Search

We present 50-fs, single-shot measurements of the x-ray thermal diffuse scattering (TDS) from copper foils that have been shocked via nanosecond laser-ablation up to pressures above 135~GPa. We hence deduce the x-ray Debye-Waller (DW) factor, providing a temperature measurement. The targets were laser-shocked with the DiPOLE 100-X laser at the High Energy Density (HED) endstation of the European X-ray Free-Electron Laser (EuXFEL). Single x-ray pulses, with a photon energy of 18 keV, were scattered from the samples and recorded on Varex detectors. Despite the targets being highly textured (as evinced by large variations in the elastic scattering), and with such texture changing upon compression, the absolute intensity of the azimuthally averaged inelastic TDS between the Bragg peaks is largely insensitive to these changes, and, allowing for both Compton scattering and the low-level scattering from a sacrificial ablator layer, provides a reliable measurement of $T/\Theta_D^2$, where $\Theta_D$ is the Debye temperature. We compare our results with the predictions of the SESAME 3336 and LEOS 290 equations of state for copper, and find good agreement within experimental errors. We thus demonstrate that single-shot temperature measurements of dynamically compressed materials can be made via thermal diffuse scattering of XFEL radation., Comment: 17 pages, 9 figures in main article; 10 pages, 5 figures in supplementary material

We have developed a new all-optical method to directly measure the pressure-volume-temperature (PVT) equation of state (EOS) of fluids and transparent solids in the diamond anvil high pressure cell by measuring the volume of the sample chamber. Our method combines confocal microscopy and white light interference with a new analysis method which exploits the mutual dependence of sample density and refractive index: Experimentally, the refractive index determines the measured sample chamber thickness (and therefore the measured sample volume/density), yet the sample density is by far the dominant factor in determining the variation in refractive index with pressure. Our analysis method allows us to obtain a set of values for the density and refractive index which are mutually consistent, and agree with the experimental data within error. We have conducted proof-of-concept experiments on a variety of samples (H$_{2}$O, CH$_{4}$, C$_{2}$H$_{6}$, C$_{3}$H$_{8}$, KCl and NaCl) at ambient temperature, and at high temperatures up to just above 500 K. Our proof-of-concept data demonstrate that our method is able to reproduce known fluid and solid EOS within error. Furthermore, we demonstrate that our method allows us to directly and routinely measure the PVT EOS of simple fluids at GPa pressures up to, at least, 514 K (the highest temperature reached in our study). A reasonable estimation of the known sources of error in our volume determinations indicates that the error is currently $\pm$ 2.7% at high temperature, and that it is feasible to reduce it to ca. $\pm$ 1% in future work., Comment: Accepted for publication in Physics of Fluids

This set of tables introduces new data for national and state-level public elementary and secondary revenues and expenditures for fiscal year (FY) 2021. Specifically, these tables include the following school finance data: (1) revenue and expenditure totals; (2) revenues by source; (3) expenditures by function and object; (4) current expenditures; (5) revenues and current expenditures per pupil; (6) expenditures from Title I funds; and (7) revenues and expenditures from COVID-19 Federal Assistance Funds. The tables chosen for this report demonstrate the range of information available when using the National Public Education Financial Survey (NPEFS). [For "Revenues and Expenditures for Public Elementary and Secondary Education: FY 20. Finance Tables. NCES 2022-301," see ED619372.]

The emergence of correlated phenomena arising from the combination of 1$\mathrm{T}$ and 1$\mathrm{H}$ van der Waals layers is the focus of intense research. Here, we synthesize a novel self-stacked 6$\mathrm{R}$ phase in NbSeTe, showing a perfect alternating 1T and 1H layers that grow coherently along the c-direction, as revealed by scanning transmission electron microscopy. Angle resolved photoemission spectroscopy shows a mixed contribution of the trigonal and octahedral Nb bands to the Fermi level. Diffuse scattering reveals temperature-independent short-range charge fluctuations with propagation vector $\mathrm{q_{CO}}$=(0.25,0), derived from the condensation of a longitudinal mode in the 1T layer. We observe that ligand disorder quenches the formation of a charge density wave. Magnetization measurements suggest the presence of an inhomogeneous, short-range magnetic order, further supported by the absence of a clear phase transition in the specific heat. These experimental analyses in combination with \textit{ab initio} calculations indicate that the ground state of 6$\mathrm{R}$-NbSeTe is described by a statistical distribution of short-range charge-modulated and spin-correlated regions driven by ligand disorder. Our results devise a route to synthesize 1$\mathrm{T}$-1$\mathrm{H}$ self-stacked bulk heterostructures to study emergent phases of matter., Comment: 12 pages, including Supplementary Information. 4 figures + 6 supplementary figures

We study loops which are universal (that is, isotopically invariant) with respect to the property of flexibility ($xy\cdot x = x\cdot yx$). We also weaken this to semi-universality, that is, loops in which every left and right isotope is flexible, but not necessarily every isotope. One of our main results is that universally flexible, inverse property loops are Moufang loops. On the other hand, semi-universally flexible, inverse property loops are diassociative. We also examine the relationship between universally flexible loops and middle Bol loops. The paper concludes with some open problems., Comment: 13pp

Phase transition theory, implemented quantitatively by thermodynamic scaling, has explained the evolution of Coronavirus extremely high contagiousness caused by a few key mutations from CoV2003 to CoV2019 identified among hundreds, as well as the later 2021 evolution to Omicron caused by 30 mutations. It also showed that the 2022 strain BA.5 with five mutations began a new path. Here we show that the early 2023 strains BKK with one stiffening mutation confirm that path, and the single flexing mutation of a later 2023 variant EG.5 strengthens it further. The few mutations of the new path have greatly reduced pandemic deaths, for mechanical reasons proposed here., Comment: 5 pages, 1 figure

This set of tables introduces new data for national and state-level public elementary and secondary revenues and expenditures for fiscal year (FY) 2020. Specifically, this report includes the following school finance data: (1) revenue and expenditure totals; (2) revenues by source; (3) expenditures by function and object; (4) current expenditures; and (5) current expenditures per pupil. The finance data used in this report are from the National Public Education Financial Survey (NPEFS), a component of the Common Core of Data (CCD). State education agencies (SEAs) in each of the 50 states; the District of Columbia; and the 5 other jurisdictions of American Samoa, Guam, the Commonwealth of the Northern Mariana Islands, Puerto Rico, and the U.S. Virgin Islands report these data annually to NCES. While the tables in this report include data for all NPEFS respondents, the figures and selected findings are limited to the 50 states and the District of Columbia. [For "Revenues and Expenditures for Public Elementary and Secondary Education: FY 19. Finance Tables. NCES 2021-302," see ED613219.]

Rhodopsin is a G-protein coupled receptor found in retinal rod cells, where it mediates monocrhromatic vision in dim light. It is one of the most studied proteins with thousands of reviewed entries in Uniprot. It has seven transmembrane segments, here examined for their hydrophobic character, and how that has evolved from chickens to humans. Elastic features associated with Proline are also discussed. Finally, differences between rhodopsin and cone opsins are also discussed., Comment: 11 pages, 5 figures, 1 table

TRPC(3,6) are two ~ 930 amino acid membrane proteins that form calcium permeant cation channels. Here we examine the differences between mammals and oviparous species. Our method is based on the concept of evolution towards criticality, a general concept we have previously applied to many proteins, especially in describing the evolution of pandemic sequences through natural selection., Comment: 7 pages, two figures

The major intrinsic protein (MIP) of the lens fiber cell membrane plays a role in lens biogenesis and maintenance. Its polypeptide chains span the membrane six times, and the protein is naturally divided into two halves. We use modern sequence analysis to identify differences between halves for humans (common to animals) and chickens (common to birds)., Comment: 6 pages, 1 Figure

We present the twisted covariant form hierarchies (TCFHs) of warped (massive) IIA AdS backgrounds. As a consequence we demonstrate that all Killing spinor form bilinears satisfy a generalisation of the conformal Killing-Yano equation with respect to the TCFH connections. We also explore some of the properties of TCFHs which include the reduced holonomy of the minimal TCFH connections for generic backgrounds. Furthermore, we investigate the interplay between TCFHs and hidden symmetries of probes propagating on IIA AdS backgrounds. We find that some of the Killing spinor form bilinears of near horizon geometries of a class of IIA intersecting brane configurations are Killing-Yano forms and so generate hidden symmetries for spinning particle probes., Comment: 29 pages

Because of their large size and widespread mechanosensitive interactions the only recently discovered titled transmembrane proteins have attracted much attention. Here we present and discuss their hydropathic profiles using a new method of sequence analysis. We find large-scale similarities and differences not obtainable by conventional sequence or structural studies. These differences support the evolution-towards-criticality conjecture popular among physicists., Comment: 10 page, two figures

With the planned turn-on of the PIP-II 800 MeV superconducting proton linac, Fermilab will potentially become the world's best laboratory at which to carry out fundamental muon measurements, sensitive searches for symmetry violation, and precision tests of theory. In preparation, we propose to develop the techniques that will be needed. An R&D and physics program is proposed at the Fermilab MeV Test Area to use the existing 400 MeV Linac to demonstrate the efficient production of a slow muonium beam using $\mu^+$ stopped in a ~100-$\mu$m-thick layer of superfluid helium, and to use that beam to measure muonium gravity., Comment: 3 pages, submitted to Fermilab

Structural Maintenance of Chromosomes, SMCs, proteins have long rod like structures immersed in water. Here we use our hydroanalytic methods based on amino acid sequences to discuss their dynamics at multiple length scales identified by evolution. The length scales are 10 to 100 times longer than used in normal studies of sequence evolution. Their hydropathic profiles exhibit many features unique to their structure and function., Comment: 1 pages, 12 figures, 1 table

This set of tables introduces new data for national and state-level public elementary and secondary revenues and expenditures for fiscal year (FY) 2019. Specifically, this report includes the following school finance data: (1) revenue and expenditure totals; (2) revenues by source; (3) expenditures by function and object; (4) current expenditures; and (5) current expenditures per pupil. The finance data used in this report are from the National Public Education Financial Survey (NPEFS), a component of the Common Core of Data (CCD). The CCD is the primary National Center for Education Statistics (NCES) database on public elementary and secondary education in the United States. [For "Revenues and Expenditures for Public Elementary and Secondary Education: FY 18. Finance Tables. NCES 2020-306," see ED607297.]

In 2022 new subvariants of Coronavirus appeared in South Africa, and spread rapidly to other parts of the world. The effects of selective evolution on increasing the already high contagiousness of CoV19 up to Omicron were previously discussed with high accuracy using concepts new to molecular biology (from mathematics and physics) that have been developed over the last few decades. Here we discuss the new subvariants, and find novel features successfully combining both improved flexibility and improved stability., Comment: 9 pages, 2 figures, 1 table

Here we examine the evolution of beta-2 microglobulin in terms of its hydropathic shapes, a theoretical construct that has revealed important trends. The dynamics of many proteins are largely driven by interactions between the protein itself and the thin water film that covers it. \b{eta}2m constitutes the basic building unit of the immunoglobulin superfamily; the evolution of its amino acid sequences from chickens to mice to humans provides new information about its multiple functions. Our hydrodynamic method involves concepts of topological shape evolution towards a critical point for optimized functions. The results are in excellent agreement with experiment for the details of the mouse-human evolution, as well as both the dangerous natural amyloid aggregation mutation D76N, and six other DN test mutations., Comment: 10 pages, 4 figures

Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by interactions between the protein itself and the thin water film that covers it. Here those interactions are connected to profiles of water waves connecting domain pivots (hydrophobic extrema), as well as a broad hydrophilic central hinge region that has evolved to provide human TTR with greater flexibility and stability. This central region has a density of single mutations related to amyloid polyneuropathy that is three times higher than other regions., Comment: 9 pages 3 figures 1 table

Improvement of protein function by evolution (natural selection) is expected on general grounds, but even with the modern database positive proof has remained a difficult problem for theory. Here we extend our recent analysis of the evolution of CoV-1 to much more contagious CoV-2, to Omicron, which appears to be qualitatively different from other recent strains like Delta. Overall the synchronized dynamics of Omicron is more elaborate than CoV-2 or its variants like Delta. The surprising result is that while Omicron could be more contagious than even Delta, it is probably much less dangerous, Comment: 10 pages, 5 figures

We present the twisted covariant form hierarchies (TCFH) of type IIA and IIB 10-dimensional supergravities and show that all form bilinears of supersymmetric backgrounds satisfy the conformal Killing-Yano equation with respect to a TCFH connection. We also compute the Killing-St\"ackel, Killing-Yano and closed conformal Killing-Yano tensors of all spherically symmetric type II brane backgrounds and demonstrate that the geodesic flow on these solutions is completely integrable by giving all independent charges in involution. We then identify all form bilinears of common sector and D-brane backgrounds which generate hidden symmetries for particle and string probe actions. We also explore the question on whether charges constructed from form bilinears are sufficient to prove the integrability of probes on supersymmetric backgrounds., Comment: 68 pages

Spike proteins, 1200 amino acids, are divided into two nearly equal parts, S1 and S2. We review here phase transition theory, implemented quantitatively by thermodynamic scaling. The theory explains the evolution of Coronavirus extremely high contagiousness caused by a few mutations from CoV2003 to CoV2019 identified among hundreds in S1. The theory previously predicted the unprecedented success of spike-based vaccines. Here we analyze impressive successes by McClellan et al., 2020, in stabilizing their original S2P vaccine to Hexapro. Hexapro has expanded the two proline mutations of S2P, 2017, to six combined proline mutations in S2. Their four new mutations are the result of surveying 100 possibilities in their detailed structure-based context Our analysis, based on only sparse publicly available data, suggests new proline mutations could improve the Hexapro combination to Octapro or beyond., Comment: 8 pages

The titled subject has attracted much interest. Here we summarize the substantial results obtained by a physical model of protein evolution based on hydropathic domain dynamics. In a recent Letter eighteen biologists suggested that the titled subject should be studied in a way inclusive of broad expertise (1). There is an even broader view that has been developed over several decades by physicists (2,3). This view is based on analyzing amino acid sequences of proteins. These sequences are now available on-line at Uniprot, and represent a treasure-trove of data (4)., Comment: 2 pages, no figures or tables

We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family in different ways, but dynamical hydropathic scaling theory is both simple and effective in providing readily transferable dynamical insights for many proteins represented in the uncounted amino acid sequences, as well as the 90 thousand static structures contained in the online Protein Data Base. Critical point theory is general, and recently it has proved to be the most effective way of describing protein networks that have evolved towards nearly perfect functionality in given environments, self-organized criticality. Darwinian evolutionary patterns are governed by common dynamical hydropathic scaling principles, which can be quantified using scales that have been developed bioinformatically by studying thousands of static PDB structures. The most effective dynamical scales involve hydropathic globular sculpting interactions averaged over length scales centered on domain dimensions. A central feature of dynamical hydropathic scaling theory is the characteristic domain length associated with a given protein functionality. Evolution has functioned in such a way that the minimal critical length scale established so far is about nine amino acids, but in some cases it is much larger. Some ingenuity is needed to find this primary length scale, as shown by the examples discussed here. Often a survey of the Darwinian evolution of a protein sequence suggests a means of determining the critical length scale. The evolution of Coronavirus is an interesting application; it identifies critical mutations., Comment: 93 pages, 37 figures. This is a review article that highlights the main ideas from arXiv:1610.04116

CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection that precedes structural rearrangements by using biomolecular evolutionary theory to identify sequence differences enhancing viral attachment rates. We find a small cluster of four single mutations which show that CoV-2 has a new feature that promotes much stronger viral attachment and enhances contagiousness. The extremely dangerous dynamics of human coronavirus infection is a dramatic example of evolutionary approach of self-organized networks to criticality. It may favor a very successful vaccine. The identified mutations can be used to test the present theory experimentally. The theory also works well for the newer strains and explains their increased contagiousness., Comment: 15 pages, 4 figures, 1 table

Intelligence is often discussed in terms of neural networks in the cerebral cortex, whose evolution has presumably been influenced by Darwinian selection. Here we present molecular evidence that one of the many kinesin motors, Kif14, has evolved to exhibit special features in its amino acid sequence that could have evolved to improve neural networks. The improvement is quantified by comparison of Kif14 sequences for 12 species. The special feature is level sets of hydrophobic extrema in water wave profiles based on several hydropathic scales. The most effective scale is a new one based on fractals, indicative of approach of globular curvatures to self-organized criticality., Comment: 7 pages, 1 figure, 1 table

Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). The principal features of the eukaryotic evolution of the cytoskeleton motor protein myosin-1 parallel those of actin and tubulin, but also show striking differences connected to its dynamical function. Optimized (long) hydropathic waves characterize the molecular level Darwinian evolution towards optimized functionality (self-organized criticality). The N-terminal and central domains of myosin-1 have evolved in eukaryotes at different rates, with the central domain hydropathic extrema being optimally active in humans. A test shows that hydropathic scaling can yield accuracies of better than 1% near optimized functionality. Evolution towards synchronized level extrema is connected to a special function of Mys-1 in humans involving Golgi complexes., Comment: 20 pages, 9 figures

What is life. Schrodingers question is discussed here for a specific protein, villin, which builds cells in tissues that detect taste and sound. Villin is represented by a sequence of 827 amino acids bound to a peptide backbone chain. We focus attention on a limited problem, the Darwinian evolution of villin sequences from chickens to humans. This biophysical problem is analyzed using a new physicical method based on thermodynamic domain scaling, a technique that bridges the gap between physical concepts, self-organized criticality, and conventional biostructural practice. It turns out that the evolutionary changes can be explained by Darwinian selection, which is not generally accepted by biologists at the protein level. The presentation is self-contained, and requires no prior experience with proteins at the molecular level., Comment: 7 pages, 3 figures

CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection which precedes structural rearrangements by using biomolecular evolutionary theory to identify sequence differences enhancing viral attachment rates. We find a small cluster of mutations which show that CoV-2 has a new feature that promotes much stronger viral attachment and enhances contagiousness. The extremely dangerous dynamics of human coronavirus infection is a dramatic example of evolutionary approach of self-organized networks to criticality. It may favor a very successful vaccine. The identified mutations can be used to test the present theory experimentally., Comment: 11 pages, 4 figures

Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). Our theoretical analysis uses hydropathic waves to identify and contrast the functional differences between the polymerizing $\alpha$ and $\beta$ tubulin monomers, which are similar in length and secondary structures, as well as having indistinguishable phylogenetic trees. We show how evolution has improved water-driven flexibility especially for $\alpha$ tubulin, and thus facilitated heterodimer microtubule assembly, in agreement with recent atomistic simulations and topological models. We conclude that the failure of phylogenetic analysis to identify functionally specific positive Darwinian evolution has been caused by 20th century technical limitations. These are overcome using 21st century quantitative mathematical methods based on thermodynamic scaling and hydropathic modular averaging. Our most surprising result is the identification of large level sets, especially in hydrophobic extrema, with both thermodynamically first- and second-order scaled water waves. Our calculations include explicitly long-range water-protein interactions described by fractals. We also suggest a much-needed corrective for large protein drug development costs., Comment: 17 pages, 5 figures

Thermodynamic profiles, based on bioinformatic hydropathicity scales and membrane-fitted sliding windows, exhibit accurately level sets of hydrophobic peaks or valleys in the constant fragment Fc of monoclonal antibodies. These sets provide a roadmap for selected short regions where a few directed amino acid mutations could produce either accelerated antibody kinetics or increased stability. These profiles may reveal dramatic differences in antibody activity, Comment: 15 pages, 5 figures

Cytoskeletons are self organized networks based on polymerized proteins, actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality self organized criticality. Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1500 amino acids away., Comment: 17 pages,6 figures

We develop a microscopic biophysical model for self-organization and reshaping of artificial tissue, that is co-driven by microscopic active forces between cells and extracellular matrix (ECM), and macroscopic forces that develop within the tissue, finding close agreement with experiment. Microscopic active forces are stimulated by $\mu$m scale interactions between cells and the ECM within which they exist, and when large numbers of cells act together these forces drive, and are affected by, macroscopic-scale self-organization and reshaping of tissues in a feedback loop. To understand this loop, there is a need to: (1) construct microscopic biophysical models that can simulate these processes for the very large number of cells found in tissues; (2) validate and calibrate those models against experimental data; and (3) understand the active feedback between cells and the extracellular matrix, and its relationship to macroscopic self-organization and reshaping of tissue. Our microscopic biophysical model consists of a contractile network representing the ECM, that interacts with a large number of cells via dipole forces, to describe macroscopic self-organization and reshaping of tissue. We solve the model using simulated annealing, finding close agreement with experiments on artificial neural tissue. We discuss calibration of model parameters. We conclude that feedback between microscopic cell-ECM dipole interactions and tissue-scale forces, is a key factor in driving macroscopic self-organization and reshaping of tissue. We discuss application of the biophysical model to simulation and rational design of artificial tissues.

Amyloid precursor with 770 amino acids dimerizes and aggregates, as do its c terminal 99 amino acids and amyloid 40,42 amino acids fragments. The titled question has been discussed extensively, and here it is addressed further using thermodynamic scaling theory to analyze mutational trends in structural factors and kinetics. Special attention is given to Family Alzheimer's Disease mutations outside amyloid 42. The scaling analysis is connected to extensive docking simulations which included membranes, thereby confirming their results and extending them to Amyloid precursor., Comment: 11 pages, 3 figures, 1 table

We describe new results from the semiconductor-laser tracking frequency gauge, an instrument that can perform sub-picometer distance measurements and has applications in gravity research and in space-based astronomical instruments proposed for the study of light from extrasolar planets. Compared with previous results, we have improved incremental distance accuracy by a factor of two, to 0.9 pm in 80 s averaging time, and absolute distance accuracy by a factor of 20, to 0.17 $\mu$m in 1000 s. After an interruption of operation of a tracking frequency gauge used to control a distance, it is now possible, using a nonresonant measurement interferometer, to restore the distance to picometer accuracy by combining absolute and incremental distance measurements., Comment: 8 pages, 4 figures. To appear in JINST. (This version with new figures 3 and 4 with improved graphic quality and performance.)

Ubiquitin tags diseased proteins and initiates an enzyme conjugation cascade, which has three stages. The first-stage enzyme Uba1 (E1) has evolved only modestly from slime mold to humans, and is > 14 times larger than Ub. Here we use critical point thermodynamic scaling theory to connect Uba1 (E1) evolution from yeast and slime mold to fruit flies and humans to subtle changes in its amino acid sequences., Comment: 12 pages, 6 figures

Ubiquitin, discovered less than 50 years ago, tags thousands of diseased proteins for destruction. It is small (only 76 amino acids), and is found unchanged in mammals, birds, fish and even worms. Key features of its functionality are identified here using critical point thermodynamic scaling theory. These include Fano interference between first- and second-order elements of globular surface shape transitions. Comparison with its closest relative, 76 amino acid Nedd8, shows that the latter lacks these features. A cracked elastic network model is proposed for the common target shared by many diseased proteins., Comment: 11pages, 4 figures