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At least 1,531 records · Page 85

Benchmarking the performance of density functional theory and point charge force fields in their description of sI methane hydrate against diffusion Monte Carlo

High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, while the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice I{sub h}, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice I{sub h} and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dark matter, long-range forces, and large-scale structure

If the dark matter in galaxies and clusters is nonbaryonic, it can interact with additional long-range fields that are invisible to experimental tests of the equivalence principle. We discuss the astrophysical and cosmological implications of a long-range force coupled only to the dark matter and find rather tight constraints on its strength. If the force is repulsive (attractive), the masses of galaxy groups and clusters (and the mean density of the universe inferred from them) have been systematically underestimated (overestimated). We explore the consequent effects on the two-point correlation function, large-scale velocity flows, and microwave background anisotropies, for models with initial scale-invariant adiabatic perturbations and cold dark matter.

Gradwohl, Ben-Ami↗

An implicit divalent counterion force field for RNA molecular dynamics

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Environmental Forcing of Super Typhoon Paka's (1997) Latent Heat Structure

The distribution and intensity of total (i.e., combined stratified and convective processes) rainrate/latent heat release (LHR) were derived for tropical cyclone Paka during the period 9-21 December, 1997 from the F-10, F-11, F-13, and F-14 Defense Meteorological Satellite Special Sensor Microwave/Imager and the Tropical Rain Measurement Mission Microwave Imager observations. These observations were frequent enough to capture three episodes of inner core convective bursts that preceded periods of rapid intensification and a convective rainband (CRB) cycle. During these periods of convective bursts, satellite sensors revealed that the rainrates/LHR: 1) increased within the inner eye wall region; 2) were mainly convectively generated (nearly a 65% contribution), 3) propagated inwards; 4) extended upwards within the middle and upper-troposphere, and 5) became electrically charged. These factors may have caused the eye wall region to become more buoyant within the middle and upper-troposphere, creating greater cyclonic angular momentum, and, thereby, warming the center and intensifying the system. Radiosonde measurements from Kwajalein Atoll and Guam, sea surface temperature observations, and the European Center for Medium Range Forecast analyses were used to examine the necessary and sufficient condition for initiating and maintaining these inner core convective bursts. For example, the necessary conditions such as the atmospheric thermodynamics (i.e., cold tropopause temperatures, moist troposphere, and warm SSTs [greater than 26 deg]) suggested that the atmosphere was ideal for Paka's maximum potential intensity (MPI) to approach super-typhoon strength. Further, Paka encountered weak vertical wind shear (less than 15 m/s ) before interacting with the westerlies on 21 December. The sufficient conditions, on the other hand, appeared to have some influence on Paka's convective burst, but the horizontal moisture flux convergence values in the outer core were weaker than some of the previously examined tropical cyclones. Also, the upper tropospheric outflow generation of eddy relative angular momentum flux convergence was 4D much less than that found during moderate tropical cyclone/trough interaction. These results indicated how important the external necessary condition and the internal forcing (i.e., CRB cycle) were in generating Paka's convective bursts as compared to the external sufficient forcing mechanisms found in higher latitude tropical cyclones. Later, as Paka began to interact with the westerlies, both the necessary (i.e., strong vertical shear and colder SSTs) and sufficient (i.e., dry air intrusion) external forcing mechanisms helped to decrease Paka's rainrate.

Rodgers, Edward B.↗

Binding of Phosphate Species to Ca 2+ and Mg 2+ in Aqueous Solution

Phosphate derivatives and their interaction with metal cations are involved in many important biological phenomena, so an accurate characterization of the phosphate-metal interaction is necessary to properly understand the role of phosphate-metal contacts in mediating biological function. Herein, we improved the standard 12-6 Lennard-Jones (LJ) potential via the usage of the 12-6-4 LJ model, which incorporates ion-induced dipole interactions. Via parameter scanning, we fine-tuned the 12-6-4 LJ polarizability values to obtain accurate absolute binding free energies for the phosphate anions H 2 PO 4 – , HPO 4 2– , PO 4 3– coordinating with Ca 2+ and Mg 2+ . First, we modified the phosphate 12-6-4 LJ parameters to reproduce the solvation free energies of the series of phosphate anions using the thermodynamic integration (TI) method. Then, using the potential mean force (PMF) method, the polarizability of the metal-phosphate interaction was obtained. We show that the free energy profiles of phosphate ions coordinated to Ca 2+ and Mg 2+ generally show similar trends at longer metal–phosphate distances, while the absolute binding energy values increased with deprotonation. The resulting parameters demonstrate the flexibility of the 12-6-4 LJ-type nonbonded model and its usefulness in accurately describing cation–anion interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Gaussian approximation potentials for accurate thermal properties of two-dimensional materials

Two-dimensional materials (2DMs) continue to attract a lot of attention, particularly for their extreme flexibility and superior thermal properties. Molecular dynamics simulations are among the most powerful methods for computing these properties, but their reliability depends on the accuracy of interatomic interactions. While first principles approaches provide the most accurate description of interatomic forces, they are computationally expensive. In contrast, classical force fields are computationally efficient, but have limited accuracy in interatomic force description. Machine learning interatomic potentials, such as Gaussian Approximation Potentials, trained on density functional theory (DFT) calculations offer a compromise by providing both accurate estimation and computational efficiency. Here, in this work, we present a systematic procedure to develop Gaussian approximation potentials for selected 2DMs, graphene, buckled silicene, and h-XN (X = B, Al, and Ga, as binary compounds) structures. We validate our approach through calculations that require various levels of accuracy in interatomic interactions. The calculated phonon dispersion curves and lattice thermal conductivity, obtained through harmonic and anharmonic force constants (including fourth order) are in excellent agreement with DFT results. HIPHIVE calculations, in which the generated GAP potentials were used to compute higher-order force constants instead of DFT, demonstrated the first-principles level accuracy of the potentials for interatomic force description. Molecular dynamics simulations based on phonon density of states calculations, which agree closely with DFT-based calculations, also show the success of the generated potentials in high-temperature simulations.

2D Materials↗

Probing new spin-independent interactions through precision spectroscopy in atoms with few electrons

The very high precision of current measurements and theory predictions of spectral lines in few-electron atoms allows us to efficiently probe the existence of exotic forces between electrons, neutrons and protons. We investigate here the sensitivity to new spin-independent interactions in transition frequencies (and their isotopic shifts) of hydrogen, helium and some heliumlike ions. We find that present data probe new regions of the force-carrier couplings to electrons and neutrons around the MeV mass range. We also find that, below few keV, the sensitivity to the electron coupling in precision spectroscopy of helium and positronium is comparable to that of the anomalous magnetic moment of the electron. Finally, we interpret our results in the dark-photon model where a new gauge boson is kinetically mixed with the photon. There, we show that helium transitions, combined with the anomalous magnetic moment of the electron, provide the strongest indirect bound from laboratory experiments above 100 keV.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analysis of Sample Acquisition Dynamics Using Discrete Element Method

The analysis presented in this paper is conducted in the framework of the Ocean Worlds Autonomy Testbed for Exploration Research and Simulation (OceanWATERS) project, currently under development at NASA Ames Research Center. OceanWATERS aims at designing a simulation environment which allows for testing autonomy of scientific lander missions to the icy moons of our solar system. Mainly focused on reproducing the end effector interaction with the inherent terrain, this paper introduces a novel discrete element method (DEM)-based approach to determine forces and torques acting on the lander’s scoop during the sample acquisition process. An accurate force feedback from the terrain on the scoop is required by fault-detection and autonomous decision-making algorithms to identify when the requested torque on the robotic arm’s joints exceeds the maximum available torque. Knowledge of the terrain force feedback significantly helps evaluating the arm’s links structural properties and properly selecting actuators for the joints. Models available in literature constitute a partial representation of the dynamics of the interaction. As an example, Balovnev derived an analytical expression of the vertical and horizontal force acting on a bucket while collecting a sample as a function of its geometry and velocity, soil parameters and reached depth. Although the model represents an adequate approximation of the two force components, it ignores the direction orthogonal to the scoop motion and neglects the torque. This work relies on DEM analysis to compensate for analytical models’ deficiencies and inaccuracies, i. e. provide force and torque 3D vectors, defined in the moving reference (body) frame attached to the scoop, at each instant of the sample collection process. Results from the first presented analysis relate to the specific OceanWATERS sampling strategy, which consists of collecting the sample through five consecutive passes with increasing depth, each pass following the same circularlinear- circular trajectory. Data is collected given a specific scoop design interacting with two types of bulk materials, which may characterize the surface of icy planetary bodies: snow and ice. Although specifically concerned with the OceanWATERS design, this first analysis provides the expected force trends for similar sampling strategies and allows to deduce phenomenological information about the general scooping process. In order to further instruct the community on the use of DEM tools as a solution to the sampling collection problem, two more analyses have been carried out, mainly focused on reducing the DEM computation time, which increases with a decrease in particle size. After running a set of identical simulations, where the only changing parameter is the size of the spherical particle, it is observed that the resulting force trajectories, starting from a given particle size, converge to the true trend. It is deducible that a further decrease in size yields negligible improvements in the accuracy, while it sensibly increases computation time. A final analysis aims at discussing limitations of approximating bulk material particles having a complex shape, e. g. ice fragments, with spheres, by comparing force trends resulting in the two cases for the same simulation scenario.

Catanoso, Damiana↗

Numerical studies of major and minor stratospheric warmings caused by orographic forcing

A primitive equation spectral model using spherical harmonics is formulated to study dynamic interactions between the troposphere and stratosphere in association with sudden stratospheric warmings. Using sigma coordinates for five tropospheric layers and log-pressure coordinates for 26 stratospheric and mesospheric layers, separate model equations for each system are combined to form single matrix governing equations. The gradual introduction of large scale topography to balanced initial states representative of observed mean winter conditions in the Northern Hemisphere is used for the generation of planetary waves during 40-day time integrations. Results of these integrations indicate that stratospheric warmings can be simulated by this orographic forcing and that mean momentum flux divergence due to zonal mean motion appears to be an essential mechanism of these simulated sudden warmings. It was found that the strength of the polar night jet can be a determining factor whether a warming becomes 'major' or 'minor'.

Koermer, J. P.↗

Bulkiness or aromatic nature of tyrosine-143 of actin is important for the weak binding between F-actin and myosin-ADP-phosphate

Highlights: •The effect of mutation of Tyr143 that becomes more exposed on assembly was examined. •Mutation of tyrosine-143 of Dictyostelium actin changed actin polymerizability. •The bulkiness or aromatic nature of Tyr143 is important for the weak binding. •The weak interaction between myosin and actin strengthened by Tyr143Trp mutation. -- Abstract: Actin filaments (F-actin) interact with myosin and activate its ATPase to support force generation. By comparing crystal structures of G-actin and the quasi-atomic model of F-actin based on high-resolution cryo-electron microscopy, the tyrosine-143 was found to be exposed more than 60 Å{sup 2} to the solvent in F-actin. Because tyrosine-143 flanks the hydrophobic cleft near the hydrophobic helix that binds to myosin, the mutant actins, of which the tyrosine-143 was replaced with tryptophan, phenylalanine, or isoleucine, were generated using the Dictyostelium expression system. It polymerized significantly poorly when induced by NaCl, but almost normally by KCl. In the presence of phalloidin and KCl, the extents of the polymerization of all the mutant actins were comparable to that of the wild-type actin so that the actin-activated myosin ATPase activity could be reliably compared. The affinity of skeletal heavy meromyosin to F-actin and the maximum ATPase activity (V{sub max}) were estimated by a double reciprocal plot. The Tyr143Trp-actin showed the higher affinity (smaller K{sub app}) than that of the wild-type actin, with the V{sub max} being almost unchanged. The K{sub app} and V{sub max} of the Tyr143Phe-actin were similar to those of the wild-type actin. However, the activation by Tyr143Ile-actin was much smaller than the wild-type actin and the accurate determination of K{sub app} was difficult. Comparison of the myosin ATPase activated by the various mutant actins at the same concentration of F-actin showed that the extent of activation correlates well with the solvent-accessible surface areas (ASA) of the replaced amino acid molecule. Because 1/K{sub app} reflects the affinity of F-actin for the myosin–ADP-phosphate intermediate (M.ADP.Pi) through the weak binding, these data suggest that the bulkiness or the aromatic nature of the tyrosin-143 is important for the initial binding of the M.ADP.Pi intermediate with F-actin but not for later processes such as the phosphate release.

60 APPLIED LIFE SCIENCES↗

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socio-economic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided from studying the binding and interaction of viral proteins with non-biological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum-, copper-, iron-, silica-, and ceria-oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ~10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. Further, this study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are non-specific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that at ambient conditions glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces and they depend on the surface tension of the liquid (water). We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetism in La{sub 0.7}Sr{sub 0.3}Mn{sub 1-x}Co{sub x}O{sub 3} (0 ≤ x ≤ 1)

We study the structural and magnetic properties of La{sub 0.7}Sr{sub 0.3}Mn{sub 1-x}Co{sub x}O{sub 3} (0 ≤ x ≤ 1). Rietveld refinement of X-ray Diffraction (XRD) pattern suggests phase purity of the polycrystalline samples with R-3c space group. Interplay of Ferromagnetic (FM) and Antiferromagnetic (AFM) interaction upon Co substitution at Mn site in La{sub 0.7}Sr{sub 0.3}MnO{sub 3} is evident from magnetic measurements. There is an optimal cobalt substitution at which the coercive field is maximum.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for “flip-flop” conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic Scale Analysis of the Carbonization Process for C/H/O/N-Based Polymers with the ReaxFF Reactive Force Field

During the carbonization process of raw polymer precursors, graphitic structures can evolve. The presence of these graphitic structures affects mechanical properties of the carbonized carbon fibers. To gain a better understanding of the chemistry behind the evolution of these structures, we performed atomistic-scale simulations using the ReaxFF reactive force field. Three different polymers were considered as a precursor: idealized ladder PAN (polyacrylonitrile), a proposed oxidized PAN, and poly(p-phenylene- 2,6-benzobisoxazole). We determined the underlying molecular details of polymer conversion into a carbon fiber structure. Because these are C/H/O/ N-based polymers, we first developed an improved force field for C/H/O/N chemistry based on the density functional theory data with a particular focus on N2 formation kinetics and its interactions with polymer-associated radicals formed during the carbonization process. Then, using this improved force field, we performed atomistic-scale simulations of the initial stage of the carbonization process for the considered polymers. On the basis of our simulation data, the molecular pathways for the formation of low-molecular-weight gas species and all-carbon ring formation were determined. We also examined the possible alignment of the developed all-carbon 6-membered ring clusters, which is crucial for the further graphitic structure evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mean-field theory for the structure of strongly interacting active liquids

Active systems, which are driven out of equilibrium by local non-conservative forces, exhibit unique behaviors and structures with potential utility for the design of novel materials. An important and difficult challenge along the path toward this goal is to precisely predict how the structure of active systems is modified as their driving forces push them out of equilibrium. Here, we use tools from liquid-state theories to approach this challenge for a classic minimal active matter model. First, we construct a nonequilibrium mean-field framework that can predict the structure of systems of weakly interacting particles. Second, motivated by equilibrium solvation theories, we modify this theory to extend it with surprisingly high accuracy to systems of strongly interacting particles, distinguishing it from most existing similarly tractable approaches. Furthermore, our results provide insight into spatial organization in strongly interacting out-of-equilibrium systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Defect Self-Elimination in Nanocube Superlattices Through the Interplay of Brownian, van der Waals, and Ligand-Based Forces and Torques

Understanding defect healing is necessary for realizing devices based on nanoparticle-superlattices with controlled electronic and optoelectronic performance. However, key questions remain regarding nanoparticle interactions and resulting assembly dynamics and defect self-elimination. In particular, for anisotropic particles, additional degrees of freedom beyond those of spherical particles, such as rotational dynamics and toques, significantly impact phenomena. Here, in this work, we investigate nanocube (NC) superlattices by employing liquid phase transmission electron microscopy, continuum theories and molecular dynamics simulations. Analyzing interparticle forces and torques due to van der Waals, Brownian, and ligand interactions, we find that the latter dominates and that the anisotropic NC morphology introduces significant torques. In imperfect regions, unbalanced forces and torques induce NC translations and rotations that are transmitted to neighboring NCs, prompting “chain interactions” in a 2D network, which lead to defect self-elimination. This fundamental understanding will further enable design and fabrication of defect-free superlattices, as well as those with tailored defects, via assembly of anisotropic particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constraining the Self-Interacting Neutrino Interpretation of the Hubble Tension

Large, nonstandard neutrino self-interactions have been shown to resolve the ~4σ tension in Hubble constant measurements and a milder tension in the amplitude of matter fluctuations. Herein we demonstrate that interactions of the necessary size imply the existence of a force carrier with a large neutrino coupling (>10 -4 ) and mass in the keV–100 MeV range. This mediator is subject to stringent cosmological and laboratory bounds, and we find that nearly all realizations of such a particle are excluded by existing data unless it carries spin 0 and couples almost exclusively to $τ$-flavored neutrinos. Furthermore, we find that the light neutrinos must be Majorana particles, and that a UV-complete model requires a nonminimal mechanism to simultaneously generate neutrino masses and appreciable self-interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Exchange Bias in Layered GdBaCo{sub 2}O{sub 5.5} Cobaltite

It is established that excess oxygen content δ influences the exchange bias (EB) in layered GdBa-Co{sub 2}O{sub 5+δ} cobaltite. The EB effect arises in p-type (δ > 0.5) cobaltite and disappears in n-type (δ < 0.5) cobaltite. The main parameters of EB in GdBaCo{sub 2}O{sub 5.52(2)} polycrystals are determined, including the field and temperature dependences of EB field H{sub EB}, blocking temperature T{sub B}, exchange coupling energy J{sub i} of antiferromagnet–ferromagnet (AFM–FM) interface, and dimensions of FM clusters. The training effect inherent in systems with EB has been studied. The results are explained in terms of exchange interaction between the FM and AFM phases. It is assumed that the EB originates from the coexistence of Co{sup 3+} and Co{sup 4+} ions that leads to the formation of monodomain FM clusters in the AFM matrix of cobaltite.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗