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We study the incubation and transition times that characterize the magnetization switching induced by spin-orbit torques in nanomagnets with perpendicular anisotropy. We present a phenomenological model to interpret the dependence of the incubation time on the amplitude of the voltage pulse and assisting magnetic field and estimate the volume of the seed domain that triggers the switching. Our measurements evidence a correlation between the incubation and transition times that is mediated by the temperature variation during the electric pulse. In addition, we discuss the stochastic distributions of the two times in terms of the energy barriers opposing the nucleation and expansion of the seed domain. We propose two models based on the log-normal and gamma functions to account for the different origin of the variability of the incubation and transition times, which are associated with a single nucleation barrier and multiple pinning sites, respectively.

A result of Allock [1](arXiv:math/9907194) states that certain orbifold braid groups contain Artin groups of type $D_n$, $\tilde{B}_n$ and $\tilde{D}_n$ as finite index subgroups. The underlying orbifolds have at most two cone points of order two. Based on [10](arXiv:2305.04273) and [12](arXiv:2305.04273), we generalize this result allowing cone points of arbitrary order. In these cases, the orbifold braid groups contain similar subgroups of finite index. We show that in many cases these subgroups can be identified as certain complex braid groups., Comment: 32 pages, 19 figures

The main result of this article is that pure orbifold braid groups fit into an exact sequence $1\rightarrow K\rightarrow\pi_1^{orb}(\Sigma_\Gamma(n-1+L))\xrightarrow{\iota_{\textrm{PZ}_n}}\textrm{PZ}_n(\Sigma_\Gamma(L))\xrightarrow{\pi_{\textrm{PZ}_n}}\textrm{PZ}_{n-1}(\Sigma_\Gamma(L))\rightarrow1.$ In particular, we observe that the kernel $K$ of $\iota_{\textrm{PZ}_n}$ is non-trivial. This corrects Theorem 2.14 in [12](arXiv:2006.07106). Moreover, we use the presentation of the pure orbifold mapping class group $\textrm{PMap}^{\textrm{id},orb}_n(\Sigma_\Gamma(L))$ from [8] to determine $K$. Comparing these orbifold mapping class groups with the orbifold braid groups, reveals a surprising behavior: in contrast to the classical case, the orbifold braid group is a proper quotient of the orbifold mapping class group. This yields a presentation of the pure orbifold braid group which allows us to read off the kernel $K$., Comment: 48 pages, 36 figures

We define orbifold mapping class groups (with marked points) and study them using their action on certain orbifold analogs of arcs and simple closed curves. Moreover, we establish a Birman exact sequence for suitable subgroups of orbifold mapping class groups. The short exact sequence allows us to deduce finite presentations of these groups. This is the basis for a similar discussion of orbifold braid groups in [6]., Comment: 47 pages, 27 figures

We prove that the infinite family of asymptotic mapping class groups of surfaces of defined by Funar--Kapoudjian and Aramayona--Funar are of type $F_\infty$, thus answering questions of Funar-Kapoudjian-Sergiescu and Aramayona-Vlamis. As it turns out, this result is a specific instance of a much more general theorem which allows to deduce that asymptotic mapping class groups of Cantor manifolds, also introduced in this paper, are of type $F_\infty$, provide the underlying manifolds satisfy some general hypotheses. As important examples, we will obtain $F_\infty$ asymptotical mapping class groups that contain, respectively, the mapping class group of every compact surface with non-empty boundary, the automorphism group of every free group of finite rank, or infinite families of arithmetic groups. In addition, for certain types of manifolds, the homology of our asymptotic mapping class groups coincides with the stable homology of the relevant mapping class groups, as studied by Harer and Hatcher--Wahl., Comment: Incorporates comments from referees. To appear in Revista Matematica Iberoamericana

Allosteric effects are often underlying the activity of proteins and elucidating generic design aspects and functional principles which are unique to allosteric phenomena represents a major challenge. Here an approach which consists in the in silico design of synthetic structures which, as the principal element of allostery, encode dynamical long-range coupling among two sites is presented. The structures are represented by elastic networks, similar to coarse-grained models of real proteins. A strategy of evolutionary optimization was implemented to iteratively improve allosteric coupling. In the designed structures allosteric interactions were analyzed in terms of strain propagation and simple pathways which emerged during evolution were identified as signatures through which long-range communication was established. Moreover, robustness of allosteric performance with respect to mutations was demonstrated. As it turned out, the designed prototype structures reveal dynamical properties resembling those found in real allosteric proteins. Hence, they may serve as toy models of complex allosteric systems, such as proteins., Comment: 12 pages, 6 figures (plus Supplementary Information)

The rotary sequential hydrolysis of metabolic machine F1-ATPase is a prominent feature to reveal high coordination among multiple chemical sites on the stator F1 ring, which also contributes to tight coupling between the chemical reaction and central {\gamma}-shaft rotation. High-speed AFM experiments discovered that the sequential hydrolysis was maintained on the F1 ring even in the absence of the {\gamma} rotor. To explore how the intrinsic sequential performance arises, we computationally investigated essential inter-subunit couplings on the hexameric ring of mitochondrial and bacterial F1. We first reproduced the sequential hydrolysis schemes as experimentally detected, by simulating tri-site ATP hydrolysis cycles on the F1 ring upon kinetically imposing inter-subunit couplings to substantially promote the hydrolysis products release. We found that it is key for certain ATP binding and hydrolysis events to facilitate the neighbor-site ADP and Pi release to support the sequential hydrolysis. The kinetically feasible couplings were then scrutinized through atomistic molecular dynamics simulations as well as coarse-grained simulations, in which we enforced targeted conformational changes for the ATP binding or hydrolysis. Notably, we detected the asymmetrical neighbor-site opening that would facilitate the ADP release upon the enforced ATP binding, and computationally captured the complete Pi release through charge hopping upon the enforced neighbor-site ATP hydrolysis. The ATP-hydrolysis triggered Pi release revealed in current TMD simulation confirms a recent prediction made from statistical analyses of single molecule experimental data in regard to the role ATP hydrolysis plays. Our studies, therefore, elucidate both the concerted chemical kinetics and underlying structural dynamics of the inter-subunit couplings that lead to the rotary sequential hydrolysis of the F1 ring., Comment: 22 pages, 6 figures

A simple force-probe setup is employed to study the mechanical properties of transcription activator-like effector (TALE) proteins in computer experiments. It is shown that their spring-like arrangement benefits superelastic behaviour which is manifested by large-scale global conformational changes along the helical axis, thus linking structure and dynamics in TALE proteins. As evidenced from the measured force-extension curves the dHax3 and PthXo1 TALEs behave like linear springs, obeying Hooke's law, for moderate global structural changes. For larger deformations, however, the proteins exhibit nonlinearities and the structures become stiffer the more they are stretched. Flexibility is not homogeneously distributed over TALE structure, but instead soft spots which correspond to the RVD loop residues and present key agents in the transmission of conformational motions are identified., Comment: 6 pages, 4 figures

ATP-binding cassette (ABC) transporters are integral membrane proteins that mediate the exchange of diverse substrates across membranes powered by ATP hydrolysis. We report results of coarse-grained dynamical simulations performed for the bacterial heme transporter HmuUV. Based on the nucleotide-free structure, we have constructed a ligand-elastic-network description for this protein and investigated ATP-induced conformational motions in structurally resolved computer experiments. As we found, interactions with nucleotides resulted in generic motions which are functional and robust. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact and the transmembrane domains were rotated. The heme channel was broadened in the ligand-bound complex and the gate to the cytoplasm, which was closed in the nucleotide-free conformation, was rendered open by a mechanism that involved tilting motions of essential transmembrane helices. Based on our findings we propose that the HmuUV transporter behaves like a `simple' mechanical device in which, induced by binding of ATP ligands, linear motions of the nucleotide-binding domains are translated into rotational motions and internal tilting dynamics of the transmembrane domains that control gating inside the heme pathway., Comment: 11 pages, 4 figures

Hepatitis C virus helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings., Comment: 22 pages, 5 figures

Operation of an X-ray spectrometer based on a spherical variable line spacing grating is analyzed using dedicated ray-tracing software allowing fast optimization of the grating parameters and spectrometer geometry. The analysis is illustrated with optical design of a model spectrometer to deliver a resolving power above 20400 at photon energy of 930 eV (Cu L-edge). With this energy taken as reference, the VLS coefficients are optimized to cancel the lineshape asymmetry (mostly from the coma aberrations) as well as minimize the symmetric aberration broadening at large grating illuminations, dramatically increasing the aberration-limited vertical acceptance of the spectrometer. For any energy away from the reference, we evaluate corrections to the entrance arm and light incidence angle on the grating to maintain the exactly symmetric lineshape. Furthermore, we evaluate operational modes when these corrections are coordinated to maintain either energy independent focal curve inclination or maximal aberration-limited spectrometer acceptance. The results are supported by analytical evaluation of the coma term of the optical path function. Our analysis gives thus a recipe to design a high-resolution spherical VLS grating spectrometer operating with negligible aberrations at large acceptance and over extended energy range.

We describe the concepts and technical realization of the high-resolution soft-X-ray beamline ADRESS operating in the energy range from 300 to 1600 eV and intended for Resonant Inelastic X-ray Scattering (RIXS) and Angle-Resolved Photoelectron Spectroscopy (ARPES). The photon source is an undulator of novel fixed-gap design where longitudinal movement of permanent magnetic arrays controls not only the light polarization (including circular and 0-180 deg rotatable linear polarizations) but also the energy without changing the gap. The beamline optics is based on the well-established scheme of plane grating monochromator (PGM) operating in collimated light. The ultimate resolving power E/dE is above 33000 at 1 keV photon energy. The choice of blazed vs lamellar gratings and optimization of their profile parameters is described. Due to glancing angles on the mirrors as well as optimized groove densities and profiles of the gratings, high photon flux is achieved up to 1.0e13 photons/s/0.01%BW at 1 keV. Ellipsoidal refocusing optics used for the RIXS endstation demagnifies the vertical spot size down to 4 um, which allows slitless operation and thus maximal transmission of the high-resolution RIXS spectrometer delivering E/dE better than 11000 at 1 keV photon energy. Apart from the beamline optics, we give an overview of the control system, describe diagnostics and software tools, and discuss strategies used for the optical alignment. An introduction to the concepts and instrumental realization of the ARPES and RIXS endstations is given.

We introduce Andreev scattering (electron-hole conversion at an interface of a normal conductor to a superconductor) at the outer vertices of a quantum star graph and examine its effect on the spectrum. More specifically we show that the density of states in Andreev graphs is suppressed near the Fermi energy where a spectral gap may occur. The size and existence of such a gap depends on one side on the Andreev scattering amplitudes and, on the other side,on the properties of the electron-electron scattering matrix at the central vertex. We also show that the bond length fluctuations have a minor effect on the spectrum near the Fermi energy., Comment: 18 pages, written for proceedings of "Analysis on Graphs and Applications" (program at the Isaac Newton Institute, Cambridge, Jan-July 2007)

Thermal perturbation theory based on the resummation scheme by Braaten and Pisarski suffers from unscreened collinear singularities whenever outer momenta become light-like. A recently proposed improvement of the hard thermal loops by an additional resummation of an asymptotic mass promises to solve this problem. Here we present a detailed investigation of the next-to-leading order plasmon self-energy. It demonstrates the applicability and consistency of the improved scheme., Comment: 9 pages, REVTEX twocolumn, two postscript figures. Talk given at the 5th International Workshop on Thermal Field Theories and Their Applications, Regensburg, August 1998. (Now REVTEX, minor typos corrected)

The conventional results for hard thermal loops, which are the building blocks of resummed perturbation theory in thermal field theories, have collinear singularities when external momenta are light-like. It is shown that by taking into account asymptotic thermal masses these singularities are removed. The thus improved hard thermal loops can be summarized by compact gauge-invariant effective actions, generalizing the ones found by Taylor and Wong, and by Braaten and Pisarski., Comment: 21 pages, LaTeX, requires elsart.sty and epsf.sty, 1 postscript figure, compressed and uuencoded, (new reference [9] added)

All the next-to-leading order contributions to the quasi-particle dispersion laws of a quark-gluon plasma which due to infrared singularities are sensitive to the magnetic-mass scale are calculated using Braaten-Pisarski resummation. These relative-order-$g\ln(g)$ corrections are shown here to generally contribute to the dynamical screening of gluonic fields with frequencies below the plasma frequency as well as to the damping of propagating gluonic and fermionic quasi-particles. In the limit of vanishing wave-vector the infrared singularities disappear, but in a way that raises the possibility for formally higher orders of the Braaten-Pisarski scheme to equally contribute at next-to-leading order when the wave-vector is of the order of or less than the magnetic-mass scale. This is argued to be a problem in particular for the fermionic damping rate., Comment: 19 pages (LaTeX), 1 figure (uuencoded postscript) included by epsf.sty

The next-to-leading order contribution $\d\P\omn (\o ,\vc q )$ to the polarization function of the hot gluon system is analysed at non-zero wave vectors $\vc q \,$. Using Braaten-Pisarski resummation and general covariant gauges, $\d\P\omn$ is found to be gauge-fixing independent and transverse on the longitudinal mass-shell. The real part of the longitudinal component $\d\P_\ell$ is UV and IR stable (for real $q$). At imaginary $q$ it is IR singular, and at the point $\o=0$, $q^2=-3m^2$ it coincides with the result of Rebhan for next-to-leading order Debye screening. When $q$ approaches the lightcone, $\d\P_\ell $ diverges like $1 / \wu {\o^2 - q^2} $, reflecting the breakdown of the Braaten-Pisarski decomposition scheme in this limit., Comment: 14 pages, LaTeX