How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations
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Biochemistry & Molecular Biology↗
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Results for “dynamic temperature”
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Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study
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59 BASIC BIOLOGICAL SCIENCES↗
Effects of unburnt reaction progress on stretch flame dynamics under elevated temperatures
Flames in practical combustors and engines are inevitably subject to the effects of upstream chemical reaction progress and stretch, induced by elevated thermodynamic conditions and flow non-uniformities, respectively. Recent shock tube experiments and simulation studies on flame propagation have shown that flame speed under engine-relevant conditions can be enhanced with non-negligible upstream chemical reaction progress, especially when low-temperature heat release is involved in the unburnt mixture. On the other hand, depending on the mixture equivalence ratio and diluents, nonequidiffusion (including the non-unity Lewis number effect and the preferential diffusion effect) can couple with the flame stretch to fundamentally affect the flame propagation, which can manifest as either facilitation or suppression. Depending on the transport property of a reacting mixture, there hence can be either inhibition or promotion from unburnt reaction progress and stretch effects on flame propagation. In the current work, through one-dimensional numerical simulations of transient planar and spherical flames of n-heptane/air under elevated thermodynamic conditions, the combined effects of upstream chemical reaction progress and stretch on flame propagation are investigated. Results show that for both lean and rich n-heptane/air mixtures, flame speed can be substantially promoted with reaction progress, while the rich mixtures can exhibit opposite stretch dependence after first-stage ignition. Different definitions of effective Lewis number are adopted to explain the change in Markstein length for spherical flame in lean and rich mixtures reformed by the low temperature chemistry. Further, this work fills an important gap in laminar premixed flame research relevant to practical combustion systems and can provide useful insight into local turbulent flame behaviors and phi-sensitivity in engine combustion.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multiscale Modeling and Experimental Insights into High-Temperature Soil Biodegradation Dynamics of Semi-Crystalline Poly(Lactic Acid) Nonwoven Fabrics
This study investigates the biodegradation of semi-crystalline poly(lactic acid) (PLA) nonwovens (NWs) in soil at 58 °C using both experimental and mathematical modeling approaches. The model utilizes a system of parabolic diffusion-reaction partial differential equations (PDEs) to elucidate chemical transformations over time and in space. It accounts for phenomena such as the diffusion of water and lactic acid monomers through the polymer matrix and into the surrounding soil, along with their microbial breakdown. It also accounts for the initial PLA crystallinity and predicts its evolution in time. The model is solved numerically for a single filament, and the results were used to shed light on PLA NW transformations observed in soil over a 180-day incubation period. Various characterization techniques, including scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and Raman spectroscopy, were employed to assess morphological changes, crystallinity, and molecular changes in the NWs throughout the experiment. By comparing the experimental data with the model predictions, the hydrolysis rate coefficient was found to be 3.37 × 10 -7 s -1 , while the rate of microbial degradation of lactic acid monomers was faster, of the order of 9.63 × 10 -7 s -1 . The findings highlight the significant role of crystallinity in the biodegradation process. The PLA degradation ceases when no amorphous material remains, and the crystallinity reaches 0.8, as observed in the experiments by day 120. Furthermore, this research contributes to a deeper understanding of PLA biodegradation dynamics and offers insights for effectively managing biodegradable materials in environmental settings.
Diffusion−reaction modeling↗
Temperature-dependent lattice dynamics in polycrystalline ZrN
Zirconium nitride holds promise for improving nuclear reactor components, where thermal conductivity is important, highlighting the need for a detailed understanding of its phonons. However, the phonon dispersion derived from previous inelastic neutron scattering data is in disagreement with modern theoretical calculations, pointing to the necessity for further experimental validation. Here, in this study, we use inelastic neutron scattering experiments on polycrystalline ZrN at 6, 100, 300, 400, and 600 K, and density functional theory (DFT) calculations to study the momentum-resolved scattering and the phonon density of states. Both experimental and theoretical results reveal a phonon cutoff energy near 65 meV, in stark disagreement with previous single-crystal neutron scattering measurements indicating a cutoff near 75 meV. The 65 meV cutoff energy is, however, in reasonable agreement with previous measurements on ZrN 0.9 . Consistency between our theoretical and experimental results confirms that ZrN is a wide phonon band gap system and that DFT provides a reliable description of its phonons.
DFT↗
Quantum Computation of Finite-Temperature Static and Dynamical Properties of Spin Systems Using Quantum Imaginary Time Evolution
Not Available
Sun, Shi-Ning (ORCID:000000025984780X)↗
Tidal–hydrological dynamics of water temperature across freshwater forested wetlands on the northeastern Pacific coast
Abstract Tidal freshwater forests were once extensive across temperate coastlines, but loss and fragmentation have made estimation of their ecosystem functions challenging. We measured water temperature for 2 years in three Sitka spruce tidal forests, a restoration site, and an adjacent emergent marsh on the Columbia River, Washington, United States. We assessed spatial variability of water temperature within sites including the effects of hydrology, differences among bay and tributary tidal forests, and differences between the tidal forests and the mainstem Columbia, the restoration site, and the emergent marsh. The tidal forests nearest to the bay had lower interior water temperatures than their channel confluences by up to 2.5°C (weekly median temperature) and 2.0°C (weekly maximum temperature), with most cooling occurring during the low‐flow months of July–September. Tributary sites had maximum temperatures up to 1.9°C cooler than bay sites and 4.2°C cooler than the mainstem. Temperatures in the two bay sites decreased by −0.16°C/100 m and −0.07°C/100 m, on average. The restoration site had the smallest within‐site temperature gradient. Differences in maximum temperatures were greatest when tidal range was low, while higher tidal ranges were associated with warmer and more variable site interiors relative to their confluences. These results suggest that water temperatures in these tidal forests can provide temperature refugia for cold water biota including salmon.
54 ENVIRONMENTAL SCIENCES↗
Negligible magnetic losses at low temperatures in liquid phase epitaxy grown Y 3 Fe 5 O 12 films
Yttrium iron garnet (Y 3 Fe 5 O 12 ; YIG) has a unique combination of low magnetic damping, high spin-wave conductivity, and insulating properties that make it a highly attractive material for a variety of applications in the fields of magnetics and spintronics. While the room-temperature magnetization dynamics of YIG have been extensively studied, there are limited reports correlating the low-temperature magnetization dynamics to the material structure or growth method. Here, in this study, we investigate liquid phase epitaxy grown YIG films and their magnetization dynamics at temperatures down to 10 K. We show there is a negligible increase in the ferromagnetic resonance linewidth down to 10 K, which is unique when compared with YIG films grown by other deposition methods. From the broadband ferromagnetic resonance measurements, polarized neutron reflectivity, and scanning transmission electron microscopy, we conclude that these liquid phase epitaxy grown films have negligible rare-earth impurities present, specifically the suppression of Gd diffusion from the Gd 3 Ga 5 O 12 (GGG) substrate into the Y 3 Fe 5 O 12 film, and therefore negligible magnetic losses attributed to the slow-relaxation mechanism. Overall, liquid phase epitaxy YIG films have a YIG/GGG interface that is five times sharper and have ten times lower ferromagnetic resonance linewidths below 50 K than comparable YIG films by other deposition methods. Thus, liquid phase epitaxy grown YIG films are ideal for low-temperature experiments/applications that require low magnetic losses, such as quantum transduction and manipulation via magnon coupling.
36 MATERIALS SCIENCE↗
Rapid eco‐phenotypic feedback and the temperature response of biomass dynamics
Biomass dynamics capture information on population dynamics and ecosystem-level processes (e.g., changes in production over time). Understanding how rising temperatures associated with global climate change influence biomass dynamics is thus a pressing issue in ecology. The total biomass of a species depends on its density and its average mass. Consequently, disentangling how biomass dynamics responds to increasingly warm and variable temperatures ultimately depends on understanding how temperature influences both density and mass dynamics. Here, we address this issue by keeping track of experimental microbial populations growing to carrying capacity for 15 days at two different temperatures, and in the presence and absence of temperature variability. We develop a simple mathematical expression to partition the contribution of changes in density and mass to changes in biomass and assess how temperature responses in either one influence biomass shifts. Moreover, we use time-series analysis (Convergent Cross Mapping) to address how temperature and temperature variability influence reciprocal effects of density on mass and vice versa. We show that temperature influences biomass through its effects on density and mass dynamics, which have opposite effects on biomass and can offset each other. We also show that temperature variability influences biomass, but that effect is independent of any effects on density or mass dynamics. Last, we show that reciprocal effects of density and mass shift significantly across temperature regimes, suggesting that rapid and environment-dependent eco-phenotypic dynamics underlie biomass responses. Overall, our results connect temperature effects on population and phenotypic dynamics to explain how biomass responds to temperature regimes, thus shedding light on processes at play in cosmopolitan and abundant microbes as the world experiences increasingly warm and variable temperatures.
54 ENVIRONMENTAL SCIENCES↗
Wireless Interrogation of High Temperature Surface Acoustic Wave Dynamic Strain Sensor
Dynamic strain sensing is necessary for high-temperature harsh-environment applications, including powerplants, oil wells, aerospace, and metal manufacturing. Monitoring dynamic strain is important for structural health monitoring and condition-based maintenance in order to guarantee safety, increase process efficiency, and reduce operation and maintenance costs. Sensing in high-temperature (HT), harsh-environments (HE) comes with challenges including mounting and packaging, sensor stability, and data acquisition and processing. Wireless sensor operation at HT is desirable because it reduces the complexity of the sensor connection, increases reliability, and reduces costs. Surface acoustic wave resonators (SAWRs) are compact, can operate wirelessly and battery-free, and have been shown to operate above 1000°C, making them a potential option for HT HE dynamic strain sensing. This paper presents wirelessly interrogated SAWR dynamic strain sensors operating around 288.8MHz at room temperature and tested up to 400°C. The SAWRs were calibrated with a high-temperature wired commercial strain gauge. The sensors were mounted onto a tapered-type Inconel constant stress beam and the assembly was tested inside a box furnace. The SAWR sensitivity to dynamic strain excitation at 25°C, 100°C, and 400°C was .439 μV/με, 0.363μV/με, and .136 μV/με, respectively. Furthermore, the experimental outcomes verified that inductive coupled wirelessly interrogated SAWRs can be successfully used for dynamic strain sensing up to 400°C.
47 OTHER INSTRUMENTATION↗
Magnetism and spin dynamics in room-temperature van der Waals magnet Fe 5 GeTe 2
Two-dimensional van der Waals (vdWs) materials have gathered a lot of attention recently. However, the majority of these materials have Curie temperatures that are well below room temperature, making it challenging to incorporate them into device applications. In this work, we synthesized a room-temperature vdW magnetic crystal Fe 5 GeTe 2 with a Curie temperature T c = 332 K, and studied its magnetic properties by vibrating sample magnetometry (VSM) and broadband ferromagnetic resonance (FMR) spectroscopy. The experiments were performed with external magnetic fields applied along the c -axis (H∥ c ) and the ab -plane (H∥ ab ), with temperatures ranging from 300 to 10 K. We have found a sizable Landé g -factor difference between the H∥ c and H∥ ab cases. In both cases, the Landé g -factor values deviated from g = 2. This indicates contribution of orbital angular momentum to the magnetic moment. The FMR measurements reveal that Fe 5 GeTe 2 has a damping constant comparable to Permalloy. With reducing temperature, the linewidth was broadened. Together with the VSM data, our measurements indicate that Fe 5 GeTe 2 transitions from ferromagnetic to ferrimagnetic at lower temperatures. Our experiments highlight key information regarding the magnetic state and spin scattering processes in Fe 5 GeTe 2 , which promote the understanding of magnetism in Fe 5 GeTe 2 , leading to implementations of Fe 5 GeTe 2 based room-temperature spintronic devices.
36 MATERIALS SCIENCE↗
Analysis of Dynamical Peculiarities in Nanoalloys at Subsystems Level: Dynamical Degrees of Freedom, Temperature Differences, and the Chameleon Effect
Abstract A novel analysis of the dynamical behavior of nanoalloy systems, as represented by model Ni/Al 13‐atom clusters, over a broad range of energies that cover the stage‐wise transition of the systems from their solid‐like to liquid‐like state is presented. Conceptually, the analysis is rooted in partitioning the systems into judiciously chosen subsystems and characterizing the latter in terms of subsystem‐specific dynamical descriptors that include dynamical degrees of freedom , root‐mean‐square bond‐length fluctuation , and element‐specific subsystem temperature . The analysis reveals a host of intriguing new peculiarities in the dynamical behavior of the Ni/Al 13‐mers, among which are what we call the chameleon effect and the difference in the temperatures of the Ni and Al subsystems at high energies, a difference that strongly depends on the cluster composition and also changes with energy. These do not have an analog in pure Ni 13 and Al 13 and are explained in terms of the coupled effects of the difference between the masses of the Ni and Al atoms (the mass effect) and of the difference in the anharmonicity of the overall interaction potential as experienced by the Ni and Al subsystems of the clusters (the potential effect).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package
Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. Here, in this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
All-Atom Molecular Dynamics Simulations of the Temperature Response of Densely Grafted Polyelectrolyte Brushes
Water acts a “good” solvent for most polyelectrolyte (PE) systems due to its high dielectric strength. Theoretical and experimental studies have highlighted some remarkably unconventional properties of strongly water-swollen PE brushes such as a reduction in brush height with increase in temperature. However, an understanding of the atomistic-scale response of the grafted PE chains as well as the local arrangement and organization of the brush-supported counterions and water molecules to changes in temperature is missing. Here, we conduct an all-atom molecular dynamics (MD) study to probe the influence of temperature on the “microstructure” of densely grafted, fully ionized polyacrylic acid (PAA) brushes. The atomistic insights obtained from our study shed light on prior experimental observations and elucidate the key role played by changes in hydrogen bonding network in dictating the hydrophilicity of the brushes. In addition to the temperature-mediated reduction in height of the PE brush layer, we study the influence of temperature on several properties of the brush-supported water molecules such as the number distribution and kinetics of water-water and water-PE hydrogen bonds (HBs), mass density, orientational tetrahedral order parameter, and the activation energy associated with the self-diffusion of water. The effect of temperature on the properties of the brush-trapped counterions is also quantified via changes in their solvation structure, counterion-water radial distribution function (RDF), and the translational mobility. Our findings unravel several hitherto unknown phenomena such as the enhanced propensity for attaining PE brush-induced “water-in-salt”-like scenarios at elevated temperatures, and an increase in the activation energy for the self-diffusion of water with increase in the degree of PE brush-induced nanoconfinement (from ‘bulk water’ to ‘sparsely grafted PE brushes’ to ‘densely grafted PE brushes’). Further, we anticipate that this work will be helpful in improving our predictive capabilities of the temperature response of water-swollen PE brushes, which would be instrumental for better design of several PE brush systems used in a multitude of applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Universal spin dynamics in infinite-temperature one-dimensional quantum magnets
Here, we address the nature of spin dynamics in various integrable and non-integrable, isotropic and anisotropic quantum spin-$S$ chains, beyond the paradigmatic $S=1/2$ Heisenberg model. In particular, we investigate the algebraic long-time decay $\propto t^{-1/z}$ of the spin-spin correlation function at infinite temperature, using state-of-the-art simulations based on tensor network methods. We identify three universal regimes for the spin transport, independent of the exact microscopic model: (i) superdiffusive with $z=3/2$, as in the Kardar-Parisi-Zhang universality class, when the model is integrable with extra symmetries such as spin isotropy that drive the Drude weight to zero, (ii) ballistic with $z=1$ when the model is integrable with a finite Drude weight, and (iii) diffusive with $z=2$ with easy-axis anisotropy or without integrability, at variance with previous observations.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Sliding friction and wear behavior of nuclear graphite in high temperature inert environment: Influence of contact load, speed and temperature
Repeated dynamic interactions of graphitic components in pebble-bed gas-cooled nuclear reactors can cause abrasive wear-induced pebble surface damage, generate hazardous fine graphite debris, and alter fuel circulation dynamics due to changes in friction behavior. Comprehensive tribological characterization of nuclear graphitic materials in conditions relevant to reactor operation is needed to assess reactor long-term safety and performance. This work reports sliding friction and wear behavior of self-mated nuclear graphite ET-10 at various elevated temperatures (650 °C and 750 °C), sliding speeds (1 and 10 mm/s) and contact loads (20 and 40 N) in a controlled argon environment. The results revealed nonmonotonic frictional behavior with a higher running-in coefficient of friction (COF) followed by a lower steady-state COF, as a result of transition from two-body abrasion to three-body abrasion along with formation of a tribofilm. A key finding of this work is the sensitivity of the running-in COF to experimental conditions; maximum running-in values were lower at either elevated temperature (0.52–0.54) or reduced sliding speed (0.51–0.54). Conversely, the steady-state COF remained invariant at approximately 0.3 across all tested parameters. Transmission electron microscopy revealed a 0.5–2.0 μm thick nanocrystalline tribofilm that was thought to be formed by the compaction of the graphitic wear debris on the contact surface during the sliding process. The nanocrystalline nature of the tribofilm was further confirmed by Raman spectroscopy. As a result, the combination of tribological testing and morphological characterization provided a mechanistic understanding of the frictional behavior of nuclear graphite upon sliding.
Friction↗