Global Simulations of Phase State and Equilibration Time Scales of Secondary Organic Aerosols with GEOS-Chem
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54 ENVIRONMENTAL SCIENCES↗
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Pressure equilibrated thermal insulation gap
A thermal structure for management of thermal energy, the thermal structure including: a first wall structure defining a first cavity; a second wall structure defining a second cavity, the second cavity in fluid communication with the first cavity; and a barrier cavity defined at least in-part by the first wall structure and the second wall structure, wherein the barrier cavity is disposed between the first cavity and the second cavity and includes a pressurized barrier fluid therein or is configured to receive the pressurized barrier fluid during operation of the thermal structure.
Erno, Daniel Jason↗
Imposing equilibrium on experimental 3-D stress fields using Hodge decomposition and FFT-based optimization
Here, we present a methodology to impose micromechanical constraints, i.e. stress equilibrium at grain and sub-grain scale, to an arbitrary (non-equilibrated) voxelized stress field obtained, for example, by means of synchrotron X-ray diffraction techniques. The method consists in finding the equilibrated stress field closest (in L 2 -norm sense) to the measured non-equilibrated stress field, via the solution of an optimization problem. The extraction of the divergence-free (equilibrated) part of a general (non-equilibrated) field is performed using the Hodge decomposition of a symmetric matrix field, which is the generalization of the Helmholtz decomposition of a vector field into the sum of an irrotational field and a solenoidal field. The combination of: a) the Euler–Lagrange equations that solve the optimization problem, and b) the Hodge decomposition, gives a differential expression that contains the bi-harmonic operator and two times the curl operator acting on the experimental stress field. These high-order derivatives can be efficiently performed in Fourier space. The method is applied to filter the non-equilibrated parts of a synthetic piecewise constant stress fields with a known ground truth, and stress fields in Gum Metal, a beta-Ti-based alloy measured in-situ using Diffraction Contrast Tomography (DCT). In both cases, the largest corrections were obtained near grain boundaries.
36 MATERIALS SCIENCE↗
Predicting Liquid–Liquid Phase Separation of Submicrometer Proxies for Atmospheric Secondary Aerosol
Liquid–liquid phase separation (LLPS) of atmospheric aerosols can significantly impact climate, air quality, and human health. However, their complex composition, small size, and history-dependent properties result in great uncertainty in the modeling of aerosol phase state and atmospheric processes. Herein, using cryogenic transmission electron microscopy (cryo-TEM), we examined model submicron aerosols composed of organic compounds and ammonium sulfate, and established a parameterization for the separation relative humidity (SRH) that accounts for chemical composition, particle size, and equilibration time. We evaluated different variables that describe chemical composition: O/C ratio, partition coefficient, solubility, molar mass, and polarizability. The O/C ratio fits the SRH of micrometer droplets best, and by using a scaling factor to translate the micrometer SRH parameterization to submicron aerosols, we incorporate the effects of size and equilibration time. The measured scaling factor for the submicron mean SRH (30nm – 1μm, 20 min equilibration times) is 0.80, the factor becomes 1 with equilibration time over 1 hour, and is equal to 0, meaning that SRH is absent, when the aerosol dry diameter is smaller than 30 nm. Furthermore, our parameterization will aid in universal SRH modeling, potentially leading to more accurate predictions of aerosol mass, optical properties, hygroscopicity, and heterogeneous chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Hyperstealth dark matter and long-lived particles
A new dark matter candidate is proposed that arises as the lightest baryon from a confining 𝑆𝑈(𝑁) gauge theory which equilibrates with the Standard Model only through electroweak interactions. Surprisingly, this candidate can be as light as a few GeV. The lower bound arises from the intersection of two competing requirements: (i) the equilibration sector of the model must be sufficiently heavy, at least several TeV, to avoid bounds from colliders, and (ii) the lightest dark meson (that may be the dark 𝜂′, 𝜎, or the lightest glueball) has suppressed interactions with the SM and must decay before big bang nucleosynthesis. The low-energy dark sector consists of one flavor that is electrically neutral and an almost electroweak singlet. The dark matter candidate is the lightest baryon consisting of 𝑁 of these light flavors leading to a highly suppressed elastic scattering rate with the Standard Model (SM). The equilibration sector consists of vectorlike dark quarks that transform under the electroweak group, ensuring that the dark sector can reach thermal equilibrium with the SM in the early Universe. The lightest dark meson lifetimes vary between 10 −3 ≲ 𝑐𝜏 ≲ 10 7 m, providing an outstanding target for LHC production and experimental detection. We delineate the interplay between the lifetime of the light mesons, the suppressed direct detection cross section of the lightest baryon, and the scale of equilibration sector that can be probed at the LHC.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Climate Sensitivity and the Direct Effect of Carbon Dioxide in a Limited-Area Cloud-Resolving Model
Even in a small domain, it can be prohibitively expensive to run cloud-resolving greenhouse gas warming experiments due to the long equilibration time. Here, a technique is introduced that reduces the computational cost of these experiments by an order of magnitude: instead of fixing the carbon dioxide concentration and equilibrating the sea surface temperature (SST), this technique fixes the SST and equilibrates the carbon dioxide concentration. Using this approach in a cloud-resolving model of radiative–convective equilibrium (RCE), the equilibrated SST is obtained as a continuous function of carbon dioxide concentrations spanning 1 ppmv to nearly 10 000 ppmv, revealing a dramatic increase in equilibrium climate sensitivity (ECS) at higher temperatures. This increase in ECS is due to both an increase in forcing and a decrease in the feedback parameter. In addition, the technique is used to obtain the direct effects of carbon dioxide (i.e., the rapid adjustments) over a wide range of SSTs. Overall, the direct effect of carbon dioxide offsets a quarter of the increase in precipitation from warming, reduces the shallow cloud fraction by a small amount, and has no impact on convective available potential energy (CAPE).
Romps, David M.↗
Lepton flavor asymmetries: from the early Universe to BBN
Large primordial lepton flavor asymmetries with almost vanishing total baryon-minus-lepton number can evade the usual BBN and CMB constraints if neutrino oscillations lead to perfect flavor equilibration. Solving the momentum averaged quantum kinetic equations (QKEs) describing neutrino oscillations and interactions, we perform the first systematic investigation of this scenario, uncovering a rich flavor structure in stark contradiction to the assumption of simple flavor equilibration. We find (i) a particular direction in flavor space, ∆ne ≃ – 2/3 (– 1)∆n μ for normal (inverted) neutrino mass hierarchy, in which the flavor equilibration is efficient and primordial asymmetries are essentially unconstrained, (ii) a minimal washout factor, ∆$n_{e}^{2}$| BBN ≤ 0.03 (0.016) ∑ α ∆$n_{α}^{2}$| ini yielding a conservative estimate for the allowed primordial asymmetries in a generic flavor direction, and (iii) particularly strong or weak washout if one of the initial flavor asymmetries vanishes due to non-adiabatic muon- or electron-driven MSW transitions. These results open up the possibility of a first-order QCD phase transition facilitated by large lepton asymmetries as well as baryogenesis from large and compensated ∆n e = ∆n μ asymmetries. Our systematic approach of deriving momentum averaged QKEs includes collision terms beyond the damping approximation, energy transfer between the neutrino and electron-photon plasma, and provides a fast and reliable way to investigate the impact of primordial lepton asymmetries at the time of BBN. We publicly release the Mathematica code COFLASY-M on https://github.com/mariofnavarro/COFLASY which solves the QKEs numerically.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Fluctuation–dissipation relation for a quantum Brownian oscillator in a parametrically squeezed thermal field
In this paper we study the nonequilibrium evolution of a quantum Brownian oscillator, modeling the internal degree of freedom of a harmonic atom or an Unruh–DeWitt detector, coupled to a nonequilibrium and nonstationary quantum field bath and inquire whether a fluctuation–dissipation relation (FDR) can exist after/if it approaches equilibration. This is a nontrivial issue because a squeezed field bath cannot reach equilibration and yet, as this work shows, the system oscillator indeed can, which is a necessary condition for FDRs. We discuss three different settings: (A) The bath field essentially remains in a squeezed thermal state throughout, whose squeeze parameter is a mode- and time-independent constant. This situation is often encountered in quantum optics and quantum thermodynamics. (B) The bath field is initially in a thermal state, but is subjected to a parametric process leading to mode- and time-dependent squeezing. This scenario is encountered in cosmology and dynamical Casimir effects. The squeezing in the bath in both types of processes will affect the oscillator’s nonequilibrium evolution. We show that at late times it approaches equilibration and this stationarity condition warrants the existence of a FDR. The trait of squeezing is marked by the oscillator’s effective equilibrium temperature, and the proportionality factor in the FDR is only related to the stationary component of the noise kernel of the bath field. Setting (C) is more subtle: A finite system–bath coupling strength can set the oscillator in a squeezed state even though the bath field is stationary and does not engage in any parametric process. The squeezing of the system in this case is in general time-dependent but becomes constant when the internal dynamics is fully relaxed. We begin with comments on the broad range of physical processes involving squeezed thermal baths and end with some remarks on the significance of FDRs in capturing the essence of quantum backreaction in nonequilibrium and stochastic systems.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Re-investigation of high-temperature phase equilibria in Fe-rich Sm–Fe–Ti alloys
Recently renewed attempts to develop high-performance rare-earth-lean permanent magnets based on the Sm(Fe,Ti) 12 compound have drawn attention to the limited knowledge about the high-temperature phase equilibria in the Sm–Fe–Ti system. Experimental investigation of equilibrated alloys with electron probe microanalysis, X-ray diffraction and thermomagnetic analysis revealed several inaccuracies in the currently accepted phase relations at 1000°C and allowed for a revision of the Fe-rich corner of the Sm–Fe–Ti phase diagram. The Sm(Fe,Ti) 12 and Sm 3 (Fe,Ti) 29 phases were found to have more extended Ti ranges of 5.1–9.7 at% and 2.8–6.9 at%, respectively. With increasing of the Ti content, the Curie temperature of the Sm(Fe,Ti) 12 remains nearly constant at 306–312°C, whereas that of the Sm 3 (Fe,Ti) 29 increases from 188°C to 207°C. The low-titanium Sm 3 (Fe,Ti) 29 phase equilibrates not only with the Sm(Fe,Ti) 12 and Sm2(Fe,Ti) 17 phases, but also with (α-Fe) solid solution. Newly demonstrated equilibrium between Sm 2 (Fe,Ti) 17 and TiFe 2 phases makes impossible the earlier reported equilibrium between the Sm 3 (Fe,Ti) 29 and Sm(Fe,Ti) 11 phases. Because of an invariant reaction at 1000 °C, the revised phase diagram also features a class II four-phase equilibrium Sm 3 (Fe,Ti) 29 + TiFe 2 + Sm(Fe,Ti) 12 + Sm 2 (Fe,Ti) 17 . Peritectic decomposition of the Sm(Fe,Ti) 11 phase, which occurs either at 1075°C or at 1087°C, was found to have among its products the Sm(Fe,Ti) 12 phase. Although no such equilibration was attempted, it must be possible to obtain above 1087°C a two-phase state composed of the Sm(Fe,Ti) 12 phase and a liquid – which is important for manufacturing of the Sm(Fe,Ti) 12 - based permanent magnets via the liquid-phase sintering.
36 MATERIALS SCIENCE↗
Edge Channel Transmission through a Quantum Point Contact in the Two-Dimensional Topological Insulator Cadmium Arsenide
Cadmium arsenide (Cd 3 As 2 ) thin films feature a two-dimensional topological insulator (2D TI) phase for certain thicknesses, which theoretically hosts a set of counterpropagating helical edge states that are characteristic of a quantum spin Hall (QSH) insulator. In devices containing electrostatically defined junctions and for magnetic fields below a critical value, chiral edge modes of the quantum Hall effect can coexist with QSH-like edge modes. In this work, we use a quantum point contact (QPC) device to characterize edge modes in the 2D TI phase of Cd 3 As 2 and to understand how they can be controllably transmitted, which is important for use in future quantum interference devices. We investigate equilibration among both types of modes and find non-spin-selective equilibration. We also demonstrate the effect of the magnetic field on suppressing equilibration. We discuss the potential role of QSH-like modes in a transmission pathway that precludes full pinch-off.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Reversibly growing crosslinked polymers with programmable sizes and properties
Growth constitutes a powerful method to post-modulate materials’ structures and functions without compromising their mechanical performance for sustainable use, but the process is irreversible. To address this issue, we here report a growing-degrowing strategy that enables thermosetting materials to either absorb or release components for continuously changing their sizes, shapes, compositions, and a set of properties simultaneously. The strategy is based on the monomer-polymer equilibrium of networks in which supplying or removing small polymerizable components would drive the networks toward expansion or contraction. Using acid-catalyzed equilibration of siloxane as an example, we demonstrate that the size and mechanical properties of the resulting silicone materials can be significantly or finely tuned in both directions of growth and decomposition. The equilibration can be turned off to yield stable products or reactivated again. During the degrowing-growing circle, material structures are selectively varied either uniformly or heterogeneously, by the availability of fillers. Our strategy endows the materials with many appealing capabilities including environment adaptivity, self-healing, and switchability of surface morphologies, shapes, and optical properties. Since monomer-polymer equilibration exists in many polymers, we envision the expansion of the presented strategy to various systems for many applications.
36 MATERIALS SCIENCE↗
Impact of mid- Z gas fill on dynamics and performance of shock-driven implosions at the OMEGA laser
Shock-driven implosions with 100% deuterium (D 2 ) gas fill compared to implosions with 50:50 nitrogen-deuterium (N 2 D 2 ) gas fill have been performed at the OMEGA laser facility to test the impact of the added mid-Ζ fill gas on implosion performance. Ion temperature (Τ ion ) as inferred from the width of measured DD-neutron spectra is seen to be 34%±6% higher for the N 2 D 2 implosions than for the D 2 -only case, while the DD-neutron yield from the D 2 -only implosion is 7.2±0.5 times higher than from the N 2 D 2 gas fill. The T ion enhancement for N 2 D 2 is observed in spite of the higher Z, which might be expected to lead to higher radiative loss, and higher shock strength for the D 2 -only versus N 2 D 2 implosions due to lower mass, and is understood in terms of increased shock heating of N compared to D, heat transfer from N to D prior to burn, and limited amount of ion-electron-equilibration-mediated additional radiative loss due to the added higher-Z material. Further, this picture is supported by interspecies equilibration timescales for these implosions, constrained by experimental observables. The one-dimensional (1D) kinetic Vlasov-Fokker-Planck code ifp and the radiation hydrodynamic simulation codes hyades (1D) and xrage [1D, two-dimensional (2D)] are brought to bear to understand the observed yield ratio. Comparing measurements and simulations, the yield loss in the N 2 D 2 implosions relative to the pure D 2 -fill implosion is determined to result from the reduced amount of D 2 in the fill (fourfold effect on yield) combined with a lower fraction of the D 2 fuel being hot enough to burn in the N 2 D 2 case. The experimental yield and T ion ratio observations are relatively well matched by the kinetic simulations, which suggest interspecies diffusion is responsible for the lower fraction of hot D 2 in the N 2 D 2 relative to the D 2 -only case. The simulated absolute yields are higher than measured; a comparison of 1D versus 2D XRAGE simulations suggest that this can be explained by dimensional effects. The hydrodynamic simulations suggest that radiative losses primarily impact the implosion edges, with ion-electron equilibration times being too long in the implosion cores. The observations of increased T ion and limited additional yield loss (on top of the fourfold expected from the difference in D content) for the N 2 D 2 versus D 2 -only fill suggest it is feasible to develop the platform for studying CNO-cycle-relevant nuclear reactions in a plasma environment.
47 OTHER INSTRUMENTATION↗
Leaf water potential measurements using the pressure chamber: Synthetic testing of assumptions towards best practices for precision and accuracy
Leaf water potential (ψ leaf ), typically measured using the pressure chamber, is the most important metric of plant water status, providing high theoretical value and information content for multiple applications in quantifying critical physiological processes including drought responses. Pressure chamber measurements of ψ leaf (ψ leafPC ) are most typical, yet, the practical complexity of the technique and of the underlying theory has led to ambiguous understanding of the conditions to optimize measurements. Consequently, specific techniques and precautions diversified across the global research community, raising questions of reliability and repeatability. Here, we surveyed specific methods of ψ leafPC from multiple laboratories, and synthesized experiments testing common assumptions and practices in ψ leafPC for diverse species: (i) the need for equilibration of previously transpiring leaves; (ii) leaf storage before measurement; (iii) the equilibration of ψ leaf for leaves on bagged branches of a range of dehydration; (iv) the equilibration of ψ leaf across the lamina for bagged leaves, and the accuracy of measuring leaves with artificially ‘elongated petioles’; (v) the need in ψ leaf measurements for bagging leaves and high humidity within the chamber; (vi) the need to avoid liquid water on leaf surfaces; (vii) the use of ‘pulse’ pressurization versus gradual pressurization; and (viii) variation among experimenters in ψ leafPC determination. Based on our findings we provide a best practice protocol to maximise accuracy, and provide recommendations for ongoing species-specific tests of important assumptions in future studies.
54 ENVIRONMENTAL SCIENCES↗
Mathematical Framework Underlying the In Situ Electrochemical Diagnosis of Adsorbed Intermediates Formed during Redox Reactions at Electrode Surfaces
Previously, we have presented an electrochemical technique wherein an electroactive tracer species is employed to probe the rate-limiting factors governing redox reactions at an electrode surface. In this technique, the electrode is first held potentiostatically to facilitate a redox process (step 1), and then the potential is released to open circuit conditions (step 2) so as to monitor the time-dependent re-equilibration of the electrode potential in the presence of the tracer. The time-dependent potential response in step 2 has been shown to contain information about diffusion—limited or desorption—limited steps, enabling in situ probing of the electrochemistry at the electrode surface during step 1. In the present contribution, a theoretical model governing the transient response in step 2 is developed for two limiting cases: diffusion—limited and desorption—limited recovery of the electrode potential. Mathematical modeling shows that, during re-equilibration, the step 2 potential transient corresponding to a case where step 1 involves surface adsorbed species which undergo desorption in step 2 exhibits a much longer time constant than that when re-equilibration occurs under diffusion limitations. The mathematical framework presented herein provides a sound fundamental basis for applying the aforementioned technique to studying adsorption-desorption processes during electrochemistry. Also, technique limitations are presented in light of the modeling findings.
25 ENERGY STORAGE↗
Sulfur speciation in dacitic melts using X-ray absorption near-edge structure spectroscopy of the S K -edge (S-XANES): Consideration of radiation-induced changes and the implications for sulfur in natural arc systems
Abstract The synchrotron technique of micro X-ray absorption near-edge structure spectroscopy at the sulfur K-edge (S-XANES) provides a unique opportunity to measure the proportion of different oxidation states of sulfur (S) in silicate glasses. Although applied extensively in the analysis of basaltic silicate glasses, few S-XANES studies have investigated variations in S oxidation states with fO2 in felsic silicate glasses. In addition, no study has systematically compared the S-XANES results obtained from the same samples at different photon flux densities to quantify the relationship between exposure time and changes in S speciation in silicate glass, as has been done for Fe and V. This study evaluates observed differences in S speciation measured in experimentally produced H2O-saturated dacitic glasses over a range of reducing to oxidizing conditions (from log fO2 = ΔFMQ-0.7 to ΔFMQ+3.3; FMQ is the fayalite-magnetite-quartz mineral redox buffer) and equilibrated at 1000 °C and 300 MPa. S-XANES spectra were collected at three different photon flux densities using three microspectroscopy beamlines. As is observed in S-XANES analyses of basaltic silicate glasses, beam-induced changes to the S6+/ΣS are observed as a function of photon flux density and beam exposure time. Our results demonstrate that silicate glasses of dacitic composition undergo beam-induced photo-reduction in samples equilibrated at ΔFMQ > +1.75 and photo-oxidation if equilibrated at ΔFMQ < +1. The time required to observe beam-induced changes in the spectra varies as a function of flux density, and our study establishes an upper photon density limit at ~1.0 × 1012 photons/µm2. The S6+/ΣS calculated from spectra collected below this absorbed photon limit at intermediate flux densities (~1–4 × 109 photons/s per µm2) are affected by beam damage, as no conditions were found to be completely free of beam-induced changes. However, the S6+/ΣS ratios calculated below the limit at intermediate flux densities are consistent with thermodynamic constraints, demonstrating that S6+/ΣS ratios calculated from S-XANES spectra can be considered reliable for estimating the oxygen fugacity. Our results carry important implications for the S budget of felsic magmas and dissolution mechanisms in evolved melts. While our results from all three flux densities show the presence of S4+ dissolved in relatively oxidized (ΔFMQ > +1.75) dacitic glass, even in the spectra exposed to the lowest photon densities, we are unable to rule out the possibility that the S4+ signal is the result of instantaneous X-ray irradiation induced beam damage using S-XANES alone. When our spectra are compared to S-XANES spectra from basaltic silicate glasses, important differences exist in the solubility of S2– and S6+ between dacitic silicate melts, pointing to differences in solubility mechanisms as melt composition changes. This study highlights the need for further investigation into beam damage systematics, presence of S4+, and the solubility mechanisms of different oxidation states of S as silicate melt composition changes.
Geochemistry & Geophysics↗
Implementation of Ion Exchange Processes for Carbon Dioxide Mineralization Using Industrial Waste Streams
Sequestration of CO 2 within stable mineral carbonates (e.g., CaCO 3 ) represents an attractive emission reduction strategy because it offers a leakage-free alternative to geological storage of CO 2 in an environmentally benign form. However, the pH of aqueous streams equilibrated with gaseous streams containing CO 2 (pH < 4) are typically lower than that which is required for carbonate precipitation (pH > 8). Traditionally, alkalinity is provided by a stoichiometric reagent (e.g., NaOH) which renders these processes environmentally hazardous and economically unfeasible. This work investigates the use of regenerable ion-exchange materials to induce alkalinity in CO 2 -saturated aqueous solutions such that the pH shift required for mineralization occurs without the need for stoichiometric reagents. Na + -H + exchange isotherms (at [H + ] = 10 −8 –10 −1 M) and rates were measured for 13X and 4A zeolites and TP-207 and TP-260 organic exchange resins in batch equilibrium and fixed-bed exchange experiments, respectively. At solutions equilibrated with CO 2 at 1.0 atm (pH = 3.9), H + exchange capacities for the materials were similar (1.7–2.4 mmol H + /g material) and resulted in pH increases from 3.9 to greater than 8.0. Multi-component mixtures using Ca 2+ and Mg 2+ cations (at 10 −3 –10 −1 M) in CO 2 -saturated water were used to probe competitive ion exchange. The presence of divalent cations in solution inhibited H + exchange, reducing capacities to as low as 0.2 mmol H + /g for both resins and zeolites. Dynamic H + exchange capacities in fixed-bed ion exchange columns were similar to equilibrium values for resins (∼1.5 mmol/g) and zeolites (∼0.8 mmol/g) using inlet solutions that were equilibrated with gaseous streams of CO 2 at 1.0 atm. However, exchange kinetics were limited by intraparticle diffusion as indicated by the increased rate parameters with increasing inlet flow rates (20–160 cm 3 min −1 ). Experimental calcite precipitation from mixing the alkaline CO 3 2− -rich water solution obtained from the ion-exchange column with a simulated liquid waste stream solution achieved thermodynamic maximum yields. The results from these studies indicate that ion exchange processes can be used as an alternative to the addition of stoichiometric bases to induce alkalinity for the precipitation of CaCO 3 , thereby opening a pathway toward sustainable and economic mineralization processes.
42 ENGINEERING↗
Solid-Density Ion Temperature from Redshifted and Double-Peaked Stark Line Shapes
Heβ spectral line shapes are important for diagnosing temperature and density in many dense plasmas. This work presents Heβ line shapes measured with high spectral resolution from solid-density plasmas with minimized gradients. The line shapes show hallmark features of Stark broadening, including quantifiable redshifts and double-peaked structure with a significant dip between the peaks; these features are compared to models through a Markov chain Monte Carlo framework. Line shape theory using the dipole approximation can fit the width and peak separation of measured line shapes, but it cannot resolve an ambiguity between electron density n e and ion temperature T i , since both parameters influence the strength of quasistatic ion microfields. Here a line shape model employing a full Coulomb interaction for the electron broadening computes self-consistent line widths and redshifts through the monopole term; redshifts have different dependence on plasma parameters and thus resolve the n e – T i ambiguity. The measured line shapes indicate densities that are 80–100% of solid, identifying a regime of highly ionized but well-tamped plasma. This analysis also provides the first strong evidence that dense ions and electrons are not in thermal equilibrium, despite equilibration times much shorter than the duration of x-ray emission; cooler ions may arise from nonclassical thermalization rates or anomalous energy transport. Furthermore, the experimental platform and diagnostic technique constitute a promising new approach for studying ion-electron equilibration in dense plasmas.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗