Helical Modulation Research Articles

MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA

Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoinflammatory disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more stably to synthetic Alu:Alu dsRNA. CryoEM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle- RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease.

Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.

By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions.

Crystal symmetry for incommensurate helical and cycloidal modulations

Crystal symmetry for incommensurate helical and cycloidal modulations

Vital role of magnetocrystalline anisotropy in cubic chiral skyrmion hosts

Magnetic anisotropy is anticipated to govern the formation of exotic spin textures reported recently in cubic chiral magnets, like low-temperature tilted conical and skyrmion lattice (SkL) states and metastable SkLs with various lattice geometry. Motivated by these findings, we quantified the cubic anisotropy in a series of CoZnMn-type cubic chiral magnets. We found that the strength of anisotropy is highly enhanced towards low temperatures. Moreover, not only the magnitude but also the character of cubic anisotropy drastically varies upon changing the Co/Mn ratio. We correlate these changes with temperature- and composition-induced variations of the helical modulation vectors, deformations of skyrmions, structural rearrangements of the metastable SkLs and the large enhancement of Gilbert damping. Similar studies on magnetic anisotropy are required for the quantitative, unified description of the known stable and metastable modulated spin textures and for the systematic exploration of novel ones in this large class of skyrmion hosts.

Martensitic transition assisted modification of the antiferromagnetic ordering in Ge-site doped MnNiGe alloys

The magnetic equiatomic alloys of the nominal compositions ${\mathrm{MnNiGe}}_{0.9}{\mathrm{Al}}_{0.1}$ and ${\mathrm{MnNiGe}}_{0.928}{\mathrm{Ga}}_{0.072}$ have been investigated through the neutron powder diffraction (NPD) technique. Both these alloys undergo a martensitic phase transition from the high-temperature hexagonal (${\mathrm{Ni}}_{2}\mathrm{In}$ type, with space group $P{6}_{3}/mmc$) austenite phase to the low-temperature orthorhombic (TiNiSi type, with space group $Pnma$) martensite phase. Our NPD analysis confirmed an incommensurate antiferromagnetic ordering of the low-temperature martensitic phase with helical modulation. The incommensurate propagation vector $\mathbf{k}$ is found to be (0.2065(1),0,0) and (0.2088(4),0,0) for Al and Ga doped alloys, respectively, at 1.5 K and shows a monotonic increase with increasing sample temperature. On the other hand, a commensurate antiferromagnetic ordering was observed for the high-temperature austenite phase. The incomplete martensitic transition allowed both these incommensurate and commensurate antiferromagnetic structures to coexist down to the lowest temperature of measurement (1.5 K).

Crystal symmetry for incommensurate helical and cycloidal modulations.

A classification of magnetic superspace groups compatible with the helical and cycloidal magnetic modulations is presented. Helical modulations are compatible with groups from crystal classes 1, 2, 222, 4, 422, 3, 32, 6 and 622, while cycloidal modulations are compatible with groups from crystal classes 1, 2, m and mm2. For each magnetic crystal class, the directions of the symmetry-allowed (non-modulated) net ferromagnetic moment and electric polarization are given. The proposed classification of superspace groups is tested on experimental studies of type-II multiferroics published in the literature.

Electromechanically reconfigurable optical nano-kirigami

Kirigami, with facile and automated fashion of three-dimensional (3D) transformations, offers an unconventional approach for realizing cutting-edge optical nano-electromechanical systems. Here, we demonstrate an on-chip and electromechanically reconfigurable nano-kirigami with optical functionalities. The nano-electromechanical system is built on an Au/SiO2/Si substrate and operated via attractive electrostatic forces between the top gold nanostructure and bottom silicon substrate. Large-range nano-kirigami like 3D deformations are clearly observed and reversibly engineered, with scalable pitch size down to 0.975 μm. Broadband nonresonant and narrowband resonant optical reconfigurations are achieved at visible and near-infrared wavelengths, respectively, with a high modulation contrast up to 494%. On-chip modulation of optical helicity is further demonstrated in submicron nano-kirigami at near-infrared wavelengths. Such small-size and high-contrast reconfigurable optical nano-kirigami provides advanced methodologies and platforms for versatile on-chip manipulation of light at nanoscale.

Competing spin modulations in the magnetically frustrated semimetal EuCuSb

The competing magnetic ground states of the itinerant magnet EuCuSb, which has a hexagonal layered structure, were studied via magnetization, resistivity, and neutron diffraction measurements on single-crystal samples. EuCuSb has a three-dimensional semimetallic band structure as confirmed by band calculation and angle-resolved photoelectron spectroscopy, consistent with the nearly isotropic metallic conductivity in the paramagnetic state. However, below the antiferromagnetic transition temperature of TN1 (8.5 K), the resistivity, especially along the hexagonal axis, increases significantly. This implies the emergence of anisotropic magnetic ordering coupled to the conducting electrons. Neutron diffraction measurements show that the Eu spins, which order ferromagnetically within each layer, are collinearly modulated (up-up-down-down) along the hexagonal axis below TN1, followed by the partial emergence of helical spin modulation below TN2 (6 K). Based on the observation of anomalous magnetoresistance with hysteretic behavior, we discuss the competing nature of the ground state inherent in a frustrated Heisenberg-like spin system with a centrosymmetric structure.

A novel CFD simulation of H2 separation by Pd-based helical and straight membrane tubes

A novel three-dimensional CFD simulation of H2 gas permeation through dense palladium (Pd) membrane was developed. Due to discontinuity of flow in a membrane, usually, gas diffusion process is simulated by introducing source and sink terms. In a novel approach, an analogy between heat and mass transfer is considered. The most important advantage of this approach is that there is no need to define sink and source terms, and the membrane thickness is considered as a solution domain without separating the geometry adjacent to the membrane. Also, it allows the modeling of multilayer membranes with different mechanisms of diffusion, separately. The effect of membrane geometry on the hydrogen separation was investigated using the straight and helical modules by defining user-defined function (UDF) and user-defined scalars (UDS). The results showed an average flux and H2 recovery enhancement of 20% and 13% for helical configuration, respectively. The influence of the feed gas and sweep gas flow rates, helix pitch, coil diameter, pressure difference, and module temperature on hydrogen separation was also investigated. The proposed simulation model was validated using the experimental data. The results indicated that this method has a maximum error of about 10% for H2 flux.

Photocatalytic ozonation of organic pollutants in wastewater using a flowing through reactor

Photocatalytic ozonation (PCO/O3) process is a promising technology for mineralizing refractory organics in wastewater. In this study, we described an efficient approach to improve the mass-transfer performance of PCO/O3 by using a helical photocatalytic module (HPM) in an annular UVC reactor. Under hydraulic retention time (HRT) of 19 min and influent phenol concentration of 33 mg/L (TOC 26 mg/L), TOC removal of 91.5% was obtained during a PCO/O3 process with HPM, while TOC removal was only 58.1% without HPM (UVC/O3). This flowing through reactor displayed good stability in a continuous test lasting 20 h. The electric energy required to reduce TOC by one order of magnitude per cubic meter of solution was calculated to be 10.23 kWh/(m3 order), which supported that the PCO/O3 process in this flowing through reactor was energy-efficient compared with other processes (24.30–68.75 kWh/(m3 order)). The steel-rolling wastewater after biological treatment was taken as a target. Under the HRT of 57 min and initial COD of 124 mg/L, COD in effluent dropped to 45.8 mg/L and met the discharge standard of pollutants for municipal wastewater treatment plant of China.

Helicity Modulation Improves the Selectivity of Antimicrobial Peptoids.

The modulation of conformational flexibility in antimicrobial peptides (AMPs) has been investigated as a strategy to improve their efficacy against bacterial pathogens while reducing their toxicity. Here, we synthesized a library of helicity-modulated antimicrobial peptoids by the position-specific incorporation of helix-inducing monomers. The peptoids displayed minimal variations in hydrophobicity, which permitted the specific assessment of the effect of conformational differences on antimicrobial activity and selectivity. Among the moderately helical peptoids, the most dramatic increase in selectivity was observed in peptoid 17, providing more than a 20-fold increase compared to fully helical peptoid 1. Peptoid 17 had potent broad-spectrum antimicrobial activity that included clinically isolated multi-drug-resistant pathogens. Compared to pexiganan AMP, 17 showed superior metabolic stability, which could potentially reduce the dosage needed, alleviating toxicity. Dye-uptake assays and high-resolution imaging revealed that the antimicrobial activity of 17 was, as with many AMPs, mainly due to membrane disruption. However, the high selectivity of 17 reflected its unique conformational characteristics, with differential interactions between bacterial and erythrocyte membranes. Our results suggest a way to distinguish different membrane compositions solely by helicity modulation, thereby improving the selectivity toward bacterial cells with the maintenance of potent and broad-spectrum activity.

Characterized helical modulation of three-dimensional Skyrmions in the spin-orbit coupled condensate

For the Bose–Einstein condensate in the non-Abelian gauge field, the atomic wavefunction obtains helical modulation, which would lead to nontrivial objects, such as three-dimensional Skyrmion. The spin–orbit coupled condensate is usually capable of supporting Skyrmion ground states, which can be well understood through the wavefunction modulation vector concept. In the present manuscript, the modulation vector is characterized both analytically and numerically with respect to the spin–orbit coupling strength. For the SU(2) symmetric condensate, the modulation vector of the wavefunction is linearly proportional to the spin–orbit coupling strength. In the presence of spin-dependent interaction, the modulus of the modulation vector is predicted to increase or decrease according to the sign of the interaction parameter, resulting in a shrunken or expanded Skyrmion. However, the Skyrmion is unstable for a certain area of the parameter space of the spin–orbit coupling and spin-dependent interaction. The condensate favors a single Skyrmion state or the Skyrmion lattice state according to the strength of the spin–orbit coupling.

Photonic Floquet topological insulators in a fractal lattice

We present Floquet fractal topological insulators: photonic topological insulators in a fractal-dimensional lattice consisting of helical waveguides. The helical modulation induces an artificial gauge field and leads to a trivial-to-topological phase transition. The quasi-energy spectrum shows the existence of topological edge states corresponding to real-space Chern number 1. We study the propagation of light along the outer edges of the fractal lattice and find that wavepackets move along the edges without penetrating into the bulk or backscattering even in the presence of disorder. In a similar vein, we find that the inner edges of the fractal lattice also exhibit robust transport when the fractal is of sufficiently high generation. Finally, we find topological edge states that span the circumference of a hybrid half-fractal, half-honeycomb lattice, passing from the edge of the honeycomb lattice to the edge of the fractal structure virtually without scattering, despite the transition from two dimensions to a fractal dimension. Our system offers a realizable experimental platform to study topological fractals and provides new directions for exploring topological physics.

Evidence for NAD+-dependent histone dynamics and tunneling associated conformational transitions in circadian deacetylase SIRT1

Circadian rhythm is a biological cycle that is involved in all processes over 24 h day and night period. Sirtuin 1 (SIRT1) is a 747 amino acid-long class III Nicotinamide adenine dinucleotide (NAD+)-dependent histone that acts as a circadian deacetylase. Here we present a detailed in-silico analysis to address comparative structure-function relationship and interaction pattern of SIRT1-NAD+/Zn+2 and SIRT1NAD+/Zn+2-acetylated histone H4 (H4KAC16) complexes. MD-based ensemble analysis suggested an overall loss of helical content (21.144–17.230%) in H4KAC16-bound SIRT1NAD+/Zn+2 due to conformational readjustments of 32 residues, as compared to SIRT1NAD+/Zn+2. Due to increased flexibility, SIRT1-specific SER275, SER442 and ARG466 residues involved in NAD+ association facilitated in the formation of a transient tunnel (17.77 Å) that was further elongated to 19.25 Å upon SIRT1NAD+/Zn+2 binding to H4KAC16. A close conformation of SIRT1NAD+/Zn+2 was achieved due to binding of H4KAC16 that results in the movement of helical module towards Zn+2 binding module together with Rossmann fold at NAD+ binding region. Furthermore, a 2-fold increase (4.31–8.82 Å) in the measured inter-atomic distance between imidazole nitrogen of conserved HIS363 and NAD+-specific 2′-hydroxyl group of ribose ring was evident in SIRT1NAD+/Zn+2-H4KAC16 complex. At 90 ns time scale, the distance between C6A of adenine ring and C2N of nicotinamide ring was more extended (19.32 Å) in SIRT1NAD+/Zn+2-H4KAC16 as compared to SIRT1NAD+/Zn+2 (11.54 Å). These data suggest that H4KAC16 binding to SIRT1 may coordinate an unusual conformational readjustment of nicotinamide ring at site-b and reposition of HIS363 to facilitate SIRT1-dependent deacetylase activity. Taken together, our findings will help in understanding the precise structural changes occurring in response to SIRT1 deacetylase activity of core histone.

Helical Magnetic Field-Induced Real-Time Plasmonic Chirality Modulation.

The astrophysical phenomenon of mimetic helical magnetic field (hB)-assisted self-assembly is herein introduced to build helical superstructures that display chiroptical properties. As a building block, magnetoplasmonic (MagPlas) Ag@Fe3O4 core-shell nanoparticles are used to guide plasmonic Ag nanoparticles onto a helical magnetic flux. The chirality of the assembled helical structures and tailored circular dichroism are successfully tuned in real time, and the handedness of the assembled structures is dynamically switched by the hB at the millisecond level, which is at least 6000-fold faster than other template-assisted methods. The peak position of circular dichroism can be reconfigured by altering the plasmonic resonance or coupling by controlling the size of the Ag core and magnetic flux density. The hB-induced chirality modulation represents a method to control the polarization state of light at the nexus of plasmonics, magnetic self-assembly, colloidal science, liquid crystals, and chirality. It presents active and dynamic chiral assemblies of magnetoplasmonic nanomaterials, enabling further practical applications in optical devices.

Emergent topological spin structures in the centrosymmetric cubic perovskiteSrFeO3

The skyrmion crystal (SkX) characterized by a multiple-q helical spin modulation has been reported as a unique topological state that competes with the single-q helimagnetic order in non-centrosymmetric materials. Here we report the discovery of a rich variety of multiple-q helimagnetic spin structures in the centrosymmetric cubic perovskite SrFeO3. On the basis of neutron diffraction measurements, we have identified two types of robust multiple-q topological spin structures that appear in the absence of external magnetic fields: an anisotropic double-q spin spiral and an isotropic quadruple-q spiral hosting a three-dimensional lattice of hedgehog singularities. The present system not only diversifies the family of SkX host materials, but furthermore provides an experimental missing link between centrosymmetric lattices and topological helimagnetic order. It also offers perspectives for integration of SkXs into oxide electronic devices.

Helical Long-Period Fiber Gratings as Wavelength-Tunable Orbital Angular Momentum Mode Generators

High-quality helical long-period fiber gratings (HLPFGs) with a coupling strength greater than 30 dB and an insertion loss less than 0.5 dB are formed by applying CO2 laser to expose an optical fiber that is simultaneously translated and rotated to relieve the residual stress of the fiber along a helical pathway, rather than twisting the fiber under a high-temperature condition. The mode coupling characteristics of this type of HLPFG are investigated for the first time. Experimental results demonstrate that the helical refractive-index modulation of the HLPFGs can generate light with orbital angular momentum (OAM) modes, where the chirality of the OAM modes is insensitive to the polarization state of the input light. The HLPFGs provide excellent torsion characteristics, and the resonant wavelengths of OAM modes can be linearly tuned when applying torsions.

Instantons in chiral magnets

We exhaustively construct instanton solutions and elucidate their properties in one-dimensional anti-ferromagnetic chiral magnets based on the $O(3)$ nonlinear sigma model description of spin chains with the Dzyaloshinskii-Moriya (DM) interaction. By introducing an easy-axis potential and a staggered magnetic field, we obtain a phase diagram consisting of ground-state phases with two points (or one point) in the easy-axis dominant cases, a helical modulation at a fixed latitude of the sphere, and a tricritical point allowing helical modulations at an arbitrary latitude. We find that instantons (or skyrmions in two-dimensional Euclidean space) appear as composite solitons in different fashions in these phases: temporal domain walls or wall-antiwall pairs (bions) in the easy-axis dominant cases, dislocations (or phase slips) with fractional instanton numbers in the helical state, and isolated instantons and calorons living on the top of the helical modulation at the tricritical point. We also show that the models with DM interaction and an easy-plane potential can be mapped into those without them, providing a useful tool to investigate the model with the DM interaction.

Sam Domains in Multiple Diseases.

The sterile alpha motif (Sam) domain is a small helical protein module, able to undergo homo- and hetero-oligomerization, as well as polymerization, thus forming different types of protein architectures. A few Sam domains are involved in pathological processes and consequently, they represent valuable targets for the development of new potential therapeutic routes. This study intends to collect state-of-the-art knowledge on the different modes by which Sam domains can favor disease onset and progression. This review was build up by searching throughout the literature, for: a) the structural properties of Sam domains, b) interactions mediated by a Sam module, c) presence of a Sam domain in proteins relevant for a specific disease. Sam domains appear crucial in many diseases including cancer, renal disorders, cataracts. Often pathologies are linked to mutations directly positioned in the Sam domains that alter their stability and/or affect interactions that are crucial for proper protein functions. In only a few diseases, the Sam motif plays a kind of "side role" and cooperates to the pathological event by enhancing the action of a different protein domain. Considering the many roles of the Sam domain into a significant variety of diseases, more efforts and novel drug discovery campaigns need to be engaged to find out small molecules and/or peptides targeting Sam domains. Such compounds may represent the pillars on which to build novel therapeutic strategies to cure different pathologies.

Permeate flux enhancement with a helical wired concentric tube in air gap membrane distillation systems

Temperature polarization plays an important role in determining the permeate flux of the membrane distillation in an air gap membrane distillation (AGMD) module. This study aimed to increase the pure water productivity of saline water desalination by applying helical wire on the circumference of a concentric-tube AGMD module to reduce the temperature polarization occurring on the smooth annulus tube of an AGMD module with a normal concentric-tube. Modeling equations of heat and mass transfer in the new design of the AGMD device with helical wire winding on the annulus of a concentric tube have been investigated theoretically and experimentally. The mathematical model proposed in this study was used to correlate a simplified equation for estimating the heat transfer coefficient and to predict the permeate flux accordingly. The effects of various operation parameters, including the feed saline water temperature, feed volumetric flow rate, air gap thickness, and helical wire pitch, on the pure water productivity were also delineated. The permeate flux enhancement for helical wire in the AGMD module could provide the maximum relative increment of up to 31.1. The temperature polarization coefficient found in this study is ranging from 0.5527 to 0.5451 for different hot feed temperature and flow rate, respectively. An optimal helical wire module was assessed when considering both permeate flux enhancement and energy utilization effectiveness. © 2020 Desalination Publications. All rights reserved.