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Intramolecular ion-pair interactions yield shape and functionality to many molecules. With proper orientation, these interactions overcome steric factors and are responsible for the compact structures of several peptides. In this study, we present a thermodynamic cycle based on isoelectronic and alchemical mutation to estimate intramolecular ion-pair interaction energy. We determine these energies for 26 benchmark molecules with common ion-pair combinations and compare them with results obtained using intramolecular symmetry-adapted perturbation theory. For systems with long linkers, the ion-pair energies evaluated using both approaches deviate by less than 2.5% in vacuum phase. The thermodynamic cycle based on density functional theory facilitates calculations of salt-bridge interactions in model tripeptides with continuum/microsolvation modeling, and four large peptides: 1EJG (crambin), 1BDK (bradykinin), 1L2Y (a mini-protein with a tryptophan cage), and 1SCO (a toxin from the scorpion venom)., version 3, experimental relevance of salt-bridge interaction energy is discussed in the introduction, and minor revisions of figures

We classify generic unfoldings of germs of antiholomorphic diffeomorphisms with a parabolic point of codimension 1 (i.e. a double fixed point) under conjugacy. These generic unfolding depend on one real parameter. The classification is done by assigning to each such germ a weak and a strong modulus, which are unfoldings of the modulus assigned to the antiholomorphic parabolic point. The weak and the strong moduli are unfoldings of the \'Ecalle-Voronin modulus of the second iterate of the germ which is a real unfolding of a holomorphic parabolic point. A preparation of the unfolding allows to identify one real analytic canonical parameter and any conjugacy between two prepared generic unfoldings preserves the canonical parameter. We also solve the realisation problem by giving necessary and sufficient conditions for a strong modulus to be realized. This is done simultaneously with solving the probem of the existence of an antiholomorphic square root to a germ of generic analytic unfolding of a holomorphic parabolic germ. As a second application we establish the condition for the existence of a real analytic invariant curve., Comment: 43 pages, 18 figures

We study Kauffman's model of folded ribbon knots: knots made of a thin strip of paper folded flat in the plane. The folded ribbonlength is the length to width ratio of such a ribbon knot. We give upper bounds on the folded ribbonlength of 2-bridge, $(2,q)$ torus, twist, and pretzel knots, and these upper bounds turn out to be linear in the crossing number. We give a new way to fold $(p,q)$ torus knots and show that their folded ribbonlength is bounded above by $2p$. This means, for example, that the trefoil knot can be constructed with a folded ribbonlength of 6. We then show that any $(p,q)$ torus knot $K$ with $p\geq q>2$ has a constant $c>0$, such that the folded ribbonlength is bounded above by $c\cdot Cr(K)^{1/2}$. This provides an example of an upper bound on folded ribbonlength that is sub-linear in crossing number., 33 pages, 26 figures. Second version corrects minor errors as well as Theorem 4: $(p,q)$ torus links with $p\geq q\geq 2$ have folded ribbonlength bounded above by $2p$

We give complete geometric invariants of cobordisms of framed fold maps. These invariants consist of two types. We take the immersion of the fold singular set into the target manifold together with information about non-triviality of the normal bundle of the singular set in the source manifold. These invariants were introduced in the author's earlier works. Secondly we take the induced stable partial framing on the source manifold whose cobordisms were studied in general by Koschorke. We show that these invariants describe completely the cobordism groups of framed fold maps into R^n. Then we are looking for dependencies between these invariants and we study fold maps of 4k-dimensional manifolds into R^2. We construct special fold maps which are representatives of the fold cobordism classes and we also compute cobordism groups. We obtain a Poincare-Hopf type formula, which connects local data of the singularities of a fold map of an oriented 4k-dimensional manifold M to the signature of M. We also study the unoriented case analogously and prove a similar formula about the twisting of the normal bundle of the fold singular set., 39 pages, 3 figures, revised

A necklace can be considered as a cyclic list of n red and n blue beads in an arbitrary order. In the necklace folding problem the goal is to find a large crossing-free matching of pairs of beads of different colors in such a way that there exists a “folding” of the necklace, that is a partition into two contiguous arcs, which splits the beads of any matching edge into different arcs. We give counterexamples for some conjectures about the necklace folding problem, also known as the separated matching problem. The main conjecture (given independently by three sets of authors) states that [Formula presented], where μ is the ratio of the maximum number of matched beads to the total number of beads. We refute this conjecture by giving a construction which proves that μ≤2−2

One of the grand challenges of utilizing machine learning for the discovery of innovative new polymers lies in the difficulty of accurately representing the complex structures of polymeric materials. Although a wide array of hand-designed polymer representations have been explored, there has yet to be an ideal solution for how to capture the periodicity of polymer structures, and how to develop polymer descriptors without the need for human feature design. In this work, we tackle these problems through the development of our periodic polymer graph representation. Our pipeline for polymer property predictions is comprised of our polymer graph representation that naturally accounts for the periodicity of polymers, followed by a message-passing neural network (MPNN) that leverages the power of graph deep learning to automatically learn chemically-relevant polymer descriptors. Across a diverse dataset of 10 polymer properties, we find that this polymer graph representation consistently outperforms hand-designed representations with a 20% average reduction in prediction error. Our results illustrate how the incorporation of chemical intuition through directly encoding periodicity into our polymer graph representation leads to a considerable improvement in the accuracy and reliability of polymer property predictions. We also demonstrate how combining polymer graph representations with message-passing neural network architectures can automatically extract meaningful polymer features that are consistent with human intuition, while outperforming human-derived features. This work highlights the advancement in predictive capability that is possible if using chemical descriptors that are specifically optimized for capturing the unique chemical structure of polymers.

The Mixed Finite Element (MFE) method is well adapted for the simulation of fluid flow in heterogeneous porous media. However, when employed for the transport equation, it can generate solutions with strong unphysical oscillations because of the hyperbolic nature of advection. In this work, a robust upwind MFE scheme is proposed to avoid such unphysical oscillations. The new scheme is a combination of the upwind edge/face centred Finite Volume (FV) method with the hybrid formulation of the MFE method. The scheme ensures continuity of both advective and dispersive fluxes between adjacent elements and allows to maintain the time derivative continuous, which permits employment of high order time integration methods via the Method of Lines (MOL). Numerical simulations are performed in both saturated and unsaturated porous media to investigate the robustness of the new upwind-MFE scheme. Results show that, contrarily to the standard scheme, the upwind-MFE method generates stable solutions without under and overshoots. The simulation of contaminant transport into a variably saturated porous medium highlights the robustness of the proposed upwind scheme when combined with the MOL for solving nonlinear problems.

Helical curling and spiral structure are very common in nature, which inspire researchers to create various forms of helical configurations and actuators. The helically deformable actuators perform asymmetric deformations and show different chirality, which means that they can be left handed or right handed. However, the mechanism of helical curling and especially how the key factors influence the chirality of the actuator have not been systematically explained and well understood. In this study, we focus on the typical double-layer soft actuator composed of an active (expansion) layer and a passive (supporting) layer and investigate the effect of key factors (expansion coefficient, Young's modulus, relative thickness) on the chirality of the helical actuation or morphing by comprehensive finite element analyses. It was found that (i) the anisotropic expansion of the active layer or (ii) the anisotropic Young's modulus of the active or the passive layer is indispensable for helical curling. In Case (i), the actuator curls along the direction of greater expansion of the active layer. In Case (ii), the actuator curls along the direction of closer moduli match of the active and passive layers, and their relative thickness also affects the helical morphing of the actuator. In practice, the above two factors may cooperate or compete with each other, and the dominant one determines the chirality. This work gives the general rules for helical morphing forms and can provide guidance for the design and preparation of spiral actuators and soft robots in the future.

Currently, DNA strand displacement is often used to build neural networks or solve logical problems. While there are few studies on the use of DNA strand displacement to solve the higher order equations. In this paper, the catalysis, degradation, annihilation and adjusted reaction modules are built through DNA strand displacement. The chemical reaction networks of the corresponding higher order equations and simultaneous equations are established through these modules, and these chemical reaction networks can be used to build analog circuits to solve binary primary simultaneous equations and binary quadratic simultaneous equations. Finally, through Visual DSD software verification, this design can realize the solution of binary primary simultaneous equations and binary quadratic simultaneous equations, which provides a reference for DNA computation in the future.

This article treats smooth weak Fano 3-folds having an extremal ray of type D. Smooth weak Fano 3-folds with an extremal ray of type D except of degree 6 are classified into 47 deformation types., Comment: 67 pages

We find an explicit formula for the conformal vector of any quantum affine W-algebra in its free field realization.

A long-standing challenge in protein biophysics is to understand protein quake in myoglobin—the structural dynamics responsible for redistributing the excess heme energy after photolysis. Despite extensive efforts, the molecular mechanism of this process remains elusive. Using the energy flow theory, we uncovered a fundamental new phenomenon: the heme energy is redistributed by energy waves with a ubiquitous fundamental frequency and two overtones. Energy waves emanate from the heme into the myoglobin backbone via a conduit of five consecutive dihedrals of the proximal histidine, then travel quickly along the backbone to reach sidechains across the protein. This mechanism is far more effective than the diffusion-based mechanism from previous studies because waves are systematic while diffusion is random. To propagate energy waves, coordinates must cooperate, resulting in collective modes that are singular vectors of the generalized work functional. These modes show task partitioning: a handful of high-energy modes generate large-scale breathing motion, which loosens up the protein matrix to enable hundreds of low-energy vibrational modes for energy transduction.

To ensure the effectiveness of the inductive power transfer (IPT) systems for high power applications, the multiple coils are being used. But the cross-couplings among the same side coils reduce the efficiency of the system. Thus, the decoupling coils are commonly used to mitigate the same side couplings in multiple transmitters and receivers system. The decoupling coils are either used outside of the main coils or concentric with the main coils. In both cases, these decoupling coils do not take part in the power transmission and have some adverse effects on the system performance. In this paper, a new IPT system with dual transmitters and dual receivers with integrated decoupling coils is introduced. Besides mitigating the mutual inductances of the same side coils, the proposed decoupling coils are also taking part in power transmission. In addition, the proposed coils also have good misalignment performance. A three-dimensional finite element analysis (FEA) tool ANSYS MAXWELL is used to investigate the proposed magnetic coupler. A scaled-down experimental setup is used to verify the feasibility of the proposed structure. The maximum dc-dc efficiency of this system is 93.14 % while delivering 700 W to the load with a 200 mm air gap.

We investigate the swelling of polymer model networks prepared at different polymer volume fractions and in solvents of different quality. We extend the existing theory to describe residual bond orientations (the vector and the tensor order parameters) for theta, good, and athermal solvents and put these relations in context with modulus at preparation conditions and the equilibrium degree of swelling. We find a good agreement with the assumption of affine swelling for the weakly entangled networks of our study. The same scaling relations (up to numerical coefficients) are obtained for the vector order parameter, m, and the tensor order parameter, S, as a function of the prepration conditions, network structure, the equilibrium degree of swelling, Q, and the modulus at swelling equilibrium, G. We obtain m\propto Q^{-2} and G\propto m^{3/2} for swelling in theta solvents and m\propto Q^{-1.08} with G\propto m^{2.14} in the good-solvent regime, in both cases independent of preparation conditions. Modulus and residual bond orientation are related by G\propto\phi_{0}m and G\propto\phi_{0}^{1.23}m as a function of the preparation polymer volume fraction \phi_{0} for theta solvents and good solvents, respectively. Computer simulations and experimental data for the good-solvent regime show good agreement with the predictions.

Due to their unique topology of having no chain ends, dilute solutions of ring polymers exhibit behaviour distinct from their linear chain counterparts. The universality of their static and dynamic properties, as a function of solvent quality $z$ in the thermal crossover regime between $\theta$ and athermal solvents, is studied here using Brownian dynamics simulations. The universal ratio $U_{\text{RD}}$ of the radius of gyration $R_g$ to the hydrodynamic radius $R_H$ is determined, and a comparative study of the swelling ratio $\alpha_g$ of the radius of gyration, the swelling ratio $\alpha_H$ of the hydrodynamic radius, and the swelling ratio $\alpha_X$ of the mean polymer stretch $X$ along the $x$-axis, for linear and ring polymers, is carried out. The ratio $U_{\text{RD}}$ for dilute ring polymer solutions is found to converge asymptotically to a constant value as $z \to \infty$, which is a major difference from the behaviour of solutions of linear chains, where no such asymptotic limit exists. Additionally, the ratio of the mean stretch along the $x$-axis to the hydrodynamic radius, $(X/R_H)$, is found to be independent of $z$ for polymeric rings, unlike in the case for linear polymers. These results indicate a fundamental difference in the scaling of static and dynamic properties of rings and linear chains in the thermal crossover regime., Comment: 20 pages, 14 figures. To appear in the Special Issue of the Journal of Rheology on Ring Polymers

We theoretically investigate the extractable work in single molecule unfolding-folding experiments with applied feedback. Using a simple two-state model, we obtain a description of the full work distribution, from discrete to continuous feedback. The effect of the feedback is captured by a detailed fluctuation theorem, accounting for the information aquired. We find analytical expressions for the average work extraction as well as an experimentally measurable bound thereof, which becomes tight in the continuous feedback limit. We further determine the parameters for maximal power, or rate of work extraction. While our two-state model only depends on a single, effective transition rate, we find quantitative agreement with Monte Carlo simulations of DNA hairpin unfolding-folding dynamics., Comment: 5 pages, 4 figures, 5 pages of supplementary information

The negative internal energetic contribution to the elastic modulus (negative energetic elasticity) has been recently observed in polymer gels. This finding challenges the conventional notion that the elastic moduli of rubberlike materials are determined mainly by entropic elasticity. However, the microscopic origin of negative energetic elasticity has not yet been clarified. Here, we consider the $n$-step interacting self-avoiding walk on a cubic lattice as a model of a single polymer chain (a subchain of a network in a polymer gel) in a solvent. We theoretically demonstrate the emergence of negative energetic elasticity based on an exact enumeration up to $n=20$ and analytic expressions for arbitrary $n$ in special cases. Furthermore, we demonstrate that the negative energetic elasticity of this model originates from the attractive polymer--solvent interaction, which locally stiffens the chain and conversely softens the stiffness of the entire chain. This model qualitatively reproduces the temperature dependence of negative energetic elasticity observed in the polymer-gel experiments, indicating that the analysis of a single chain can explain the properties of negative energetic elasticity in polymer gels., Comment: 6 pages, 5 figures (main text); 21 pages, 4 figures (Supplemental Material)

High-performance osmotic energy conversion requires both large ionic throughput and high ionic selectivity, which can be significantly promoted by exterior surface charges simultaneously, especially for short nanopores. Here, we investigate the enhancement of ionic diffusion by charged exterior surfaces under various conditions and explore corresponding effective charged areas. From simulations, ionic diffusion is promoted more significantly by exterior surface charges through nanopores with a shorter length, wider diameter, and larger surface charge density, or under higher salt gradients. Effective widths of the charged ring regions near nanopores are reversely proportional to the pore length and linearly dependent on the pore diameter, salt gradient, and surface charge density. Due to the important role of effective charged areas in the propagation of ionic diffusion through single nanopores to cases with porous membranes, our results may provide useful guidance to the design and fabrication of porous membranes for practical high-performance osmotic energy harvesting., 24 Pages,5 figures

This paper investigates the secrecy outage performance of a downlink cooperative nonorthogonal multiple access- (NOMA-) assisted hybrid satellite-terrestrial network, where a satellite source communicates with two terrestrial users based on NOMA, in the presence of a terrestrial eavesdropper. We assume that there is no direct link between the satellite source and the far terrestrial user, and the near terrestrial user acts as a relay to forward the information to the far terrestrial user. The near user is assumed to support both half-duplex mode and the full-duplex mode for information relaying. We derive the closed-form exact expressions for the secrecy outage probability (SOP) of the near user, as well as the closed-form approximate expressions for the SOP of the far user based on the Gaussian-Chebyshev quadrature. Theoretical results are validated by conducting simulations. The impacts of various system parameters on the performance comparison between the half-duplex mode and full-duplex mode are investigated. Particularly, the full-duplex mode is shown to outperform the half-duplex mode when the received signal-to-noise ratio (SNR) at the near user is low or the residual self-interference is low.

金沢大学ナノ生命科学研究所, Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid–liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe., Embargo Period 12 months / CC BY-NC-ND 4.0

To understand the relationships between channel size and ion selectivity, we have developed a new type of artificial ion channel based on pore-forming helical polymers consisting of phenanthroline-...

Biosensor behaviour is characterised by non-linear differential equations that describe well-defined physical, chemical, and biological processes. Mathematical modelling of these biosensors is highly desirable since they have many applications. These models enable the prediction of a variety of their properties. In this study, the cyclic conversion of the substrate in an amperometric biosensor with an oxidase enzyme membrane electrode is studied using a mathematical model. The governing parameters for the Michaelis–Menten kinetics of enzymatic reactions are the enzyme kinetic and diffusion rates across the enzymatic layer. In this paper, we solved the non-linear equations analytically and numerically for all experimental values of parameters. This problem is simulated in MATLAB® v2016b software using the PDE solver. Our analytical solutions are compared to simulation results to validate the proposed model.

Homogeneous magnetic field is widely used in various applications, and Helmholtz and Merritt coils are the most commonly used homogeneous field generators. However, only the field homogeneity at the center point is concerned in their design, which leads to restriction for most applications where a certain volume of homogeneous field is required. This indicates that traditional coil configurations can be further optimized. Based upon a comprehensive definition of homogeneous field, improved three-coil and four-coil configurations are proposed in this paper. Practical formulae with normalized coil parameters are given to provide a convenient tool for designers. These formulae establish relationships between coil parameters and the required homogeneous field. The accuracy of the formulae is verified by the finite-element analysis. Comparisons with Merritt coils show that, when getting the same homogeneous field, the improved coils can reduce both power loss and conductor mass by up to 24.8%. Through a comparison among main coil configurations, the improved four-coil configuration is recommended for homogeneous magnetic field generation. For high-intensity magnetic field applications, the winding cross-section effect is analyzed. At last, experiments are performed to verify the theoretical analysis, and the reason why the improved coils have better performance than traditional ones is revealed.

Coil design and operating frequency are key factors impacting the efficiency of inductive power transfer system. This paper presents the modeling of PCB spiral coils, design optimization and analysis on coil geometry and operating frequency for medium voltage applications, such as auxiliary power supplies for medium voltage converters. Analytic model considering the geometric distribution of the magnetic field is proposed to calculate with high accuracy equivalent electrical parameters of coils. For a defined design space and constraints, a large number of coils are designed in order to determine their performances and select optimal coil geometries. Selected coil designs are prototyped and experimentally verified under design-specific conditions. In addition, further characterization is performed considering variations of several parameters that can be encountered in practice.

Silk is a semidilute solution of randomly coiled associating polypeptide chains that crystallize following the stretch-induced disruption, in the strong extensional flow of extrusion, of the solvation shell around their amino acids. We propose that natural silk spinning exploits both the exponentially broad stretch distribution generated by associating polymers in extensional flow and the criterion of a critical concentration of sufficiently stretched chains to nucleate flow-induced crystallization. To investigate the specific-energy input needed to reach this criterion in start-up flow, we have coupled a model for the Brownian dynamics of a bead-spring-type chain, whose beads represent coarse-grained Gaussian chain segments, to the stochastic, strain-dependent binding and unbinding of their associations. We have interpreted the simulations with the aid of analytic calculations on simpler, tractable models with the same essential physical features. Our simulations indicate that the associations hamper chain alignment in the initial slow flow, but, on the other hand, facilitate chain stretching at low specific work at later, high rates. We identify a minimum in the critical specific work at a strain rate just above the stretch transition (i.e., where the mean stretch diverges), which we explain in terms of analytical solutions of a two-state master equation. We further discuss how the silkworm appears to exploit the chemical tunability of the associations to optimize chain alignment and stretching in different locations along the spinning duct: this delicate mechanism also highlights the potential biomimetic industrial benefits of chemically tunable processing of synthetic association polymers.

The topology of polymers plays an essential role in their chemical, physical and biological properties. However, their effects on chirality-related functions remain unclear. Here, we reported the topology-controlled chirality expression in the chiral supramolecular system for the first time. Two topological supramolecular polymers, hyperbranched (HP) and linear (LP) supramolecular polymers produced by the host–guest interactions of branched and linear monomers, respectively, exhibited completely different chirality expressions despite the same molecular chirality of their monomers. Significantly, due to the branch points and strong steric hindrance existing in HP, cis-HP showed an enhanced and sign-inverted Cotton effect in the n–π* bands compared with cis-LP, as a result that the distinctive chirality induction and transfer were controlled by the topological skeletons. This topology-controlled chirality induction and transfer in the photoswitchable supramolecular polymers not only enables us to elucidate the in-depth effects of topology on the chiral expression in biopolymers but also inspires the design of chiroptical and bioinspired materials.

This paper tackles the topic of conformable Laplace transform. The authors aim at discussing its existence by exploring and providing the kind of functions that possess a conformable Laplace transform. Furthermore, the comparison theorem of conformable improper integrals is presented to further explain and justify the existence of conformable Laplace transform for some functions. The uniqueness is also established in order to determine the inverse of conformable Laplace transform for functions. Moreover, we present a table of the conformable Laplace transform of the usual functions. Finally, as an application, we use the conformable Laplace transform for solving some fractional differential equations.

Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism which enables lower error at the cost of higher energy dissipation. Elucidating physicochemical constraints for global minimization of dissipation and error is important for understanding enzyme evolution. Here, we identify theoretically a fundamental error-cost bound which tightly constrains the performance of proofreading networks under any parameter variations preserving the rate discrimination between substrates. The bound is kinetically controlled, i.e. completely determined by the difference between the transition state energies on the underlying free energy landscape. The importance of the bound is analyzed for three biological processes. DNA replication by T7 DNA polymerase is shown to be nearly optimized, i.e. its kinetic parameters place it in the immediate proximity of the error-cost bound. The isoleucyl-tRNA synthetase (IleRS) of E. coli also operates close to the bound, but further optimization is prevented by the need for reaction speed. In contrast, E. coli ribosome operates in a high-dissipation regime, potentially in order to speed up protein production. Together, these findings establish a fundamental error-dissipation relation in biological proofreading networks and provide a theoretical framework for studying error-dissipation trade-off in other systems with biological discrimination., 14 (main text)+ 19 (supporting information) pages, 6+4 figures

Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are non-ergodic, including bistable Holliday junctions and part of a bistable origami. Taking an origami compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results establish an efficient framework to study free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications., 4 figures, 7 SI figures, 3 SI tables, 2 SI discussions, methods

An interior penalty discontinuous Galerkin method is devised to approximate minimizers of a linear folding model by discontinuous isoparametric finite element functions that account for an approximation of a folding arc. The numerical analysis of the discrete model includes an a priori error estimate in case of an accurate representation of the folding curve by the isoparametric mesh. Additional estimates show that geometric consistency errors may be controlled separately if the folding arc is approximated by piecewise polynomial curves. Various numerical experiments are carried out to validate the a priori error estimate for the folding model.

Characterizing critical current IC of Nb3Sn strands as function of a strain is very important for large high field superconducting magnet applications such as the superconducting outsert coil of the series-connected hybrid at the NHMFL and the ITER magnets. Apparatuses for measuring IC versus longitudinal strain and transverse stress have been developed and used at the NHMFL. We have characterized the IC strain sensitivities of a few candidate strands for the series-connected-hybrid. In addition, IC irreversibility strains are measured for the recently developed ITER high JC strands. The different strain sensitivities for different strands are discussed., 4 pages, 6 figures

We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the internal-to-Cartesian process relies on correctly predicting chemically subtle correlations among the internal coordinates themselves, and learning these correlations increases the fidelity of the Cartesian representation. This general problem has been solved with machine learning for proteins, but with appropriately formulated data is extensible to any type of chain biomolecule including RNA, DNA, and lipids. We show that the internal-to-Cartesian process relies on correctly predicting chemically subtle correlations among the internal coordinates themselves, and learning these correlations increases the fidelity of the Cartesian representation. We developed a machine learning algorithm, Int2Cart, to predict bond lengths and bond angles from backbone torsion angles and residue types of a protein, and allows reconstruction of protein structures better than using fixed bond lengths and bond angles, or a static library method that relies on backbone torsion angles and residue types on a single residue. The Int2Cart algorithm has been implemented as an individual python package at https://github.com/THGLab/int2cart.

Let $ \mathcal{A} $ be a commutative and semisimple Banach algebra with identity norm one and $ G $ be an abelian locally compact Hausdorff group. In this paper, we study BSE-Property for $L^1(G,\mathcal A)$ and show that $L^1(G,\mathcal A)$ is a BSE algebra if and only if $\mathcal A$ is so., arXiv admin note: text overlap with arXiv:2206.07123

Isoflux tension propagation (IFTP) theory and Langevin dynamics (LD) simulations are employed to study the dynamics of channel-driven polymer translocation in which a polymer translocates into a narrow channel and the monomers in the channel experience a driving force fc. In the high driving force limit, regardless of the channel width, IFTP theory predicts τ ∝ f βc for the translocation time, where β = −1 is the force scaling exponent. Moreover, LD data show that for a very narrow channel fitting only a single file of monomers, the entropic force due to the subchain inside the channel does not play a significant role in the translocation dynamics and the force exponent β = −1 regardless of the force magnitude. As the channel width increases the number of possible spatial configurations of the subchain inside the channel becomes significant and the resulting entropic force causes the force exponent to drop below unity., Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe; 1292

We describe the Amber tool for proving and refuting the termination of a class of probabilistic while-programs with polynomial arithmetic, in a fully automated manner. Amber combines martingale theory with properties of asymptotic bounding functions and implements relaxed versions of existing probabilistic termination proof rules to prove/disprove (positive) almost sure termination of probabilistic loops. Amber supports programs parameterized by symbolic constants and drawing from common probability distributions. Our experimental comparisons give practical evidence of Amber outperforming existing state-of-the-art tools., Accepted to FM 2021

This paper utilizes computer simulations to physical science and applications. High-temperature plasmas and macromolecules are reviewed first including magnetic reconnection in space and DNA translocation of the human body. The second topic is that water and salt-added saline solution are heated in elevated temperatures by microwaves, while the ice is frozen in complete ice structures and cannot be heated. The third topic is that a carbon-gold compound is driven by relativistic electromagnetic radiations and is accelerated as a nanotube accelerator.

Theoretical expressions for the intrinsic viscosity, the Huggins coefficient, zero-shear viscosity, and storage and loss moduli for stiff-chain polymer solutions are reviewed. Especially, the mean-field Green function method is explained in detail to consider the intermolecular collision effect on the rheological properties of concentrated stiff-chain polymer solutions, by applying the method to monodisperse and polydisperse straight cylinders and monodisperse fuzzy cylinder models. The theoretical expressions reviewed are compared with experimental results for aqueous solutions of two rigid helical polysaccharides, schizophyllan and xanthan.

Hypothesis Mixtures of colloids and supramolecular polymers may exhibit stimuli-responsive phase behaviour. However, in theoretical descriptions of such systems, the polymers are commonly described either as flexible chains or as rigid rods, while in experimental systems supramolecular polymers usually fall in between these two limits. We expect the flexibility of the polymers to have a profound effect on the stimuli-responsive phase behaviour. Theory We propose a general approach to predict the phase behaviour of colloidal hard spheres mixed with covalent or supramolecular polymers of arbitrary persistence length using free volume theory and an interpolation between flexible and rigid chains. Findings The binodals are predicted to shift to lower monomer concentrations as the persistence length is increased, making the polymers more efficient depletants. The persistence length is therefore an additional degree of freedom for manipulating the phase behaviour of colloid–polymer mixtures. We show that by manipulating the persistence length of temperature responsive supramolecular polymers, a wide range of phase diagrams with various topologies can be obtained. For example, we find phase diagrams with a critical point but no triple point or displaying two triple points for temperature-sensitive supramolecular polymers mixed with hard spheres.

The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of a protein in a protein folding system. We plotted the various energies against the root mean square deviation, required as a reference structure. Herein, we replotted the various energies against the end-to-end distance between the N- and C-termini, which is not a required reference and is experimentally measurable. The solvation free energies for all proteins tend to be low as the end-to-end distance increases, whereas the conformational energies tend to be low as the end-to-end distance decreases. The end-to-end distance is one of interesting measures to study the behavior of proteins.

The title compound, C7H7N3S, which has potential biological activity, can be used as a ligand in metal complexation. This compound exists as the thione tautomer in the crystal phase, which is confirmed by the study of its molecular structure. The amino group has pyramidal configuration. In the crystal phase, the two independent molecules in the asymmetric unit form tetramers as a result of N—H...S hydrogen bonds. These tetramers are linked by N—H...N hydrogen bonds, forming chains/tubes in the [010] direction. The Hirshfeld surface analysis showed that the highest contribution to the total surface is provided by H...H interactions as well as S...H/H...S and C...H/H...C contacts associated with X—H...S hydrogen bonds and X—H...C(π) interactions.

The aim of this review is to present a summary of the published papers of the heat transfer and pressure drop characteristics for single-phase flow in helically coiled tubes. The effect of geometrical parameters such as curvature ratio, coil pitch and working conditions such as Reynolds number, Dean number, flow rate and flow arrangement on heat transfer and pressure drop in helically coiled tubes are determined in the light of the experimental, numerical and analytical studies in the literature. Also, the effect of using nanofluids in comparison with conventional fluids, using enhanced surfaces such as corrugated, micro-finned, dimpled with regards to smooth surfaces and wire coil insert usage in helically coiled tubes are discussed. The correlations proposed for determination of Nusselt number and friction factor in helically coiled tubes are presented in detail separately under laminar and turbulent flow regimes. The studies show that usage of helically coiled tube merely gives higher heat transfer rate and pressure drop in comparison to straight one, additionally, the heat transfer performance increases with the inclusion of the combination of other passive heat transfer enhancement methods to helically coiled tube. Moreover, the subject of single-phase flow in helically coiled tubes is ascertained to be worth researching due to the fact that there are limited number of studies and is still no empirical or analytical model/correlation in the case of using enhanced surfaces and wire coil insert. Forthcoming researches on this issue in the near future will be considered as pioneer ones in literature.

By using neutron crystallography, we determined the precise three-dimensional structure of a copper-containing nitrite reductase (CuNIR), a protein enzyme involved in the nitrogen cycle. Our data visualizes the positions of hydrogen atoms at the catalytic site and a hydroxide-bound state of CuNIR, which has been proposed by quantum chemical calculations. Other experimental findings including a tight hydrogen bond on a possible electron transfer pathway also supports previous results from theoretical chemistry.

In this paper, a new method for pesticide detection based on porous silicon microcavities was proposed. First, the aptamer of acetamiprid was fixed in the functionalized porous silicon microcavity. Then, the complementary strand of the aptamer modified with graphene quantum dots was hybridized with the aptamer, and the effective refractive index of the porous silicon microcavity increased. When acetamiprid was added, it bound to the aptamer due to its stronger specificity. The aptamer separated from the complementary strand of the coupled graphene quantum dots and bound to acetamiprid, resulting in a decrease in the effective refractive index, and its central wavelength of reflection spectrum was blue shifted, and the blueshift increased with the increase of acetamiprid concentration. The relationship between the change in central wavelength and the concentration of acetamiprid was analysed, and the detection limit of acetamiprid was 151 nm.

In this paper, a dual-loop active shielding coil directly connected in series with the primary coil is proposed to reduce the leakage magnetic field while eliminating the additional coupling between the shielding coil and the receiving coil of a wireless electric vehicle (EV) charging system. Parameter design strategy featuring system efficiency improvement and shielding coil cost reduction using multi-objective optimization algorithm is proposed. Finally, a 1.5 kW with 19 cm air gap prototype is fabricated to verify the analytical results and investigate the influence of the shielding coil over the system parameters. The results prove that the proposed active shielding coil shows its advantage on the system transmission performance and the shielding effectiveness on the target surface comparing to conventional aluminum shielding.

Sensor layout of biomagnetic measurement systems is measured using a multiple coil array that generates a magnetic signal. However, the results of the sensor array measurement included the error of the coil array because the coil array was not calibrated. In this paper, we proposed a calibration method to obtain the effective geometry and uncertainty of the coil array. The calibration was performed based on the X-ray CT measurements and numerical analysis of the position and shape of the coils. The differences between the designed and calibrated coil array geometries were 0.6 mm, 0.7°, and 0.3 mm with respect to the center position, orientation of the normal vector, and radius of the coils, respectively. The uncertainty of the calibration was 0.3 mm and 1.70 in terms of the dimension and orientation, respectively. We measured the sensor array layout of a magnetoencephalography (MEG) system using a calibrated coil array geometry. The source localization accuracy of the MEG system was improved compared with that of the sensor array layout obtained using the designed coil array geometry. We revealed the necessity of calibrating the coil array, regardless of the precision of the fabrication.

Physics and physical chemistry are an important thread in computational protein design, complementary to knowledge-based tools. They provide molecular mechanics scoring functions that need little or no ad hoc parameter readjustment, methods to thoroughly sample equilibrium ensembles, and different levels of approximation for conformational flexibility. They led recently to the successful redesign of a small protein using a physics-based folded state energy. Adaptive Monte Carlo or molecular dynamics schemes were discovered where protein variants are populated as per their ligand-binding free energy or catalytic efficiency. Molecular dynamics have been used for backbone flexibility. Implicit solvent models have been refined, polarizable force fields applied, and many physical insights obtained.

The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently, optical sensors have been shown to allow noninvasive time-resolved measurements of the dynamic polarizability of single-molecules. Here we introduce a method to efficiently predict the dynamic polarizability from the atomic configuration of a given macromolecule. This provides a means to connect the measured dynamic polarizability to the underlying structure of the molecule, and therefore to connect temporal measurements to structural dynamics. To illustrate the methodology we calculate the change in polarizability as a function of time based on conformations extracted from molecular dynamics simulations and using different conformations of motor proteins solved crystalographically. This allows us to quantify the magnitude of the changes in polarizablity due to thermal and functional motions.

For amorphous polymers, restoring forces are generated by the progressive orientation of the macromolecular chains in the stretching direction leading to a decrease in the system entropy. Orienting the chains in the future stretching direction thus reduces the entropy variation induced by the stretching and limits the entropic restoring force magnitude. Entropic restoring forces created during stretching have been correlated to the number of junction points by previous studies. Reducing the entanglement density (i.e., the number of junction points) is supposed to limit the entropic restoring force magnitude. In this study, the influence of blend ratio of low molecular weight wax and orientation level on the mechanical properties of the thin films, especially the elastic recovery, were evaluated. Elastic energy strain recovery was calculated from hysteresis curve obtained during 60% loading (stretch) and unloading (recovery) cycle and compared to rheological and orientation measurement. It has been shown that a decrease in entanglement density can minimize elastic recovery, Nevertheless, a compromise must be found, in order to limit the permanent deformation caused by chain flow. Macromolecular orientation is also a way to adjust the film mechanical properties. A LDPE 3 × 3 biaxial orientation leads to a 25% reduction in transversal direction elastic recovery (compared to MDO cast film) without altering machine direction mechanical behavior. However, for ethylene vinyl acetate, the uniaxial macromolecular orientation seems to impact the film behavior in the transverse direction by causing a smaller inter-atom distance, favoring a higher bond strength. The latter acts as transient physical nodes, increasing entropic restoring forces.

Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of intermediate states from non-equilibrium pulling experiments. From the kinetic rates, we also extract the force-dependent kinetic barriers and the equilibrium folding energies. We apply our method to DNA hairpins with multiple folding pathways and intermediates. The experimental results agree with theoretical predictions. Furthermore, the proposed non-equilibrium single-molecule approach permits us to characterize kinetic and thermodynamic properties of native, unfolded, and intermediate states that cannot be derived from equilibrium hopping experiments., Comment: 8 pages, 5 figures

Here, we focus on a common class of enzymes that have multiple substrate binding sites (multisite enzymes) and analyze their capacity to generate bistable dynamics in the reaction networks that they are embedded in. These networks include both substrate–product–substrate cycles and substrate-to-product conversion with subsequent product consumption. Using mathematical techniques, we show that the inherent binding and catalysis reactions arising from multiple substrate–enzyme complexes create a potential for bistable dynamics in such reaction networks. We construct a generic model of an enzyme with n-substrate binding sites and derive an analytical solution for the steady-state concentration of all enzyme–substrate complexes. By studying these expressions, we obtain a mechanistic understanding of bistability, derive parameter combinations that guarantee bistability, and show how changing specific enzyme kinetic parameters and enzyme levels can lead to bistability in reaction networks involving multisite enzymes. Thus, the presented findings provide a biochemical and mathematical basis for predicting and engineering bistability in multisite enzymes.\ud \ud