Kaveh Edalati, Jacqueline Hidalgo-Jimenez, Thanh Tam Nguyen
The origin of life is yet a compelling scientific mystery that has sometimes been attributed to high-pressure impacts by small solar system bodies such as comets, meteoroids, asteroids, and transitional objects. High-pressure torsion (HPT) is an innovative method with which to simulate the extreme conditions of astronomical impacts and offers insights relevant to prebiotic chemistry. In the present study, we investigated the polymerization and stability of adenosine monophosphate (AMP), a key precursor to ribonucleic acid (RNA), in dry and hydrated conditions (10 wt% water) under 6 GPa at ambient and boiling water temperatures. Comprehensive analyses with the use of X-ray diffraction, Raman spectroscopy, Fourier-transform infrared spectroscopy, nuclear magnetic resonance, scanning electron microscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry revealed no evidence of polymerization, while AMP partly transformed to other organic compounds such as nucleobase-derived fragments of adenine, phosphoribose fragments, dehydrated adenosine, protonated adenosine, and oxidized adenosine. The torque measurements during HPT further highlight the mechanical behavior of AMP under extreme conditions. These findings suggest that, while HPT under the conditions tested does not facilitate polymerization, the formation of various compounds from AMP confirms the significance of astronomical impacts on the prebiotic chemistry of RNA on early Earth. Keywords: Ribonucleic acid (RNA), Origin of life; Phase transformations; Chemical reactions, Small solar system bodies
Deep learning, a subfield of machine learning, has gained importance in various application areas in recent years. Its growing popularity has led it to enter the natural sciences as well. This has created the need for molecular representations that are both machine-readable and understandable to scientists from different fields. Over the years, many chemical molecular representations have been constructed, and new ones continue to be developed as computer technology advances and knowledge of molecular complexity increases. This paper presents some of the most popular digital molecular representations inspired by natural language processing (NLP) and used in chemical informatics. In addition, the paper discusses some notable AI-based applications that use these representations. This paper aims to provide a guide to structural representations that are important for the application of AI in chemistry and materials science from the perspective of an NLP researcher. This review is a reference tool for researchers with little experience working with chemical representations who wish to work on projects at the interface of these fields.
Lukas Felix, Daniel Kitzmann, Brice-Olivier Demory
et al.
Recent JWST measurements allow access to the near-infrared spectrum of the sub-Neptune TOI-270 d, for which two different interpretations, a high-metallicity miscible envelope and a lower metallicity hycean world, are currently in conflict. Here, we reanalyze the published data and reproduce previously retrieved molecular abundances based on an independent data reduction and a different retrieval framework. The aim of this study is to refine the understanding of TOI-270 d and highlight considerations for JWST data analysis. Additionally, we test the impact of data resolution on atmospheric retrieval calculations. We reduce one JWST NIRSpec G395H and one NIRISS SOSS GR700XD transit dataset using the Eureka! pipeline and a custom MCMC-based light curve fitting algorithm at the instruments' native resolutions. The atmospheric composition is estimated with the updated BeAR retrieval code across a grid of retrieval setups and spectral resolutions. Our transit spectrum is consistent with previous studies, except at the red end of the NIRISS data. Our retrievals support a higher mean molecular weight atmosphere for TOI-270 d. We provide refined abundance constraints and find statistically favored model extensions indicating either sulfur-rich chemistry with species such as CS2, CS, and H2CS, or the possible presence of CH3Cl or CH3F. However, Bayesian inference cannot distinguish between these scenarios due to similar opacities below 4 microns. Our analysis reinforces TOI-270 d as a highly interesting warm sub-Neptune for atmospheric studies, with a complex chemistry in a cloud-free upper atmosphere. However, its exact nature remains uncertain and warrants further detailed photochemical modeling and observations.
Optically addressable spin systems, such as nitrogen-vacancy centers in diamond, have been widely studied for quantum sensing applications. In this work, we demonstrate that certain flavoproteins, specifically cryptochrome and iLOV, which generate spin correlated radical pairs upon optical excitation, also exhibit optically detected magnetic resonance (ODMR). Remarkably, the iLOV protein, commonly used in cellular imaging, displays ODMR contrast approaching 50%. We present initial applications including widefield magnetic field sensing and spatial modulation of photoluminescence using radiofrequency pulses and magnetic field gradients. Our results establish radical pairs in proteins as a novel platform for optically addressable spin systems, offering the key advantages of molecular designability and genetic encodability. Moreover, due to the spin-selective nature of radical pair chemistry, the results lay the groundwork for future radiofrequency-based manipulation of biological systems.
Irina A. Okkelman, Hang Zhou, Sergey M. Borisov
et al.
Abstract Increased micro- and nanoplastic (MNP) pollution poses significant health risks, yet the mechanisms of their accumulation and effects on absorptive tissues remain poorly understood. Addressing this knowledge gap requires tractable models coupled to dynamic live cell imaging methods, enabling multi-parameter single cell analysis. We report a new method combining adult stem cell-derived small intestinal organoid cultures with live fluorescence lifetime imaging microscopy (FLIM) to study MNP interactions with gut epithelium. To facilitate this, we optimized live imaging of porcine and mouse small intestinal organoids with an ‘apical-out’ topology. Subsequently, we produced a set of pristine MNPs based on PMMA and PS (<200 nm, doped with deep-red fluorescent dye) and evaluated their interaction with organoids displaying controlled epithelial polarity. We found that nanoparticles interacted differently with apical and basal membranes of the organoids and showed a species-specific pattern of cellular uptake. Using a phasor analysis approach, we demonstrate improved sensitivity of FLIM over conventional intensity-based microscopy. The resulting ‘fluorescence lifetime barcoding’ enabled distinguishing of different types of MNP and their interaction sites within organoids. Finally, we studied short (1 day)- and long (3 day)-term exposure effects of PMMA and PS-based MNPs on mitochondrial function, total cell energy budget and epithelial inflammation. We found that even pristine MNPs could disrupt chemokine production and mitochondrial membrane potential in intestinal epithelial cells. The presented FLIM approach will advance the study of MNP toxicity, their biological impacts on gastrointestinal tissue and enable the tracing of other fluorescent nanoparticles in live organoid and 3D ex vivo systems.
Zhong-Xia Shang, Han-Sen Zhong, Yu-Kun Zhang
et al.
In this work, we give a hybrid quantum-classical algorithm for solving electronic structure problems of molecules using only linear quantum optical systems. The variational ansatz we proposed is a hybrid of non-interacting Boson dynamics and classical computational chemistry methods, specifically, the Hartree-Fock method and the Configuration Interaction method. The Boson part is built by a linear optical interferometer which is easier to realize compared with the well-known Unitary Coupled Cluster (UCC) ansatz composed of quantum gates in conventional VQE and the classical part is merely classical processing acting on the Hamiltonian. We called such ansatzes Boson Sampling-Classic (BS-C). The appearance of permanents in the Boson part has its physical intuition to provide different kinds of resources from commonly used single-, double-, and higher-excitations in classical methods and the UCC ansatz to exploring chemical quantum states. Such resources can help enhance the accuracy of methods used in the classical parts. We give a scalable hybrid homodyne and photon number measurement procedure for evaluating the energy value which has intrinsic abilities to mitigate photon loss errors and discuss the extra measurement cost induced by the no Pauli exclusion principle for Bosons with its solutions. To demonstrate our proposal, we run numerical experiments on several molecules and obtain their potential energy curves reaching chemical accuracy.
The ground state of second-quantized quantum chemistry Hamiltonians provides access to an important set of chemical properties. Wavefunctions based on ML architectures have shown promise in approximating these ground states in a variety of physical systems. In this work, we show how to achieve state-of-the-art energies for molecular Hamiltonians using the the neural network backflow wave-function. To accomplish this, we optimize this ansatz with a variant of the deterministic optimization scheme based on SCI introduced by [Li, et. al JCTC (2023)] which we find works better than standard MCMC sampling. For the molecules we studied, NNBF gives lower energy states than both CCSD and other neural network quantum states. We systematically explore the role of network size as well as optimization parameters in improving the energy. We find that while the number of hidden layers and determinants play a minor role in improving the energy, there is significant improvements in the energy from increasing the number of hidden units as well as the batch size used in optimization with the batch size playing a more important role.
Abstract Damage and fracture of archaeological potteries not only jeopardize the long-term preservation but also hinder their exhibition. To repair these pottery sherds effectively, this study introduces a novel inorganic phosphate-based adhesive and evaluates its effectiveness through a series of experiments. To determine the optimal base adhesive, the paper investigates the influence of varying weight ratios of the H2O–H3PO4 system and the Al(OH)3–H3PO4 system on properties including tensile lap-shear strength, microstructure, high-temperature resistance and phase composition. However, the original black color of the traditional CuO–phosphate adhesive limits its application. The innovation of this study lies in the addition of nano-TiO2 to the adhesive, which not only improves the bonding strength but also adjusts the color of the adhesive. This study has defined the optimal formulation (i.e., base adhesive = m[Al(OH)3]:m[H3PO4] = 7:100, filler = 10wt% nano-TiO2), and the final product shows no residual acid in adhesives. Additionally, the fracture surfaces are successfully bonded with a high strength of 3.56 MPa. Various ageing tests including dry-thermal ageing, hygrothermal ageing and UV irradiation ageing are conducted to assess the ageing resistance of the inorganic phosphate-based adhesive. The results indicate strong tolerance of adhesive to high temperature and high humidity environment. Preliminary applications in archaeological pottery restoration suggest that the inorganic phosphate-based adhesive offers considerable promise for repairing shattered pottery. Graphical Abstract
Abstract Quantifying small amounts of the 17-hydroxyprogesterone in various matrix is crucial for different purposes. In this study, a commercial polydimethylsiloxane stir bar was used to extract hormone from water and urine samples. Analysis was performed by high-performance liquid chromatography using a UV detector. The response surface methodology was used to optimize the desorption and extraction steps, with predicted optimal point relative errors of 1.25% and 6.40%, respectively. The optimized method was validated with a linear range of 1.21–1000.00 for aqueous and 2.43–2000.00 ng mL–1 for urine samples. The coefficient of determination was 0.9998 and 0.9967, and the detection limit of the proposed method was obtained to be 0.40 and 0.80 ng mL–1 for aqueous and urine samples, respectively. The recovery percentage and relative standard deviation within a day and between three days after the addition of three different concentration levels of the standard to the control sample were 87–103% and 0.4–3.6% for aqueous and 87.5–101% and 0.1–5.2% for urine samples, respectively. The results show that the proposed method can be appropriate and cost-effective for extracting and analyzing this hormone. In addition, using three different tools, the greenness of the proposed method was proven.
Abstract Heritage sites in Alexandria, Egypt, are some of the UNESCO world heritage sites at high risk from geo-environmental hazards, in particular caused by sea level rise and heavy rain due to the climate change. Recently, safeguarding UNESCO world subterranean and built heritage draws more attention. After recent environmental catastrophies in Alexandria, sustainable conservation materials and stabilizing configurations of underground monumental structures has also become urgent and highly demanded. Based on typical damage due to the heavy weathering caused by the ground water table and salt, this paper offers a guide for engineers and conservators, where rock structures consolidation and stabilizing configurations to protect these structures in the static state and against strong seismic events is presented. In this paper, typical geotechnical problems and damage to the Catacombs of of Kom El-Shoqafa are presented first, followed by an experimental evaluation methodology that includes spectroscopic and morphological characterization in addition to the mechanical testing of untreated and treated rock samples with synthetic organosilicone and acrylic compounds. The effectiveness of the new silica-based consolidants was evaluated in terms of the amount of solid adsorbed, mechanical properties (e.g., surface hardness, ultrasonic velocity, modulus of elasticity and modulus of compressive strength), and resistance to salt crystallization. The treated groups showed better mechanical strength than the control group. The ability of the treated samples to resist climate change negative impact was also greatly improved. According to laboratory tests, new silica-based hardeners and hydrophobic materials have great potential for strengthening weathered Calcarenitic rock structures. It was observed that the rock samples containing the modified binder (MTMOS + Wacher BS 15) reach higher mechanical strength parameters. After the experimental study (testing procedures), FEM analysis was performed using PLAXIS 2D code to validate the silica-based consolidants and verify their efficiency in improving the response of rock structures in static and seismic states against strong earthquake events. The results of this work confirm the high potential of low-cost injection techniques and stabilizing configurations (pre- stressed anchors and concrete friction piles) technology, confirming the possibility of achieving significant improvement in the geotechnical properties of Calcarenitic rock structures and enhancing the seismic performance of underground archaeological structures using low-cost injection technology that is easy to manufacture.
Assalamu’alaikum Wr. Wb.
Alhamdulillahirabbil ‘alamin. The next edition of the Borneo Journal of Pharmacy (Borneo J Pharm) was published in February 2024. This edition contains ten articles: Pharmacognosy-Phytochemistry, Analytical Pharmacy-Medicinal Chemistry, and Clinical-Community Pharmacy. This edition includes writings from four countries: India, Indonesia, South Africa, and Thailand. The authors come from several institutions, including Universitas Muhammadiyah Kalimantan Timur, Universitas Gadjah Mada, Khon Kaen University, Universitas Muhammadiyah Surakarta, University of the Witwatersrand, Universitas Sanata Dharma, Universitas Halu Oleo, Universitas Bhakti Kencana, Universitas Negeri Gorontalo, Sekolah Tinggi Farmasi Mahaganesha, Universitas Tanjungpura, National Research and Innovation Agency of the Republic of Indonesia, Universitas Surabaya, Universitas Airlangga, Universitas Indonesia, M. S. Ramaiah University of Applied Sciences, and Universitas Muhammadiyah Yogyakarta.
Editorial boards are fully aware that this edition has room for improvement. Hence, with all humility, we are willing to accept constructive suggestions and feedback for improvements to the publication for the next editions. The editorial board would like to thank all editors, reviewers, and contributors of the scientific articles who have provided the repertoire in this issue. We hope all parties, especially the contributors, can re-participate in the publication in the next edition in May 2024.
Wassalamu’alaikum Wr. Wb.
Protoplanetary disks around Herbig AeBe stars are exciting targets for studying the chemical environments where giant planets form. Save for a few disks, however, much of Herbig AeBe disk chemistry is an open frontier. We present a Submillimeter Array (SMA) $\sim$213-268 GHz pilot survey of mm continuum, CO isotopologues, and other small molecules in disks around five Herbig AeBe stars (HD 34282, HD 36112, HD 38120, HD 142666, and HD 144432). We detect or tentatively detect $^{12}$CO 2--1 and $^{13}$CO 2--1 from four disks; C$^{18}$O 2--1 and HCO$^+$ 3--2 from three disks; HCN 3--2, CS 5--4, and DCO$^+$ 3--2 from two disks; and C$_2$H 3--2 and DCN 3--2 from one disk each. H$_2$CO 3--2 is undetected at the sensitivity of our observations. The mm continuum images of HD 34282 suggest a faint, unresolved source $\sim$5\farcs0 away, which could arise from a distant orbital companion or an extended spiral arm. We fold our sample into a compilation of T Tauri and Herbig AeBe/F disks from the literature. Altogether, most line fluxes generally increase with mm continuum flux. Line flux ratios between CO 2--1 isotopologues are nearest to unity for the Herbig AeBe/F disks. This may indicate emitting layers with relatively similar, warmer temperatures and more abundant CO relative to disk dust mass. Lower HCO$^+$ 3--2 flux ratios may reflect less ionization in Herbig AeBe/F disks. Smaller detection rates and flux ratios for DCO$^+$ 3--2, DCN 3--2, and H$_2$CO 3--2 suggest smaller regimes of cold chemistry around the luminous Herbig AeBe/F stars.
Quantum computing is emerging as a new computational paradigm with the potential to transform several research fields, including quantum chemistry. However, current hardware limitations (including limited coherence times, gate infidelities, and limited connectivity) hamper the straightforward implementation of most quantum algorithms and call for more noise-resilient solutions. In quantum chemistry, the limited number of available qubits and gate operations is particularly restrictive since, for each molecular orbital, one needs, in general, two qubits. In this study, we propose an explicitly correlated Ansatz based on the transcorrelated (TC) approach, which transfers -- without any approximation -- correlation from the wavefunction directly into the Hamiltonian, thus reducing the number of resources needed to achieve accurate results with noisy, near-term quantum devices. In particular, we show that the exact transcorrelated approach not only allows for more shallow circuits but also improves the convergence towards the so-called basis set limit, providing energies within chemical accuracy to experiment with smaller basis sets and, therefore, fewer qubits. We demonstrate our method by computing bond lengths, dissociation energies, and vibrational frequencies close to experimental results for the hydrogen dimer and lithium hydride using just 4 and 6 qubits, respectively. Conventional methods require at least ten times more qubits for the same accuracy.
Ruhee D'Cunha, Matthew Otten, Matthew R. Hermes
et al.
State preparation for quantum algorithms is crucial for achieving high accuracy in quantum chemistry and competing with classical algorithms. The localized active space unitary coupled cluster (LAS-UCC) algorithm iteratively loads a fragment-based multireference wave function onto a quantum computer. In this study, we compare two state preparation methods, quantum phase estimation (QPE) and direct initialization (DI), for each fragment. We analyze the impact of QPE parameters, such as the number of ancilla qubits and Trotter steps, on the prepared state. We find a trade-off between the methods, where DI requires fewer resources for smaller fragments, while QPE is more efficient for larger fragments. Our resource estimates highlight the benefits of system fragmentation in state preparation for subsequent quantum chemical calculations. These findings have broad applications for preparing multireference quantum chemical wave functions on quantum circuits, particularly via QPE circuits.
Eleonora Bianchi, Anthony Remijan, Claudio Codella
et al.
We report a comprehensive study of the cyanopolyyne chemistry in the prototypical prestellar core L1544. Using the 100m Robert C. Byrd Green Bank Telescope (GBT) we observe 3 emission lines of HC$_3$N, 9 lines of HC$_5$N, 5 lines of HC$_7$N, and 9 lines of HC$_9$N. HC$_9$N is detected for the first time towards the source. The high spectral resolution ($\sim$ 0.05 km s$^{-1}$) reveals double-peak spectral line profiles with the redshifted peak a factor 3-5 brighter. Resolved maps of the core in other molecular tracers indicates that the southern region is redshifted. Therefore, the bulk of the cyanopolyyne emission is likely associated with the southern region of the core, where free carbon atoms are available to form long chains, thanks to the more efficient illumination of the interstellar field radiation. We perform a simultaneous modelling of the HC$_5$N, HC$_7$N, and HC$_9$N lines, to investigate the origin of the emission. To enable this analysis, we performed new calculation of the collisional coefficients. The simultaneous fitting indicates a gas kinetic temperature of 5--12 K, a source size of 80$\arcsec$, and a gas density larger than 100 cm$^{-3}$. The HC$_5$N:HC$_7$N:HC$_9$N abundance ratios measured in L1544 are about 1:6:4. We compare our observations with those towards the the well-studied starless core TMC-1 and with the available measurements in different star-forming regions. The comparison suggests that a complex carbon chain chemistry is active in other sources and it is related to the presence of free gaseous carbon. Finally, we discuss the possible formation and destruction routes in the light of the new observations.
Hanane Fatma Chentouf, Fouzia Rahli, Zineb Benmechernene
et al.
Abstract Background Eighty-three strains of Leuconostoc mesenteroides were isolated from Algerian raw camel milk. Based on morphological, biochemical, and physiological characters tests, strains were identified as Ln. mesenteroides subsp. mesenteroides. Seven strains had a remarkable antagonistic and probiotic characterization. The present study aims at identifying these strains by means of 16 s rRNA gene sequencing and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), extending phenotypic and genotypic studies done previously. Results The phyloproteomic dendrograms of the studied strains based on MALDI-TOF MS provided the same identification with more intraspecific information from the 16S rRNA gene sequencing based on phylogenetic analysis. The latter were in agreement with the previous biochemical/physiological identification, the seven isolated strains were Ln. mesenteroides subsp. mesenteroides. Conclusions Remarkably, MALDI-TOF MS fingerprinting was found to be effective enough as 16S rRNA gene sequencing identification, allowing faster and more reliable analysis than biochemical/physiological methods.
Variational optimization of neural-network representations of quantum states has been successfully applied to solve interacting fermionic problems. Despite rapid developments, significant scalability challenges arise when considering molecules of large scale, which correspond to non-locally interacting quantum spin Hamiltonians consisting of sums of thousands or even millions of Pauli operators. In this work, we introduce scalable parallelization strategies to improve neural-network-based variational quantum Monte Carlo calculations for ab-initio quantum chemistry applications. We establish GPU-supported local energy parallelism to compute the optimization objective for Hamiltonians of potentially complex molecules. Using autoregressive sampling techniques, we demonstrate systematic improvement in wall-clock timings required to achieve CCSD baseline target energies. The performance is further enhanced by accommodating the structure of resultant spin Hamiltonians into the autoregressive sampling ordering. The algorithm achieves promising performance in comparison with the classical approximate methods and exhibits both running time and scalability advantages over existing neural-network based methods.
Hans Hon Sang Chan, Richard Meister, Tyson Jones
et al.
First quantized, grid-based methods for chemistry modelling are a natural and elegant fit for quantum computers. However, it is infeasible to use today's quantum prototypes to explore the power of this approach, because it requires a significant number of near-perfect qubits. Here we employ exactly-emulated quantum computers with up to 36 qubits, to execute deep yet resource-frugal algorithms that model 2D and 3D atoms with single and paired particles. A range of tasks is explored, from ground state preparation and energy estimation to the dynamics of scattering and ionisation; we evaluate various methods within the split-operator QFT (SO-QFT) Hamiltonian simulation paradigm, including protocols previously-described in theoretical papers as well as our own novel techniques. While we identify certain restrictions and caveats, generally the grid-based method is found to perform very well; our results are consistent with the view that first quantized paradigms will be dominant from the early fault-tolerant quantum computing era onward.