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At least 343 records · Page 19

Molecular interactions from the density functional theory for chemical reactivity: Interaction chemical potential, hardness, and reactivity principles

In the first paper of this series, the authors derived an expression for the interaction energy between two reagents in terms of the chemical reactivity indicators that can be derived from density functional perturbation theory. While negative interaction energies can explain reactivity, reactivity is often more simply explained using the “|dμ| big is good” rule or the maximum hardness principle. Expressions for the change in chemical potential (μ) and hardness when two reagents interact are derived. A partial justification for the maximum hardness principle is that the terms that appear in the interaction energy expression often reappear in the expression for the interaction hardness, but with opposite sign.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Organizing principles for vegetation dynamics

Understanding vegetation dynamics is very challenging because of the multitude of contributing processes at 64widely different spatial and temporal scales. In this Perspective we propose that understanding of vegetation dynamics can be improved, permitting better predictions, based on organizing principles that constrain plant and ecosystem be haviour: natural selection, self-organization, and entropy maximization. Although these ideas are increasingly used,a limited common understanding of their theoretical basis has prevented their full potential to be realized. We explain the power of natural selection-based optimality to predict photosynthesis and carbon allocation responses to multiple environmental drivers, and how individual plasticity leads to the predictable self-organization of forest canopies. We show how models of natural selection acting on a few key traits can generate realistic plant communities, and how entropy maximization can distinguish between stochastic and deterministic drivers of vegetation patterns. In combination with empirical exploration of patterns in plant functional variation, these principles can accelerate the development of dynamic vegetation models as well as trait-based ecology resting on strengthened theoretical and empirical foundations.

Geosciences↗

Larger than uncorrelated vacancy diffusion contributions in chemically disordered crystalline materials

Arising from a variational approach to compute diffusion coefficients, we introduce “superkinetic kinosons”, which are contributions to the diffusion flux of mobile defects and atomic species by single jump mechanisms that can exceed their uncorrelated values. In vacancy-mediated diffusion in crystalline random and high entropy materials, these contributions primarily arise from intermittent jumps of slow moving atoms that remove the vacancy out of correlation traps and enable a quantification of such effects on the diffusion coefficients. They can be significant contributors to diffusion, even when faster moving atoms have infinite percolation networks. Furthermore, their existence and importance provide fundamental insights about underlying aspects of vacancy diffusion such as formation of localized correlation traps and deviation of vacancy diffusion from percolation behavior.

36 MATERIALS SCIENCE↗

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape 1,2,3 , have activity against diverse sarbecoviruses 4,5,6,7 , and be highly protective through viral neutralization 8,9,10,11 and effector functions 12,13 . Understanding how these properties relate to each other and vary across epitopes would aid the development of therapeutic antibodies and guide vaccine design. Here we comprehensively characterize escape, breadth and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a potent RBM antibody (S2E12 8 ) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth and potency among antibodies that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.

60 APPLIED LIFE SCIENCES↗

Model reduction methods for nuclear emulators

The field of model order reduction (MOR) is growing in importance due to its ability to extract the key insights from complex simulations while discarding computationally burdensome and superfluous information. We provide an overview of MOR methods for the creation of fast & accurate emulators of memory- and compute-intensive nuclear systems, focusing on eigen-emulators and variational emulators. As an example, we describe how 'eigenvector continuation' is a special case of a much more general and well-studied MOR formalism for parameterized systems. We continue with an introduction to the Ritz and Galerkin projection methods that underpin many such emulators, while pointing to the relevant MOR theory and its successful applications along the way. Here, we believe that this guide will open the door to broader applications in nuclear physics and facilitate communication with practitioners in other fields.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Thermodynamically consistent semi-compressible fluids: a variational perspective

This paper presents (Lagrangian) variational formulations for single and multicomponent semi-compressible fluids with both reversible (entropy-conserving) and irreversible (entropy-generating) processes. Semi-compressible fluids are useful in describing low-Mach dynamics, since they are soundproof. These models find wide use in many areas of fluid dynamics, including both geophysical and astrophysical fluid dynamics. Specifically, the Boussinesq, anelastic and pseudoincompressible equations are developed through a unified treatment valid for arbitrary Riemannian manifolds, thermodynamic potentials and geopotentials. By design, these formulations obey the 1st and 2nd laws of thermodynamics, ensuring their thermodynamic consistency. This general approach extends and unifies existing work, and helps clarify the thermodynamics of semi-compressible fluids. To further this goal, evolution equations are presented for a wide range of thermodynamic variables: entropy density s, specific entropy η, buoyancy b, temperature T, potential temperature θ and a generic entropic variable χ; along with a general definition of buoyancy valid for all three semicompressible models and arbitrary geopotentials. Finally, the elliptic equation for the pressure perturbation (the Lagrange multiplier that enforces semi-compressibility) is developed for all three equation sets in the case of reversible dynamics, and for the Boussinesq/anelastic equations in the case of irreversible dynamics; and some discussion is given of the difficulty in formulating it for the pseudoincompressible equations with irreversible dynamics.

97 MATHEMATICS AND COMPUTING↗

Understanding the Selective Deposition of Li Metal on Nonuniform Electrode Surfaces Using Atomic Force Microscopy

The use of lithium metal in secondary batteries has been impeded by its tendency to form dendrites: branching conductive structures of metal that can lead to capacity loss and, ultimately, internal shorts in the battery. Patterned electrodes, in addition to artificially increasing the current density of cells by increasing the surface area available for reaction, also generate a nonuniform electric field in the vicinity of the electrode surface. This nonuniform electric field, though rapidly screened by the electrolyte, can promote inhomogeneous deposition and Solid Electrolyte Interphase formation. As the consequence of these effects is not theoretically apparent since Solid Electrolyte Interphase volume and conductivity changes can, in principle, offset variations in local current density, we have performed experiments to examine the deposition of Li on nonuniform electrode surfaces using Atomic Force Microscopy. In this work, we measure the local variations in topography, SEI thickness, and composition, and discuss their implications for the formation of dendrites in Li metal.

25 ENERGY STORAGE↗

BUQEYE guide to projection-based emulators in nuclear physics

The BUQEYE collaboration (Bayesian Uncertainty Quantification: Errors in Your effective field theory) presents a pedagogical introduction to projection-based, reduced-order emulators for applications in low-energy nuclear physics. The term emulator refers here to a fast surrogate model capable of reliably approximating high-fidelity models. As the general tools employed by these emulators are not yet well-known in the nuclear physics community, we discuss variational and Galerkin projection methods, emphasize the benefits of offline-online decompositions, and explore how these concepts lead to emulators for bound and scattering systems that enable fast and accurate calculations using many different model parameter sets. We also point to future extensions and applications of these emulators for nuclear physics, guided by the mature field of model (order) reduction. All examples discussed here and more are available as interactive, open-source Python code so that practitioners can readily adapt projection-based emulators for their own work.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

What is H sub 0/ques/

Zero order Hamiltonian in perturbation theory for eigenvalue problems of atom in magnetic field

EIGENVALUE↗

Canonical fluid thermodynamics

The space-time integral of the thermodynamic pressure plays the role of the thermodynamic potential for compressible, adiabatic flow in the sense that the pressure integral for stable flow is less than for all slightly different flows. This stability criterion can be converted into a variational minimum principle by requiring the molar free-enthalpy and the temperature, which are the arguments of the pressure function, to be generalized velocities, that is, the proper-time derivatives of scalar spare-time functions which are generalized coordinates in the canonical formalism. In a fluid context, proper-time differentiation must be expressed in terms of three independent quantities that specify the fluid velocity. This can be done in several ways, all of which lead to different variants (canonical transformations) of the same constraint-free action integral whose Euler-Lagrange equations are just the well-known equations of motion for adiabatic compressible flow.

Schmid, L. A.↗

A Stability Analysis of Cylindrical Panels Using a Finite Element Formulation

A cylindrical finite element suitable for the linear stability analysis of cylindrical shells is developed. Energy principles and variational methods lead to a problem formulation which lends itself to physical interpretations of the governing matrices of the finite element. By properly grouping the terms which result from taking the second variation of the potential energy of the element, it is possible to identify three distinct types of matrices. The first matrix is the conventional stiffness matrix; the second is an initial stress stiffness matrix; and the third is an initial displacement stiffness matrix. With the assumption of linearity, the buckling problem is stated in terms of the classical linear real eigenvalue equation. This problem formulation was programmed on the CDC 6600 series computer. The computer program is used to analyze the buckling of a variety of structures. Columns, arches, flat plates and curved panels with and without cutouts are considered.

Snyder, R. E.↗

The stability of solar coronal loops with realistic photospheric boundary conditions

Finite-length effects are the primary influence for the MHD stability of coronal loops. This paper gives a new physical description of the photospheric boundary conditions, and the first complete and uniformly convergent initial-perturbation set. A general energy-principle (or variational) stability analysis is then developed. The results of this calculation show that large classes of cylindrical-symmetry perturbations, those with separable contributions to the energy integral, are completely stable. Comparisons are also made with other more restrictive formulations of this problem.

Van Hoven, G.↗

Contribution to the theory of propeller vibrations

This report presents a calculation of the torsional frequencies of revolving bars with allowance for the air forces. Calculation of the flexural or bonding frequencies of revolving straight or tapered bars in terms of the angular velocity of revolution. Calculation on the basis of Rayleigh's principle of variation. There is also a discussion of error estimation and the accuracy of results. The author then provides an application of the theory to screw propellers for airplanes and the discusses the liability of propellers to damage through vibrations due to lack of uniform loading.

Liebers, F↗