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At least 739 records · Page 41

Polarisabilities of long conjugated chain molecules with density functional response methods: The role of coupled and uncoupled response

The longitudinal component of the dipole-dipole polarisability of polyacetylene molecules containing 4 to 20 carbon atoms has been calculated with density-functional theory (DFT) response methods. In order to analyse the effect of the uncoupled and coupled contributions to the response matrix, a number of different sets of orbitals were combined with different approximations for the Hessian matrix. This revealed a surprising result: a qualitatively correct increase of the polarisability with the chain length can already be reproduced on the uncoupled level if the response matrix is constructed from Hartree-Fock (HF) or exact-exchange (EXX) DFT orbitals. The nonlocal HF and the local EXX exchange potentials both produce a displacement of charge from the chain ends to the centre of the polyacetylene molecule compared to DFT methods using standard exchange-correlation potentials. In this way, the reduced increase of the transition dipole moments along the molecular axis counteracts the decrease of the occupied-virtual orbital energy gaps and leads to a linear dependence of the polarisabilities (normalised by the number of carbon atoms) on the chain length. A new DFT response approach is tested which utilises unitary transformed Hartree-Fock orbitals as input and which resolves the failure of standard DFT response methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A chain-of-states acceleration method for the efficient location of minimum energy paths

We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths (MEPs) associated to barrier-crossing events in poly-atomic systems, which we call the acceleration method. The path is parametrized in terms of a continuous variable t ∈ [0, 1] that plays the role of time. In contrast to previous chain-of-states algorithms such as the nudged elastic band or string methods, where the positions of the states in the chain are taken as variational parameters in the search for the MEP, our strategy is to formulate the problem in terms of the second derivatives of the coordinates with respect to t, i.e., the state accelerations. We show this to result in a very simple and efficient method for determining the MEP. We describe the application of the method to a series of test cases, including two low-dimensional problems and the Stone-Wales transformation in C{sub 60}.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Tunneling magnetoresistance of silicon chains

The tunneling magnetoresistance (TMR) of a silicon chain sandwiched between nickel electrodes was examined by using first-principles density functional theory. The relative orientation of the magnetization in a parallel-alignment (PA) configuration of two nickel electrodes enhanced the current with a bias less than 0.4 V compared with that in an antiparallel-alignment configuration. Consequently, the silicon chain-nickel electrodes yielded good TMR characteristics. In addition, there was polarized spin current in the PA configuration. The spin polarization of sulfur atoms functioning as a linking bridge between the chain and nickel electrode played an important role in the magnetic effects of the electric current. Moreover, the hybridization of the sulfur 3p orbital and σ-conjugated silicon 3p orbital contributed to increasing the total current.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Computational simulations of solvation force and squeezing out of dodecane chain molecules in an atomic force microscope

Understanding the squeeze out behaviors of liquid films at nanometer scale in an atomic force microscope (AFM) has been a significant interest since the 1990s. We carry out all-atom static-mode AFM simulations in a liquid-vapor molecular dynamics ensemble to investigate the solvation force oscillation and squeeze out mechanisms of a confined linear dodecane fluid between a gold AFM tip and a mica substrate. Solvation force oscillations are found to be associated with the layering transition of the liquid film and unstable jumps of the AFM tip. Detailed structural analyses and molecular animations show that the local permeation of chain molecules and the squeeze out of molecules near the edge of contact promote the layering transition under compression. The confinement-induced slow down dynamics is manifested by the decrease in diffusivity and increase in rotational relaxation times. Furthermore, the persistent diffusive behavior of dodecane chain molecules even in the single-monolayer film is attributed to the chain sliding motions in the film due to the substantial vacancy space and thermal fluctuations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Layered nested Markov chain Monte Carlo

A configurational sampling algorithm based on nested layerings of Markov chains (Layered Nested Markov Chain Monte Carlo or L-NMCMC) is presented for simulations of systems characterized by rugged free energy landscapes. The layerings are generated using a set of auxiliary potential energy surfaces. The implementation of the method is demonstrated in the context of a rugged, two-dimensional potential energy surface. The versatility of the algorithm is next demonstrated on a simple, many body system, namely, a canonical Lennard-Jones fluid in the liquid state. In that example, different layering schemes and auxiliary potentials are used, including variable cutoff distances and excluded volume tempering. In addition to calculating a variety of properties of the system, it is also shown that L-NMCMC, when combined with a free-energy perturbation formalism, provides a straightforward means to construct approximate free-energy surfaces at no additional computational cost using the sampling distributions of each auxiliary Markov chain. In conclusion, the proposed L-NMCMC scheme is general in that it could be complementary to any number of methods that rely on sampling from a target distribution or methods that exploit a hierarchy of time scales and/or length scales through decomposition of the potential energy.

97 MATHEMATICS AND COMPUTING↗

The effect of chain stiffness and salt on the elastic response of a polyelectrolyte

Here, We present simulations of the force-extension curves of strong polyelectrolytes with varying intrinsic stiffness as well as specifically treating hyaluronic acid, a polyelectrolyte of intermediate stiffness. Whereas fully flexible polyelectrolytes show a high-force regime where extension increases nearly logarithmically with force, we find that the addition of even a small amount of stiffness alters the short-range structure and removes this logarithmic elastic regime. This further confirms that the logarithmic regime is a consequence of the short-ranged “wrinkles” in the flexible chain. As the stiffness increases, the force-extension curves tend toward and reach the wormlike chain behavior. Using the screened Coulomb potential and a simple bead-spring model, the simulations are able to reproduce the hyaluronic acid experimental force-extension curves for salt concentrations ranging from 1 to 500 mM. Furthermore, the simulation data can be scaled to a universal curve like the experimental data. The scaling analysis is consistent with the interpretation that, in the low-salt limit, the hyaluronic acid chain stiffness scales with salt with an exponent of –0.7, rather than either of the two main theoretical predictions of –0.5 and –1. Furthermore, given the conditions of the simulation, we conclude that this exponent value is not due to counterion condensation effects, as had previously been suggested.

36 MATERIALS SCIENCE↗

Chiral symmetry and scale invariance breaking in spin chains

The effects of the Dzyaloshinsky-Moriya interaction on finite size one-dimensional (1D) magnetic chains are investigated as a function of their length. The magnetic configuration the system adopts for varying boundary conditions are explored analytically, which leads to the appearance of chiral configurations that play a crucial role. The coercive and exchange bias fields show an unexpected chain length dependence, caused by the boundary conditions and by chiral symmetry breaking, which in turn leads to the breakdown of scale-invariance. Our treatment yields results in agreement with experimental evidence and ongoing research on phthalocyanine iron chains bonded to hydrogen.

36 MATERIALS SCIENCE↗

Evidence of short chains in liquid sulfur

High energy x-ray pair distribution function measurements show the average coordination number of the first shell in liquid sulfur is 1.86 ± 0.04 across the λ-transition, not precisely 2.0 as widely accepted. This indicates that upon melting, liquid sulfur does not comprise solely of S 8 rings but also possesses a significant number of short chains. Intensities of the pre-peak and first diffraction peak of the x-ray structure factor and third peak height of the pair distribution function all show deviations at the λ-transition temperature T λ , associated with the break-up of S 8 rings and the start of oligomer polymerization. A significant number of non-bonded or loosely bonded “interstitial atoms,” with an average coordination number of 0.20 ± 0.005, are also observed in the so-called “forbidden zone” between the first and second shells upon melting. The number of interstitial atoms is found to decrease to a minimum at the λ-transition, but the majority persist into the high temperature polymerized liquid. Furthermore, the existence of short chains and nearby interstitial atoms represent the two main factors required to initiate the S 8 -ring to chain transition, as proposed by recent molecular dynamics simulations.

Chemical bonding↗

A discretized representation for Monte Carlo simulation of deformed semiflexible chains

In this study, we present a novel orientation discretization approach based on the rhombic triacontahedron for Monte Carlo simulations of semiflexible polymer chains, aiming at enhancing structural analysis through rheo-small-angle scattering (rheo-SAS). Our approach provides a more accurate representation of the geometric features of semiflexible chains under deformation, surpassing the capabilities of traditional lattice structures. Validation against the Kratky–Porod chain system demonstrated superior consistency, underscoring its potential to significantly improve the precision of uncovering geometric details from rheo-SAS data. Further, this approach opens new avenues for investigating the conformations of semiflexible polymers and mechanically induced phase transitions in more complex polymer structures, offering deeper insights into their behavior under various conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fission Chain Restart Theory

We present that fast nanosecond timescale neutron and gamma-ray counting can be performed with a (liquid) scintillator array. Fission chains in metal evolve over a timescale of tens of nanoseconds. If the metal is surrounded by moderator, neutrons leaking from the metal can thermalize and diffuse in the moderator. With finite probability, the diffusing neutrons can return to the metal and restart the fast fission chain. The timescale for this restart process is microseconds. A theory describing time evolving fission chains for metal surrounded by moderator, including this restart process, is presented. Finally, this theory is sufficiently simple for it to be implemented for real-time analysis.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Frustrated magnetism in the spin–chain metal Yb 2 Fe 12 P 7

Here, magnetization measurements for magnetic fields ${{\mu}_{0}}H$ up to 60 T are reported for the noncentrosymmetric spin–chain metal Yb 2 Fe 12 P 7 . These measurements reveal behavior that is consistent with Ising-like spin chain magnetism that produces pronounced spin degeneracy. In particular, we find that although a Brillouin field dependence is observed in M ( H ) for $H\bot ~c$ with a saturation moment that is close to the expected value for free ions of Yb 3+ , non-Brillouin-like behavior is seen for $H~\parallel ~c$ with an initial saturation moment that is nearly half the free ion value. In addition, hysteretic behavior that extends above the ordering temperature ${{T}_{\text{M}}}$ is seen for $H~\parallel ~c$ but not for $H~\bot ~c$ , suggesting out-of-equilibrium physics. This point of view is strengthened by the observation of a spin reconfiguration in the ordered state for $H~\parallel ~c$ which is only seen for $T\leqslant {{T}_{\text{M}}}$ and after polarizing the spins. Together with the heat capacity data, these results suggest that the anomalous low temperature phenomena that were previously reported are driven by spin degeneracy that is related to the Ising-like one dimensional chain-like configuration of the Yb ions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera

In vitro display technologies based on phage and yeast have a successful history of selecting single-chain variable fragment (scFv) antibodies against various targets. However, single-chain antibodies are often unstable and poorly expressed in Escherichia coli. Here, we explore the feasibility of converting scFv antibodies to an intrinsically fluorescent format by inserting the monomeric, stable fluorescent protein named thermal green, between the light- and heavy-chain variable regions. Our results show that the scTGP format maintains the affinity and specificity of the antibodies, improves expression levels, allows one-step fluorescent assay for detection of binding and is a suitable reagent for epitope binning. We also report the crystal structure of an scTGP construct that recognizes phosphorylated tyrosine on FcεR1 receptor of the allergy pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Exact statistics of helical wormlike chains with twist-bend coupling

Here, we present a solution for the Green's function for the general case of a helical wormlike chain with twist-bend coupling and demonstrate the applicability of our solution for evaluating general structural and mechanical chain properties. We find that twist-bend coupling renormalizes the persistence length and the force-extension curves relative to wormlike chains. Analysis of intrinsically twisted polymers shows that incorporation of twist-bend coupling results in the oscillatory behavior in principal tangent correlations that are observed in some studies of synthetic polymers. The exact nature of our solution provides a framework to evaluate the role of twist-bend coupling on polymer properties, such as DNA bound to histones and motivates the reinterpretation of existing biopolymer experimental data.

Ghosh, Ashesh [University of California, Berkeley,↗

Unexpected magnetic phase in the weakly ordered spin- 1 2 chain cuprate Sr 2 CuO 3

The magnetic phase diagram of a spin-$\frac{1}{2}$ chain antiferromagnet Sr 2 CuO 3 is studied by an ultrasound phase-sensitive detection technique. The system is in the extreme proximity of the Luttinger-liquid quantum-critical point and we observe an unusually strong effect of magnetic field, which is very weak compared to the in-chain interaction, on the Néel ordering temperature. Inside the ordered phase, we detect an unexpected, field-induced continuous phase transition. The transition is accompanied by softening of magnetic excitation observed by electron-spin resonance, which in previous work [E. G. Sergeicheva et al., Phys. Rev. B 95, 020411(R) (2017)] was associated with a longitudinal (amplitude) mode of the order parameter. These results suggest a transition from a transverse collinear antiferromagnet to an amplitude-modulated spin-density-wave phase in a very weak magnetic field, which is unexpected for a system of weakly coupled Heisenberg spin-$\frac{1}{2}$ chains.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Thermal control across a chain of electronic nanocavities

Here, we study a chain of alternating hot and cold electronic nanocavities—connected to one another via resonant-tunneling quantum dots—with the intent of achieving precise thermal control across the chain. This is accomplished by positioning the dots' energy levels such that a predetermined distribution of heat currents is realized across the chain in the steady state. The number of electrons in each cavity is conserved in the steady state which constrains the cavities' chemical potentials. We determine these chemical potentials analytically in the linear response regime where the energy differences between the dots' resonant levels and the neighboring chemical potentials are much smaller than the thermal energy. In this regime, the thermal control problem can be solved exactly, while, in the general case, thermal control can only be achieved in a relative sense, that is, when one only preassigns the ratios between different heat currents. We apply our results to two different cases: We first demonstrate that a “heat switch” can be easily realized with three coupled cavities, and then we show that our linear response results can provide accurate results in situations with a large number of cavities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Magnetic properties of a staggered S = 1 chain with an alternating single-ion anisotropy direction

Materials composed of spin-1 antiferromagnetic (AFM) chains are known to adopt complex ground states that are sensitive to the single-ion-anisotropy (SIA) energy ( D ), and intrachain ( J 0 ) and interchain ( J 1 , 2 ′ ) exchange energy scales. While theoretical and experimental studies have extended this model to include various other energy scales, the effect of the lack of a common SIA axis is not well explored. Here we investigate the magnetic properties of Ni ( pyrimidine ) ( H 2 O ) 2 ( NO 3 ) 2 , a chain compound where the tilting of Ni octahedra leads to a twofold alternation of the easy-axis directions along the chain. Muon-spin relaxation measurements indicate a transition to long-range order at T N = 2.3 K and the magnetic structure is initially determined to be antiferromagnetic and collinear using elastic neutron diffraction experiments. Inelastic neutron scattering measurements were used to find J 0 = 5.107 ( 7 ) K , D = 2.79 ( 1 ) K , J 1 ′ = 0.00 ( 5 ) K , J 2 ′ = 0.18 ( 3 ) K , and a rhombic anisotropy energy E = 0.19 ( 9 ) K . Mean-field modeling reveals that the ground state structure hosts spin canting of ϕ ≈ 6 . 5 ∘ , which is not detectable above the noise floor of the elastic neutron diffraction data. Monte Carlo simulation of the powder-averaged magnetization, M ( H ) , is then used to confirm these Hamiltonian parameters, while single-crystal M ( H ) simulations provide insight into features observed in the data. Published by the American Physical Society 2025

Vaidya, S. (ORCID:000000033975497X)↗

Topological insulating phases of non-Abelian anyonic chains

Boundary conformal field theory is brought to bear on the study of topological insulating phases of non- Abelian anyonic chains. These phases display protected anyonic end modes. We consider spin-1/2 su(2)t chains at any level k, focusing on the most prominent examples: the case k = 2 describes Ising anyons (equivalent to Majorana fermions) and k = 3 corresponds to Fibonacci anyons. The method we develop is quite general and rests on a deep connection between boundary conformal field theory and topological symmetry. This method tightly constrains the nature of the topological insulating phases of these chains for general k. Emergent anyons which arise at domain walls are shown to have the same braiding properties as the physical quasiparticles. This suggests a "solid-stat.e" topological quantum computation scheme in which emergent anyons are braided by tuning the couplings of non-Abelian quasiparticles in a fixed network.

DeGottardi, Wade↗

Majorana spin in magnetic atomic chain systems

In this study, we establish that Majorana zero modes emerging from a topological band structure of a chain of magnetic atoms embedded in a superconductor can be distinguished from trivial localized zero energy states that may accidentally form in this system using spin-resolved measurements. To demonstrate this key Majorana diagnostics, we study the spin composition of magnetic impurity induced in-gap Shiba states in a superconductor using a hybrid model. By examining the spin and spectral densities in the context of the Bogoliubov-de Gennes (BdG) particle-hole symmetry, we derive a sum rule that relates the spin densities of localized Shiba states with those in the normal state without superconductivity. Extending our investigations to a ferromagnetic chain of magnetic impurities, we identify key features of the spin properties of the extended Shiba state bands, as well as those associated with a localized Majorana end mode when the effect of spin-orbit interaction is included. We then formulate a phenomenological theory for the measurement of the local spin densities with spin-polarized scanning tunneling microscopy (STM) techniques. By combining the calculated spin densities and the measurement theory, we show that spin-polarized STM measurements can reveal a sharp contrast in spin polarization between an accidental-zero-energy trivial Shiba state and a Majorana zero mode in a topological superconducting phase in atomic chains. We further confirm our results with numerical simulations that address generic parameter settings.

Majorana fermions↗