Experimental Discovery Research Articles

HemoNet: Predicting hemolytic activity of peptides with integrated feature learning.

Quantifying the hemolytic activity of peptides is a crucial step in the discovery of novel therapeutic peptides. Computational methods are attractive in this domain due to their ability to guide wet-lab experimental discovery or screening of peptides based on their hemolytic activity. However, existing methods are unable to accurately model various important aspects of this predictive problem such as the role of N/C-terminal modifications, D- and L- amino acids, etc. In this work, we have developed a novel neural network-based approach called HemoNet for predicting the hemolytic activity of peptides. The proposed method captures the contextual importance of different amino acids in a given peptide sequence using a specialized feature embedding in conjunction with SMILES-based fingerprint representation of N/C-terminal modifications. We have analyzed the predictive performance of the proposed method using stratified cross-validation in comparison with previous methods, non-redundant cross-validation as well as validation on external peptides and clinical antimicrobial peptides. Our analysis shows the proposed approach achieves significantly better predictive performance (AUC-ROC of 88%) in comparison to previous approaches (HemoPI and HemoPred with AUC-ROC of 73%). HemoNet can be a useful tool in the search for novel therapeutic peptides. The python implementation of the proposed method is available at the URL: https://github.com/adibayaseen/HemoNet.

Classifying Charge Carrier Interaction in Highly Compressed Elements and Silane.

Since the pivotal experimental discovery of near-room-temperature superconductivity (NRTS) in highly compressed sulphur hydride by Drozdov et al. (Nature 2015, 525, 73–76), more than a dozen binary and ternary hydrogen-rich phases exhibiting superconducting transitions above 100 K have been discovered to date. There is a widely accepted theoretical point of view that the primary mechanism governing the emergence of superconductivity in hydrogen-rich phases is the electron–phonon pairing. However, the recent analysis of experimental temperature-dependent resistance, R(T), in H3S, LaHx, PrH9 and BaH12 (Talantsev, Supercond. Sci. Technol. 2021, 34, accepted) showed that these compounds exhibit the dominance of non-electron–phonon charge carrier interactions and, thus, it is unlikely that the electron–phonon pairing is the primary mechanism for the emergence of superconductivity in these materials. Here, we use the same approach to reveal the charge carrier interaction in highly compressed lithium, black phosphorous, sulfur, and silane. We found that all these superconductors exhibit the dominance of non-electron–phonon charge carrier interaction. This explains the failure to demonstrate the high-Tc values that are predicted for these materials by first-principles calculations which utilize the electron–phonon pairing as the mechanism for the emergence of their superconductivity. Our result implies that alternative pairing mechanisms (primarily the electron–electron retraction) should be tested within the first-principles calculations approach as possible mechanisms for the emergence of superconductivity in highly compressed lithium, black phosphorous, sulfur, and silane.

Recent progress on 2D magnets: Fundamental mechanism, structural design and modification

The two-dimensional (2D) magnet, a long-standing missing member in the family of 2D functional materials, is promising for next-generation information technology. The recent experimental discovery of 2D magnetic ordering in CrI3, Cr2Ge2Te6, VSe2, and Fe3GeTe2 has stimulated intense research activities to expand the scope of 2D magnets. This review covers the essential progress on 2D magnets, with an emphasis on the current understanding of the magnetic exchange interaction, the databases of 2D magnets, and the modification strategies for modulation of magnetism. We will address a large number of 2D intrinsic magnetic materials, including binary transition metal halogenides; chalogenides; carbides; nitrides; oxides; borides; silicides; MXene; ternary transition metal compounds CrXTe3, MPX3, Fe-Ge-Te, MBi2Te4, and MXY (M = transition metal; X = O, S, Se, Te, N; Y = Cl, Br, I); f-state magnets; p-state magnets; and organic magnets. Their electronic structure, magnetic moment, Curie temperature, and magnetic anisotropy energy will be presented. According to the specific 2D magnets, the underlying direct, superexchange, double exchange, super-superexchange, extended superexchange, and multi-intermediate double exchange interactions will be described. In addition, we will also highlight the effective strategies to manipulate the interatomic exchange mechanism to improve the Curie temperature of 2D magnets, such as chemical functionalization, isoelectronic substitution, alloying, strain engineering, defect engineering, applying electronic/magnetic field, interlayer coupling, carrier doping, optical controlling, and intercalation. We hope this review will contribute to understanding the magnetic exchange interaction of existing 2D magnets, developing unprecedented 2D magnets with desired properties, and offering new perspectives in this rapidly expanding field.

Sensorless Human-Robot Collaborative Assembly Considering Load and Friction Compensation

The collaboration of humans and robots can combine human flexibility with the efficiency of robots, so that robots can accomplish a variety of complex tasks, such as handling and assembly. However, most robots have poor collaboration capabilities and rely on expensive sensors to obtain the force interaction information of limited space range. To solve this problem, a human-robot collaborative assembly scheme without using additional force/torque sensors is proposed in this letter. First, a load identification and compensation method that does not require the load model is proposed to realize the decoupling of load force and human-robot interaction force. Next, to realize a compliant dragging effect of robots, an improved LuGre friction model is proposed based on the experimental discovery that the motion of the load has a non-negligible effect on the friction torque of robot joints. Finally, the kinesthetic teaching experiments of compliant assembly using a universal 6-DOF collaborative robot have been completed by designing a task-determined adaptive impedance control algorithm. The experimental results prove that the proposed scheme can effectively improve the safety, compliance, and flexibility of the loaded robots compared with the existing position-encoded robots, indicating its great potential for industry application.

On the unity between observational and experimental causal discovery

In “Flagpoles anyone? Causal and explanatory asymmetries”, James Woodward supplements his celebrated interventionist account of causation and explanation with a set of new ideas about causal and explanatory asymmetries, which he extracts from some cutting-edge methods for causal discovery from observational data. Among other things, Woodward draws interesting connections between observational causal discovery and interventionist themes that are inspired in the first place by experimental causal discovery, alluding to a sort of unity between observational and experimental causal discovery. In this paper, I make explicit what I take to be the implicated unity. Like experimental causal discovery, observational causal discovery also relies on interventions (or exogenous variations, to be more accurate), albeit interventions that are not carried out by investigators and hence need to be detected as part of the inference. The observational patterns appealed to in observational causal discovery are not only surrogates for would-be interventions, as Woodward sometimes puts it; they also serve to mark relevant interventions that actually happen in the data generating process.

Diabatic description of bottomoniumlike mesons

We apply the diabatic approach, specially suited for a QCD based study of conventional (quark-antiquark) and unconventional (quark-antiquark + meson-meson) meson states, to the description of hidden-bottom mesons. A spectral analysis of the $I=0$, $J^{++}$ and $1^{--}$ resonances with masses up to about $10.8$ GeV is carried out. Masses and widths of all the experimentally known resonances, including conventional and unconventional states, can be well reproduced. In particular, we predict a significant $B\bar{B}^{\ast}$ component in $\Upsilon(10580)$. We also predict the existence of a not yet discovered unconventional $1^{++}$ narrow state, with a significant $B_{s}\bar{B}_{s}^{\ast}$ content making it to decay into $\Upsilon(1S)\phi$, whose experimental discovery would provide definite support to our theoretical analysis.

Thermoelectrics by Computational Design: Progress and Opportunities

The performance of thermoelectric materials is determined by their electrical and thermal transport properties that are very sensitive to small modifications of composition and microstructure. Discovery and design of next-generation materials are starting to be accelerated by computational guidance. We review progress and challenges in the development of accurate and efficient first-principles methods for computing transport coefficients and illustrate approaches for both rapid materials screening and focused optimization. Particularly important and challenging are computations of electron and phonon scattering rates that enter the Boltzmann transport equations, and this is where there are many opportunities for improving computational methods. We highlight the first successful examples of computation-driven discoveries of high-performance materials and discuss avenues for tightening the interaction between theoretical and experimental materials discovery and optimization.

Sesamolin Protects Mice From Ovariectomized Bone Loss by Inhibiting Osteoclastogenesis and RANKL-Mediated NF-κB and MAPK Signaling Pathways.

This article was submitted to Experimental Pharmacology and Drug Discovery, a section of the journal Frontiers in Pharmacology. Postmenopausal osteoporosis (PMOP), which increases the risk of fracture, is the most common bone disease in women. PMOP not only increases the risk of death but also imposes a financial burden on countless families. At present, most of the drugs used to treat osteoporosis have significant side effects, so it is important to find effective anti-osteoporosis medications without major side effects. Sesamolin (Ses) is a kind of natural lignan extracted from sesame oil. Many researches have shown that Ses has anti-inflammatory, antioxidative, and anticancer effects, however it is still unknown whether it has any effect on osteoporosis. In this research, we explored the therapeutic effect of Ses in the process of osteoclast formation and bone resorption and found that Ses effectively inhibited osteoclast formation in vitro through TRAcP staining and hydroxyapatite resorption assays. Through Western blot analysis of the NF-κB pathway, MAPK pathway, c-Fos and NFATc1, it was found that Ses not only effectively inhibited the activation of NF-κB and MAPK signaling pathways induced by RANKL but also significantly reduced the protein expression of c-Fos and NFATc1. Several genes specifically expressed in osteoclasts were determined by qPCR, and Ses was also found to play a significant inhibitory role on the expression of these genes. Besides, an osteoporosis model induced in ovariectomized (OVX) mice was employed to verify that Ses could effectively reduce bone loss caused by estrogen deficiency in vivo. In conclusion, Ses showed promise as a new treatment for postmenopausal osteoporosis.

Observation of domain wall bimerons in chiral magnets

Topological defects embedded in or combined with domain walls have been proposed in various systems, some of which are referred to as domain wall skyrmions or domain wall bimerons. However, the experimental observation of such topological defects remains an ongoing challenge. Here, using Lorentz transmission electron microscopy, we report the experimental discovery of domain wall bimerons in chiral magnet Co-Zn-Mn(110) thin films. By applying a magnetic field, multidomain structures develop, and simultaneously, chained or isolated bimerons arise as the localized state between the domains with the opposite in-plane components of net magnetization. The multidomain formation is attributed to magnetic anisotropy and dipolar interaction, and domain wall bimerons are stabilized by the Dzyaloshinskii-Moriya interaction. In addition, micromagnetic simulations show that domain wall bimerons appear for a wide range of conditions in chiral magnets with cubic magnetic anisotropy. Our results promote further study in various fields of physics.

High-temperature antiferromagnetism in Yb based heavy fermion systems proximate to a Kondo insulator

Given the parallelism between the physical properties of Ce and Yb based magnets and heavy fermions due to the electron-hole symmetry, it has been rather odd that the transition temperature of the Yb based compounds is normally very small, as low as $\sim$ 1 K or even lower, whereas Ce counterparts may often have the transition temperature well exceeding 10 K. Here, we report our experimental discovery of the transition temperature reaching 20 K for the first time in a Yb based compound at ambient pressure. The Mn substitution at the Al site in an intermediate valence state of $\alpha$-YbAlB$_{4}$ not only induces antiferromagnetic transition at a record high temperature of 20 K but also transforms the heavy fermion liquid state in $\alpha$-YbAlB$_{4}$ into a highly resistive metallic state proximate to a Kondo insulator.

Flexoelectricity in soft elastomers and the molecular mechanisms underpinning the design and emergence of giant flexoelectricity

Soft robotics requires materials that are capable of large deformation and amenable to actuation with external stimuli such as electric fields. Energy harvesting, biomedical devices, flexible electronics, and sensors are some other applications enabled by electroactive soft materials. The phenomenon of flexoelectricity is an enticing alternative that refers to the development of electric polarization in dielectrics when subjected to strain gradients. In particular, flexoelectricity offers a direct linear coupling between a highly desirable deformation mode (flexure) and electric stimulus. Unfortunately, barring some exceptions, the flexoelectric effect is quite weak and rather substantial bending curvatures are required for an appreciable electromechanical response. Most experiments in the literature appear to confirm modest flexoelectricity in polymers although perplexingly, a singular work has measured a "giant" effect in elastomers under some specific conditions. Due to the lack of an understanding of the microscopic underpinnings of flexoelectricity in elastomers and a commensurate theory, it is not currently possible to either explain the contradictory experimental results on elastomers or pursue avenues for possible design of large flexoelectricity. In this work, we present a statistical-mechanics theory for the emergent flexoelectricity of elastomers consisting of polar monomers. The theory is shown to be valid in broad generality and leads to key insights regarding both giant flexoelectricity and material design. In particular, the theory shows that, in standard elastomer networks, combining stretching and bending is a mechanism for obtaining giant flexoelectricity, which also explains the aforementioned, surprising experimental discovery.

Brief Review of the Results Regarding the Possible Underlying Mechanisms Driving the Neutrinoless Double Beta Decay

Since the experimental discovery of neutrino oscillations, the search for the neutrinoless double beta (0νββ) decay has intensified greatly, as this particular decay mode, if experimentally discovered, could offer a testing ground for Beyond Standard Model (BSM) theories related to the yet hidden fundamental properties of neutrinos and the possibility of violating of some fundamental symmetries. In this work we make a brief review of the nuclear matrix elements and phase space factors calculations performed mainly by our group. Next, using these calculations and the most recent experimental half-life limits, we revise the constraints on the BSM parameters violating the lepton number corresponding to four mechanisms that could contribute to 0νββ decay. Finally, using the values obtained for the BSM parameters from one of the most sensitive double-beta decay experiments, we provide a comparison with the sensitivities of other experiments.

Crick's Adaptor Hypothesis and the Discovery of Transfer RNA: Experiment Surpassing Theoretical Prediction

Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids are incorporated into growing protein chains. Independently from and concomitantly with Crick’s hypothesis, Mahlon Hoagland and Paul Zamecnik conducted experiments with no guiding theory that culminated in discoveries of the actual adaptors, transfer RNA (tRNA) molecules, and their amino acids charging enzymes. This paper traces the parallel histories of Crick’s adaptor hypothesis and of the experimental discovery of tRNA and compares their relative impacts on the scientific community. Remarkably, despite the brilliance of Crick’s confirmed prognostication, it had marginal impact on practicing scientists. Conversely, Hoagland and Zamecnik’s experimental discoveries and their evidence-based model of protein synthesis had immediate and enduring impact. I discuss possible explanations for the different impacts of the theoretical prediction and experimental identifications of the same entities.

Weyl, Dirac and high-fold chiral fermions in topological quantum matter

Quantum materials hosting Weyl fermions have opened a new era of research in condensed matter physics. First proposed in 1929 in particle physics, Weyl fermions have yet to be observed as elementary particles. In 2015, Weyl fermions were detected as collective electronic excitations in the strong spin-orbit coupled material tantalum arsenide, TaAs. This discovery was followed by a flurry of experimental and theoretical explorations of Weyl phenomena in materials. Weyl materials naturally lend themselves to the exploration of the topological index associated with Weyl fermions and their divergent Berry curvature field, as well as the topological bulk-boundary correspondence giving rise to protected conducting surface states. Here, we review the broader class of Weyl topological phenomena in materials, starting with the observation of emergent Weyl fermions in the bulk and of Fermi arc states on the surface of the TaAs family of crystals by photoemission spectroscopy. We then discuss some of the exotic optical and magnetic responses observed in these materials, as well as the progress in developing some of the related chiral materials. We discuss the conceptual development of high-fold chiral fermions, which generalize Weyl fermions, and we review the observation of high-fold chiral fermion phases by taking the rhodium silicide, RhSi, family of crystals as a prime example. Lastly, we discuss recent advances in Weyl-line phases in magnetic topological materials. With this Review, we aim to provide an introduction to the basic concepts underlying Weyl physics in condensed matter, and to representative materials and their electronic structures and topology as revealed by spectroscopic studies. We hope this work serves as a guide for future theoretical and experimental explorations of chiral fermions and related topological quantum systems with potentially enhanced functionalities.

Controlling chaos by the system size

Despite the ubiquity of physical systems evolving on time-dependent spatial domains, understanding their regular and chaotic dynamics is still in a rudimentary state. While chaos implies that the system’s behavior can be altered by small perturbations, this sensitivity proves to be useful for control purposes. Here we report on the experimental discovery of a novel mechanism to control chaos by time-variation of the system (spatial domain) size: depending upon the rate of the latter, the chaotic state may be completely prevented. Our experimental observations are disentangled with theoretical insights and numerical modeling, which also reveals the ability to control spatio-temporal chaos, thus making the findings relevant to a wide range of natural phenomena.

Diabatic description of charmoniumlike mesons. II. Mass corrections and strong decay widths

From a diabatic bound state approach to $J^{PC}=1^{--}$ and $(0,1,2)^{++}$ charmoniumlike resonances below $4.1$ GeV, formulated in terms of ${c\overline{c}}$ and closed meson-meson channels, we calculate mass shifts and widths due to open meson-meson channels. This calculation does not involve any new free parameter, so comparison of our predictions with existing data provides a direct test of our approach. Further mass corrections are also estimated and good agreement with the measured masses comes out. As for the calculated widths, overall reasonable, they point out to the need of some refinement of our current bound state approximation for an accurate description of data. These results give additional support to the diabatic approach in QCD as an adequate framework for a complete unified description of conventional and unconventional charmoniumlike resonances. In this respect, the experimental discovery of a predicted $2^{++}$ resonance with a mass around $4$ GeV would be of special relevance.

Application of Artificial Neural Network(ANN) and Feature Selection Algorithm(FSA) on the ATLAS Experiment Data to Identify Higgs Boson

From the 1950s, physicists started to smash particles together to temporarily form new smaller particles for observing and studying. With further development and enormous experiments, physicists had successfully built the Large Hadron Collider, which became the key hardware for proton colliding. The historical research and experiment in this field have provided us a number of referring data from the LHC experiment and the detailed information of the LHC upgrade to LH-LHC during the previous several years. The Higgs Boson detected by ATLAS Detector in 2013 was significant to scientific research, and its associated dataset could form a new hypothesis to predict the universe rule for small particles. In this study, both Artificial Neural Network(ANN) and Feature Selection Algorithm(FSA) are applied to the ATLAS experiment data to identify Higgs Boson, including the characteristics and fitness for the current model of nature. The study is based on the experiment result of head-on collisions of protons of extraordinarily high energy. The study is aimed to explore the potential of both methods of ANN and FSA to improve the significance of the experiment study and discovery. It will benefit further study to develop the full potential and the enormous scope of physics opportunities given by LHC.

Discovery of Two-Dimensional Electromagnetic Plasma Waves

We report the experimental discovery of "superluminal" electromagnetic 2D plasma waves in the electromagnetic response of a high-quality GaAs/AlGaAs two-dimensional electron system on a dielectric substrate. We measure the plasma wave spectrum on samples with different electron density. It is established that, at large two-dimensional densities, there is a strong hybridization between the plasma and the Fabry-Perot light modes. In the presence of a perpendicular magnetic field, the plasma resonance is shown to split into two modes, each corresponding to a particular sense of circular polarization. Experimental results are found to be in good agreement with the theory.

Integrating Computational and Experimental Workflows for Accelerated Organic Materials Discovery.

Organic materials find application in a range of areas, including optoelectronics, sensing, encapsulation, molecular separations, and photocatalysis. The discovery of materials is frustratingly slow however, particularly when contrasted to the vast chemical space of possibilities based on the near limitless options for organic molecular precursors. The difficulty in predicting the material assembly, and consequent properties, of any molecule is another significant roadblock to targeted materials design. There has been significant progress in the development of computational approaches to screen large numbers of materials, for both their structure and properties, helping guide synthetic researchers toward promising materials. In particular, artificial intelligence techniques have the potential to make significant impact in many elements of the discovery process. Alongside this, automation and robotics are increasing the scale and speed with which materials synthesis can be realized. Herein, the focus is on demonstrating the power of integrating computational and experimental materials discovery programmes, including both a summary of key situations where approaches can be combined and a series of case studies that demonstrate recent successes.

Experimental investigation on the susceptibility of minimal networks to a change in topology and number of oscillators.

Understanding the global dynamical behavior of a network of coupled oscillators has been a topic of immense research in many fields of science and engineering. Various factors govern the resulting dynamical behavior of such networks, including the number of oscillators and their coupling schemes. Although these factors are seldom significant in large populations, a small change in them can drastically affect the global behavior in small populations. In this paper, we perform an experimental investigation on the effect of these factors on the coupled behavior of a minimal network of candle-flame oscillators. We observe that strongly coupled oscillators exhibit the global behavior of in-phase synchrony and amplitude death, irrespective of the number and the topology of oscillators. However, when they are weakly coupled, their global behavior exhibits the intermittent occurrence of multiple stable states in time. We report the experimental discovery of partial amplitude death in a network of candle-flame oscillators, in addition to the observation of other dynamical states including clustering, chimera, and weak chimera. We also show that closed-loop networks tend to hold global synchronization for longer duration as compared to open-loop networks.