Recent Experiments Research Articles

Fluctuating Chromatin Facilitates Enhancer-Promoter Communication by Regulating Transcriptional Clustering Dynamics.

Enhancers regulate gene expression by forming contacts with distant promoters. Phase-separated condensates or clusters formed by transcription factors (TFs) and cofactors are thought to facilitate these enhancer-promoter (E-P) interactions. Using polymer physics, we developed distinct coarse-grained chromatin models that produce similar ensemble-averaged Hi-C maps but with "stable" and "dynamic" characteristics. Our findings, consistent with recent experiments, reveal a multistep E-P communication process. The dynamic model facilitates E-P proximity by enhancing TF clustering and subsequently promotes direct E-P interactions by destabilizing the TF clusters through chain flexibility. Our study promotes physical understanding of the molecular mechanisms governing E-P communication in transcriptional regulation.

Superconductivity in a background of topological spin texture

Abstract Motivated by a recent experiment on high-temperature superconductors [Nature 615, 405 (2023)], we perform a theoretical study to distinguish the nature of the topological spin texture in the superconducting phase of an underdoped cuperate. We propose a phenomenological tight-binding model of electrons with spin-singlet pairing hopping in the background of topological spin texture on the square lattice. Two types of topological spin texture relevant to the experiment are considered, i.e. Bloch Skyrmion and sinusoidal vortex, and the mean-field theory is employed. We discover an emergent $d_{xy}$-wave component in imaginary part of gap function for Skyrmion, but there is not for vortex. For Skyrmion, each coherent peak in the local density of states splits into two spatial uniform peaks, while for vortex, it splits into two spatial modulated peaks. Our study reveals the qualitatively different consequences of two types of topological spin texture, and can be possibly detected in the further STM expriment.

Superconductivity in the pressurized nickelate La3Ni2O7 in the vicinity of a BEC–BCS crossover

Ever since the discovery of high-temperature superconductivity in cuprates, gaining microscopic insights into the nature of pairing in strongly correlated systems has remained one of the greatest challenges in modern condensed matter physics. Following recent experiments reporting superconductivity in the bilayer nickelate La3Ni2O7 (LNO) with remarkably high critical temperatures of Tc = 80 K, it has been argued that the low-energy physics of LNO can be described by the strongly correlated, mixed-dimensional bilayer t–J model. Here we investigate this bilayer system and utilize density matrix renormalization group techniques to establish a thorough understanding of the model and the magnetically induced pairing through comparison to the perturbative limit of dominating inter-layer spin couplings. In particular, this allows us to explain appearing finite-size effects, firmly establishing the existence of long-range superconducting order in the thermodynamic limit. By analyzing binding energies, we predict a BEC–BCS crossover as a function of the Hamiltonian parameters. We find large binding energies of the order of the inter-layer coupling that suggest strikingly high critical temperatures of the Berezinskii–Kosterlitz–Thouless transition, raising the question of whether (mixD) bilayer superconductors possibly facilitate critical temperatures above room temperature.

Investigating the Substrate Oxidation Mechanism in Lytic Polysaccharide Monooxygenase: H2O2- versus O2-Activation.

Lytic polysaccharide monooxygenases (LPMOs) form a copper-dependent family of enzymes classified under the auxiliary activity (AA) superfamily. The LPMOs are known for their boosting of polysaccharide degradation through oxidation of the glycosidic bonds that link the monosaccharide subunits. This oxidation has been proposed to be dependent on either O2 or H2O2 as cosubstrate. Theoretical investigations have previously supported both mechanisms, although this contrasts with recent experiments. A possible explanation is that the theoretical results critically depend on how the Cu active site is modeled. This has also led to different results even when employing only H2O2 as cosubstrate. In this paper, we investigate both the O2- and H2O2-driven pathways, employing LsAA9 as the underlying LPMO and a theoretical model based on a quantum mechanics/molecular mechanics (QM/MM) framework. We ensure to consistently include all residues known to be important by using extensive QM regions of up to over 900 atoms. We also investigate several conformers that can partly explain the differences seen in previous studies. We find that the O2-driven reaction is unfeasible, in contrast with our previous QM/MM calculations with smaller QM regions. Meanwhile, the H2O2-driven pathway is feasible, showing that for LsAA9, only H2O2 is a viable cosubstrate as proposed experimentally.

Measurement of spherical tokamak plasma compression in the PCS-16 magnetized target fusion experiment

Abstract A sequence of magnetized target fusion (MTF) devices built by General Fusion have compressed magnetically confined deuterium plasmas inside imploding aluminum liners. Here we describe the best-performing compression experiment, PCS-16, which was the fifth of the most recent experiments that compressed a spherical tokamak plasma configuration. In PCS-16 the plasma remained axisymmetric with δBpol/Bpol < 20% to a high radial compression factor (CR > 8) with significant poloidal flux conservation (77% up to CR = 1.7, and ≈30% up to CR = 8.65) and a total compression time of 167 μs. Magnetic energy of the plasma increased from 0.96 kJ poloidal and 17 kJ toroidal to a peak of 1.14 kJ poloidal and 29.9 kJ toroidal during the compression, while thermal energy was in the range of 350 ± 25 J. Plasma equilibrium was a low-β state with βtor ≈ 4% and βpol ≈ 15%. Ingress of impurities from the lithium coated aluminum wall was not a dominant effect. Neutron yield from D-D fusion increased significantly during compression. Thermodynamics during the early phase of compression (CR < 1.7) were consistent with increasing Ohmic heating of the electrons due to a geometric rise in the current density at near-constant resistivity, and with increasing ion cooling that approximately matched ion compressional heating power. Ion cooling by electrons was significant because the electrons were cooler than the ions (Te = 200 eV, Ti = 600 eV). Magnetohydrodynamic simulation was used to model the emergence of instabilities that increased electron thermal transport in the final phase of compression. Conditions for ideal stability were actively maintained during compression through a current ramp applied to the central shaft, and after this current ramp reached its peak two-thirds of the way through compression we measured a transition in plasma behavior across multiple diagnostics.

Carbamic acid and its dimer: A computational study.

A recent work by Marks et al. on the formation of carbamic acid in NH -CO interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.

Bismuth-based ternary chalcogenides Pt3Bi4X9 (X = S, Se) as promising thermoelectric materials

We present a theoretical investigation of thermoelectric transport properties of bismuth-based ternary chalcogenides Pt3Bi4X9 (X = S, Se), which has low thermal conductivity and promising zT as discovered in a recent experiment [Wang et al., J. Am. Chem. Soc. 146, 7352 (2024)], using density functional theory combined with the Boltzmann transport equation within rigid band approximation. We find that the high density of states of valence bands near the Fermi level yields high p-type Seebeck coefficient. The lower effective mass of electron in Pt3Bi4S9 leads to high mobility and long relaxation time, and hence the high n-type electrical conductivity. In contrast, the effective mass of electron is much higher than that of hole in Pt3Bi4Se9 due to the flatted conduction band, which in turn gives rise to higher p-type electrical conductivity. As a result, the p-type zT is much higher than n-type in Pt3Bi4Se9, with an optimal value of 0.5 at 300 K. Considering the experimental carrier concentration for Pt3Bi4S9 (−1.4 × 1019 cm−3) and Pt3Bi4Se9 (−0.898 × 1019 cm−3), calculated n-type zT at 773 K are 0.52 and 0.04, respectively, which are consistent well with the experimental values. Our calculations uncover the upper limit thermoelectric zT of Pt3Bi4X9 and also highlight them as promising thermoelectric materials.

Revisiting the assessment of magnetic texture of Rare-Earth Magnets: The role of coercivity

A crucial figure of merit of rare-earth magnets is their magnetic texture, because it is closely related to the maximum remanence a magnet can achieve, hence assessing the magnetic texture is pivotal in terms of magnet’s performance. Fernengel et al. (1996) developed a methodology based on magnetometry, which allows for a quick determination of the texture by calculating the degree of alignment 〈cosθ〉 from the remanent magnetization in directions parallel and perpendicular to the texture axis of the magnet. Although this method provided reliable values, its application was limited to magnets with high degrees of alignment (〈cosθ〉 > 95 %), a restriction that was corrected by Quispe et al. (2020). Nevertheless, recent experiments have indicated that the magnetometry technique can introduce errors in texture assessment when the magnet presents high levels of coercivity. This work presents an approach that incorporates a correction factor into the magnetometry technique, accounting for the effect of the coercivity and circumventing this error source in texture assessment. The proposed methodology has been successfully applied to magnets with varying levels of coercivity.

Antifungal peptide-loaded alginate microfiber wound dressing evaluated against Candida albicans in vitro and ex vivo

Invasive fungal infections have high mortality rates, and many current antimycotics are limited by host toxicity and drug resistance. Recent experiments in our laboratory have demonstrated the antifungal activity of dKn2-7, a synthetic peptide, against Candida albicans. The purpose of the current study was to develop a wound dressing capable of dKn2-7 release for extended periods to help combat fungal infection in wounds. dKn2-7 was incorporated into calcium alginate microfibers, an excipient with known wound healing and hemostatic properties. dKn2-7 release rates from the fibers were dependent on drug loading, but all formulations exhibited a burst release with 41–71 % of total release in the first 15 min and 84–96 % release by 24 h. Calcium release at 15 min was similar to that of a commercial hemostatic dressing, indicating dKn2-7 loading would not adversely affect the hemostatic capability of the alginate fibers. In vitro antifungal studies indicated a dose dependent effect with fibers loaded at ≥20 µg/mg causing significant planktonic killing and ≥30 µg/mg causing significant biofilm killing. Viable fungal counts in biofilms grown on ex vivo porcine skin declined by 99 % following 500 µg/mg fiber treatment. Skin histology indicated no significant differences in tissue damage between treatment groups and controls. Results confirm calcium alginate microfibers are capable of binding and subsequently releasing dKn2-7 over a 24-h period when rehydrated. Furthermore, dKn2-7 released from the fibers was able to significantly reduce biofilms in an ex vivo model with minimal toxicity, indicating these dKn2-7 loaded fiber dressings may be effective at controlling C. albicans biofilm infections in vivo.

Model of Faraday waves in a cylindrical container with force detuning

Recent experiments by Shao et al. [“Surface wave pattern formation in a cylindrical container,” J. Fluid Mech. 915, A19 (2021)] have revealed complex wave dynamics on the surface of a liquid bath in a vertically vibrated cylindrical container that are related to the presence of a meniscus on the container sidewall. We develop a corresponding theoretical model for this system by detuning the driving acceleration of the container, which results in an inhomogeneous Mathieu equation that governs the wave dynamics whose spatial structure is defined by the mode number pair (n,m), with n and m the radial and azimuthal mode numbers, respectively. Asymmetric m≠0 modes are unaffected by the detuning parameter, which is related to the meniscus shape and satisfy a homogeneous Mathieu equation with the shape of the instability tongues computed by the Floquet theory. The Poincaré–Lindstedt method is used to compute the instability tongues for the axisymmetric m=0 modes, which have a lower threshold acceleration and larger bandwidth that depend upon the detuning parameter. Our model results explicitly show how the shape of the meniscus and spatial structure of the wave determine the temporal response and are in good agreement with prior experimental observations for both pure modes and mixed modes.

Impact of grain size on the performance of WSe2 FETs revealed by first-principles calculations

We theoretically investigate the grain size dependence of the mobility of WSe2 FETs, and the experimental results which have been recently reported. A larger grain size (LG) WSe2 has been modeled by a single monolayer WSe2 of infinite length. We model a smaller grain size (SG) WSe2 as a partial monolayer of WSe2 with a zigzag edge WSe2 nanoribbon. Our results show that the step edges of the partial monolayer WSe2 function as electron traps. Moreover, the effective mass of SG WSe2 appears to be much larger than that of LG WSe2 because of hybridization with gap states originating from step edges at the conduction band minimum. These results coincide with recent experiments that show that the on-currents of the SG WSe2 are much lower than those of the LG WSe2. Hence, our calculated results indicate that LG fabrication is essential for advanced large-scale integration (LSI) using WSe2 FETs.

Brief History of the Uncontrolled Manifold Hypothesis and Its Role in Motor Control

BACKGROUND: The apparent problem of motor redundancy was replaced by the principle of abundance and turned into a theoretical framework and associated toolbox for exploration of performance-stabilizing synergies. AIM and METHOD: We review briefly the development of the main methods within the UCM framework and some of the main findings, both basic and clinical. The UCM framework is naturally merged with the theory of hierarchical movement control with spatial referent coordinates. RESULTS: The UCM framework has established itself as a productive framework for the analysis of movement control, in particular as related to stability of salient performance variables. It led to the discovery of novel phenomena such as trade-offs within hierarchical systems, anticipatory synergy adjustments, synergies within systems of different complexity from single muscles to the whole body. It has also led to promising results offering sensitive biomarkers to various neurological disorders. Recent experiments suggest the existence of three main levels of organization of performance-stabilizing synergies tentatively associated with cortical, subcortical, and spinal circuitry. CONCLUSION: Currently, this approach is in its adulthood. Further progress may be expected in focusing on spaces of neural control variables, developing the method for analysis across species, and expanding the range and depth of clinical studies.

Improvement of aerosol spray scavenging efficiency by pre-injecting electrically charged water mist

Efficient aerosol scavenging is crucial for gas purification to reduce environmental pollution in various chemical industries. In nuclear reactor decommissioning, especially for damaged reactors after severe accidents like Fukushima Daiichi, controlling radioactive aerosol generation and dispersion is essential. Radioactive aerosols sizing from 0.1 to 1 μm are expected during containment cleaning and fuel debris retrieval processes. To ensure safe decommissioning and mitigate environmental radioactivity, a containment water spray system is used for aerosol scavenging. However, conventional water spray has low efficiency for these submicron aerosols. Our recent experiments at UTARTS demonstrated that pre-injection of water mist enhances scavenging efficacy by increasing aerosol size and hydrophilicity through aerosol-mist agglomeration prior to spraying. On this basis, in this study, we introduced an innovative method using electrically charged water mist, which significantly facilitates aerosol-mist agglomeration through additional electrostatic coagulation, further improving scavenging efficacy (maximum 35 % in current configurations). The present experimental results attained under various mist conditions and charging configurations provided insights into optimizing the mist charging system. Our developed technology is expected to be useful in radioactive aerosol control during damaged reactor decommissioning and has potential applications in other environmental chemical engineering processes.

Six-Letter DNA Nanotechnology: Incorporation of Z-P Base Pairs into Self-Assembling 3D Crystals.

Artificially expanded genetic information systems (AEGIS) were developed to expand the diversity and functionality of biological systems. Recent experiments have shown that these expanded DNA molecular systems are robust platforms for information storage and retrieval as well as useful for basic biotechnologies. In tandem, nucleic acid nanotechnology has seen the use of information-based "semantomorphic" encoding to drive the self-assembly of a vast array of supramolecular devices. To establish the effectiveness of AEGIS toward nanotechnological applications, we investigated the ability of a six-letter alphabet composed of A:T, G:C and synthetic Z:P (Z, 6-amino-3-(1'-β-d-2'-deoxy ribofuranosyl)-5-nitro-(1H)-pyridin-2-one; P, 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-(8H)-4-one) base pairs to engage in 3D self-assembly. We found that crystals could be programmably assembled from AEGIS oligomers. We conclude that unnatural base pairs can be used for the topological self-assembly of crystals. We anticipate the expansion of AEGIS-based nucleic acid nanotechnologies to enable the development of novel nanomaterials, high-fidelity signal cascades, and dynamic nanoscale devices.

Revealing the Response of Structure and Decomposition Behaviors of 1, 1′‐Azobis‐1, 2, 3‐Triazole to Pressure: A Theoretical Study

ABSTRACT1, 1′‐azobis‐1, 2, 3‐triazole (C4H4N8, N8) is a novel nitrogen‐rich energetic material with excellent detonation performance, which has received widespread interest. Inspired by recent theories and experiments, the dependence of structural, vibrational, and electronic properties on high pressure up to 10 GPa was systematically investigated using periodic DFT calculations. It was found that the optimized structure belonged to the cis‐N8 structure through comparing the theoretical IR with experimental IR spectra. The third‐order Birch–Murnaghan equation of state for N8 was obtained up to 10 GPa, where the bulk modulus and its pressure derivative were 10.91 GPa and 7.689, respectively. More importantly, the pressure dependence of Laplacian bond order indicated that the five‐membered ring opening was the first step in the decomposition process, and that high pressure could inhibit the decomposition process of N8 due to the reinforcement of non‐covalent interactions. The present work could deepen the understanding of the energetic materials N8 under high pressure, and is of great significance to the blasting and detonation applications of N8.

Bounds on the superconducting transition temperature

I summarize recent progress on obtaining rigorous upper bounds on superconducting transition temperature [Formula: see text] in two dimensions independent of pairing mechanism or interaction strength. These results are derived by finding a general upper bound for the superfluid stiffness for a multi-band system with arbitrary interactions, with the only assumption that the external vector potential couples to the kinetic energy and not to the interactions. This bound is then combined with the universal relation between the superfluid stiffness and the Berezinskii–Kosterlitz–Thouless [Formula: see text] in 2D. For parabolic dispersion, one obtains the simple result that [Formula: see text], which has been tested in recent experiments. More generally, the bounds are expressed in terms of the optical spectral weight and lead to stringent constraints for the [Formula: see text] of low-density, strongly correlated superconductors. Results for [Formula: see text] bounds for models of flat-band superconductors, where the kinetic energy vanishes and the vector potential must couple to interactions, are briefly summarized. Upper bounds on [Formula: see text] in 3D remains an open problem, and I describe how questions of universality underlie the challenges in 3D.

Upregulation of the sodium potassium pump current supresses ectopic activity after stem cell delivery in the human-based heart after myocardial infarction

Abstract Background Cell therapy is being explored to restore the damaged and intrinsically irreparable human heart. Whilst preclinical studies showed improvements in cardiac function after injury, they also highlighted a critical pro-arrhythmic window when delivered cells produce ectopy-induced ventricular tachycardia. Recent experiments investigating the cells in vivo maturation suggested upregulation of the inward rectifier potassium current (IK1) and knock-out of the funny current (If) and sodium calcium exchanger (INaCa) to supress the arrhythmias[1]. Purpose Whilst promising, such modifications may impact the cells’ calcium dynamics and ultimately, their efficacy. The goal of this study is to identify novel ionic targets that improve therapy safety whilst maintaining efficacy by employing the unique predictive capabilities of modelling and simulation. Methods For this, we used our established modelling and simulation framework of cell therapy in the chronically infarcted human heart with Purkinje, validated against experimental and clinical data from the action potential to the ECG. We incorporated experimentally observed gene expression of in vivo cell maturation[1] into our framework to reproduce human pluripotent stem cell-induced cardiomyocyte (hPSC-CM) electrophysiology at day 0 and day 14 after injection. To consider variability amongst experimentally reported hPSC-CMs, we also created a fast-beating hPSC-CM model by upregulating the SERCA pump current, If and INaCa. Results Our results showed that while day 0 hPSC-CMs did not cause spontaneous activity, day 14 hPSC-CMs produced ectopic beats in the ventricles every 1.5s. The rapid beating hPSC-CM phenotype at day 14 elicited tachycardia through spontaneous beating and intermittent re-entrant wavefronts (see Figure 1). Next, we demonstrated 65% upregulation of the sodium-potassium pump current (INaK) together with a 50% increase in IK1 and knock-out of If as a novel pathway to quiescence. Importantly, our simulations highlighted that compared to INaCa knock-out, an increase in INaK allowed for physiological calcium transients. Conclusion To conclude, in this work we have utilised modelling and simulation of the injured human heart to 1) capture pre-clinically observed arrhythmias after cell therapy and 2) identify INaK upregulation as a novel target to mitigate safety concerns, whilst preserving efficacy.

Molecular dynamics study of N,N'-di-n-alkyl-3,4,9,10-perylenetetracarboxylic diimide (PTCDI)/rubrene interface: Why the charge transfer at the interface is optimized depending on the alkyl chain length of PTCDI.

Molecular dynamics simulations were performed to investigate the interfacial structure of the N,N'-di-n-alkyl-3,4,9,10-perylenetetracarboxylic diimide (PTCDI)/rubrene interface, which represents the donor/acceptor interface in new types of organic light-emission diodes. In particular, the interfacial structure was examined for different alkyl chain lengths of PTCDI (Cn-PTCDI) at n = 4, 8, and 13, in order to elucidate the observed maximum charge transfer efficiency at the C8-PTCDI/rubrene interface in a recent experiment. The results revealed that the molecular conformation of the acceptor (Cn-PTCDI) molecules at the interface undergoes changes depending on the alkyl chain length when interacting with the rubrene molecule. It was found that the closest complex between Cn-PTCDI and rubrene is formed at n = 8, consistent with the experimental observation. In addition, the interfacial structures of Cn-PTCDI/air and rubrene/air were examined and compared to gain insights into the inherent stability associated with the intermolecular interactions at the interface.

The fate of weakly bound light nuclei in central collider experiments: A challenge in favor of a late continuous decoupling mechanism

Arguments are presented that the reaction products of central high energy nuclear collisions up to collider energies can rigorously be interpreted in terms of a continuous decoupling mechanism based on continuous equations of motion. The various aspects of the collision dynamics are investigated in terms of the individual decoupling processes. Thereby each observed particle decouples during its own temporal decoupling window. This includes a “very late” decoupling of the faintly bound Hypertritons observed in recent ALICE experiments. The success of the strategy is based upon 200 years old wisdom and leads to a revised interpretation of the entire decoupling process.

Large Chiral Orbital Texture and Orbital Edelstein Effect in Co/Al Heterostructure.

Recent experiments by S. Krishnia et al. [Nano Lett. 2023, 23, 6785] reported an unprecedentedly large enhancement of torques upon inserting thin Al layer in Co/Pt heterostructure that suggested the presence of a Rashba-like interaction at the metallic Co/Al interface. Based on first-principles calculations, we reveal the emergence of a large helical orbital texture in reciprocal space at the interfacial Co layer, whose origin is attributed to the orbital Rashba effect due to the formation of the surface states at the Co/Al interface and where spin-orbit coupling is found to produce smaller contributions with a higher-order winding of the orbital moments. Our results unveil that the orbital texture gives rise to a nonequilibrium orbital accumulation producing large current-induced torques, thus providing an essential theoretical background for the experimental data and advancing the use of orbital transport phenomena in all-metallic magnetic systems with light elements.