-lives (T1/2) at 80 °C by 1.2- and 1.6-fold, respectively, and their melting temperatures (Tm) rose by 3.4 and 2.5 °C, respectively, without any loss in activity relative to the wild type. Via an integration of structural analysis and molecular dynamics simulations, we elucidated the underlying mechanism facilitating the concurrent enhancement of both thermostability and enzymatic activity.

Exploring Host-Guest Interactions within a 600 kDa DegP Protease Cage Complex Using Hydrodynamics Measurements and Methyl-TROSY NMR.

The DegP protease-chaperone operates within the periplasm of Gram-negative bacteria, where it assists in the regulation of protein homeostasis, promotes virulence, and is essential to survival under stress. To carry out these tasks, DegP forms a network of preorganized apo oligomers that facilitate the capture of substrates within distributions of cage-like complexes which expand to encapsulate clients of various sizes. Although the architectures of DegP cage complexes are well understood, little is known about the structures, dynamics, and interactions of client proteins within DegP cages and the relationship between client structural dynamics and function. Here, we probe host-guest interactions within a 600 kDa DegP cage complex throughout the DegP activation cycle using a model α-helical client protein through a combination of hydrodynamics measurements, methyl-transverse relaxation optimized spectroscopy-based solution nuclear magnetic resonance studies, and proteolytic activity assays. We find that in the presence of the client, DegP cages assemble cooperatively with few intermediates. Our data further show that the N-terminal half of the bound client, which projects into the interior of the cages, is predominantly unfolded and flexible, and exchanges between multiple conformational states over a wide range of time scales. Finally, we show that a concerted structural transition of the protease domains of DegP occurs upon client engagement, leading to activation. Together, our findings support a model of DegP as a highly cooperative and dynamic molecular machine that stabilizes unfolded states of clients, primarily via interactions with their C-termini, giving rise to efficient cleavage.

Femtosecond Electron Diffraction Reveals Local Disorder and Local Anharmonicity in Thermoelectric SnSe.

In addition to long-range periodicity, local disorder, with local structures deviating from the average lattice structure, dominates the physical properties of phonons, electrons, and spin subsystems in crystalline functional materials. Experimentally characterizing the 3D atomic configuration of such a local disorder and correlating it with advanced functions remains challenging. Using a combination of femtosecond electron diffraction, structure factor calculations, and time-dependent density functional theory molecular dynamics simulations, the static local disorder and its local anharmonicity in thermoelectric SnSe are identified exclusively. The ultrafast structural dynamics reveal that the crystalline SnSe is composed of multiple locally correlated configurations dominated by the static off-symmetry displacements of Sn (≈0.4 Å) and such a set of locally correlated structures is termed local disorder. Moreover, the anharmonicity of this local disorder induces an ultrafast atomic displacement within 100 fs, indicating the signature of probable THz Einstein oscillators. The identified local disorder and local anharmonicity suggest a glass-like thermal transport channel, which updates the fundamental insight into the long-debated ultralow thermal conductivity of SnSe. The method of revealing the 3D local disorder and the locally correlated interactions by ultrafast structural dynamics will inspire broad interest in the construction of structure-property relationships in material science.

A fast actuated soft gripper based on shape memory alloy wires

The application of shape memory alloy (SMA) actuated soft grippers is limited by their slow recovery speed. In order to further expand their application range, as one of the solutions to address this limitation, this paper proposes a fast actuated soft gripper based on SMA wire active heat dissipation and elastic rib combination to meet the rapid actuation and recovery. The structure primarily consists of a heat dissipation module capable of winding SMA wire and a soft structure resembling a scorpion tail with embedded supper elastic SMA wire. The geometric structure model, dynamics and SMA constitutive model and finite element model of the soft gripper are established, and the lateral deformation of soft bionic scorpion tail end is analyzed through simulations and experiments. In addition, the force in designed soft gripper tip and its ability to grasp different objects are also studied through experiments. The results show that the addition of a cooling fan increased the recovery rate by about 25%, and the force in soft bionic scorpion tail end can reach about 0.12 N. The designed soft gripper can successfully grasp objects with different softness, shape, size and weight. It lays a theoretical foundation and technical support for the development of soft grippers actuated by SMA in the future.

SOFR term structure dynamics—Discontinuous short rates and stochastic volatility forward rates

AbstractThe Secured Overnight Funding Rate (SOFR) has become the risk‐free rate benchmark in US dollars, thus term structure models should reflect key features exhibited by SOFR and forward rates implied by SOFR futures. We construct a multifactor, stochastic volatility term structure model which incorporates these features. Calibrating to options on SOFR futures, we achieve a reasonable fit to the market across maturities and strikes in a single model. This also provides novel insights into SOFR term rate behavior (and implied volatilities) within their accrual periods, and a model mechanism by which interest rate mean reversion arises from monetary policy.

Na4Fe1.5Mn1.5(PO4)2(P2O7): A low-cost and earth-abundant cathode for robust sodium storage

The mixed compounds of phosphates and pyrophosphates are attractive cathodes for sodium-ion batteries (SIBs) owing to their robust open framework structure and superior diffusion dynamics. However, most reported mixed phosphate cathodes generally suffer from low operating potential. Herein, we develop a bimetallic Na4Fe1.5Mn1.5(PO4)2(P2O7)/C-rGO (NFMPP/C-rGO) cathode, which possesses two working plateaus at 2.92 and 3.95 V. The obtained NFMPP/C-rGO demonstrates a stable high capacity of over 120 mAh g−1 at 0.1 C. In-situ XRD characterization discloses a solid solution reaction for the Fe2+/3+ redox couple and a two-phase reaction for the Mn2+/3+ redox couple. First-principles calculations reveal the migration of Na+ in NFMPP has low barriers. This work provides a new, low-cost, earth-abundant, and stable cathode choice for practical SIBs.

Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration

Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.

Study on influence coefficients of hydrodynamic force on dynamic response of deep-water pier under earthquake

The hydrodynamic force generated by the interaction between deep-water pier and water under earthquake exerts a significant influence on the dynamic response of the pier. At present, there is a lack of characterization methods to measure the influence degree of pier-water interaction on the dynamic response of the deep-water pier. Based on the structural dynamics theory and considering the coupling effect of pier-water interaction, the dynamic equilibrium equations for the deep-water pier under earthquake are established, and the solutions are deduced and validated by the finite element simulation results. Then the comprehensive analysis of influence mechanism is conducted. Further, the displacement influence coefficients and internal force influence coefficients are proposed to evaluate the influence degree of hydrodynamic force on dynamic response of deep-water piers. Validation shows that the proposed coefficients have high accuracy, indicating the important application of the proposed coefficients in seismic design of deep-water piers in real practice.

Effects of Xylanase A double mutation on substrate specificity and structural dynamics

While protein activity is traditionally studied with a major focus on the active site, the activity of enzymes has been hypothesized to be linked to the flexibility of adjacent regions, warranting more exploration into how the dynamics in these regions affects catalytic turnover. One such enzyme is Xylanase A (XylA), which cleaves hemicellulose xylan polymers by hydrolysis at internal β-1,4-xylosidic linkages. It contains a “thumb” region whose flexibility has been suggested to affect the activity. The double mutation D11F/R122D was previously found to affect activity and potentially bias the thumb region to a more open conformation. We find that the D11F/R122D double mutation shows substrate-dependent effects, increasing activity on the non-native substrate ONPX2 but decreasing activity on its native xylan substrate. To characterize how the double mutant causes these kinetics changes, nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations were used to probe structural and flexibility changes. NMR chemical shift perturbations revealed structural changes in the double mutant relative to the wild-type, specifically in the thumb and fingers regions. Increased slow-timescale dynamics in the fingers region was observed as intermediate-exchange line broadening. Lipari-Szabo order parameters show negligible changes in flexibility in the thumb region in the presence of the double mutation. To help understand if there is increased energetic accessibility to the open state upon mutation, alchemical free energy simulations were employed that indicated thumb opening is more favorable in the double mutant. These studies aid in further characterizing how flexibility in adjacent regions affects the function of XylA.

Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements

RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1’s unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.

Resonant multiphoton processes and excitation limits to structural dynamics.

Understanding the chemical reactions that give rise to functional biological systems is at the core of structural biology. As techniques are developed to study the chemical reactions that drive biological processes, it must be ensured that the reaction occurring is indeed a biologically relevant pathway. There is mounting evidence indicating that there has been a propagation of systematic error in the study of photoactive biological processes; the optical methods used to probe the structural dynamics of light activated protein functions have failed to ensure that the photoexcitation prepares a well-defined initial state relevant to the biological process of interest. Photoexcitation in nature occurs in the linear (one-photon per chromophore) regime; however, the extreme excitation conditions used experimentally give rise to biologically irrelevant multiphoton absorption. To evaluate and ensure the biological relevance of past and future experiments, a theoretical framework has been developed to determine the excitation conditions, which lead to resonant multiphoton absorption (RMPA) and thus define the excitation limit in general for the study of structural dynamics within the 1-photon excitation regime. Here, we apply the theoretical model to bacteriorhodopsin (bR) and show that RMPA occurs when excitation conditions exceed the linear saturation threshold, well below typical excitation conditions used in this class of experiments. This work provides the guidelines to ensure excitation in the linear 1-photon regime is relevant to biological and chemical processes.

Real-time tracking of three-dimensional atomic dynamics of Pt trimer on TiO2 (110).

Single and multi-atoms supported on oxide substrates ultimately increase the efficiency of noble metal atom use, and moreover, catalytic activity and selectivity are also improved substantially. However, single and multi-atoms are unstable under catalytic conditions, and these metal atoms spontaneously aggregate and grow into nanoparticles. Catalytic performance is strongly related to local atomic configurations, and hence, it is essential to determine the three-dimensional (3D) atomic structures of multi-atoms on the substrate and their structural dynamics. Here, we show the real-time tracking of the 3D structural evolution of a Pt trimer on TiO2 (110) substrate at a high temperature, using high-spatiotemporal-resolution scanning transmission electron microscopy, where sub-angstrom spatial resolution is maintained, while the temporal resolution reaches 40 milliseconds. With the aid of prior structural knowledge of a Pt trimer for 3D reconstruction, the present method could open the way to characterize in situ atomic-scale structural dynamics, especially meta-stable structural transition.