Molecular System Research Articles

Classification of complex local environments in systems of particle shapes through shape symmetry-encoded data augmentation.

Detecting and analyzing the local environment is crucial for investigating the dynamical processes of crystal nucleation and shape colloidal particle self-assembly. Recent developments in machine learning provide a promising avenue for better order parameters in complex systems that are challenging to study using traditional approaches. However, the application of machine learning to self-assembly on systems of particle shapes is still underexplored. To address this gap, we propose a simple, physics-agnostic, yet powerful approach that involves training a multilayer perceptron (MLP) as a local environment classifier for systems of particle shapes, using input features such as particle distances and orientations. Our MLP classifier is trained in a supervised manner with a shape symmetry-encoded data augmentation technique without the need for any conventional roto-translations invariant symmetry functions. We evaluate the performance of our classifiers on four different scenarios involving self-assembly of cubic structures, two-dimensional and three-dimensional patchy particle shape systems, hexagonal bipyramids with varying aspect ratios, and truncated shapes with different degrees of truncation. The proposed training process and data augmentation technique are both straightforward and flexible, enabling easy application of the classifier to other processes involving particle orientations. Our work thus presents a valuable tool for investigating self-assembly processes on systems of particle shapes, with potential applications in structure identification of any particle-based or molecular system where orientations can be defined.

Tuneable Current Rectification Through a Designer Graphene Nanoribbon.

Unimolecular current rectifiers are fundamental building blocks in organic electronics. Rectifying behavior has been identified in numerous organic systems due to electron-hole asymmetries of orbital levels interfaced by a metal electrode. As a consequence, the rectifying ratio (RR) determining the diode efficiency remains fixed for a chosen molecule-metal interface. Here, wepresent a mechanically tunable molecular diode exhibiting an exceptionally large rectification ratio (>105) and reversible direction. The molecular system comprises a 7-armchair graphene nanoribbon (GNR) doped with a single unit of substitutional diboron within its structure, synthesized with atomic precision on a gold substrate by on-surface synthesis. The diboron unit creates half-populated in-gap bound states and splits the GNR frontier bands into two segments, localizing the bound state in a double barrier configuration. By suspending these GNRs freely between the tip of a low-temperature scanning tunneling microscope and the substrate, wedemonstrate unipolar hole transport through the boron in-gap state's resonance. Strong current rectification is observed, associated with the varying widths of the two barriers, which can be tuned by altering the distance between tip and substrate. This study introduces an innovative approach for the precise manipulation of molecular electronic functionalities, opening new avenues for advanced applications in organicelectronics. This article is protected by copyright. All rights reserved.

Two-Dimensional Projected-Momentum Covariance Mapping for Coulomb Explosion Imaging.

We introduce projected-momentum covariance mapping, an extension of recoil-frame covariance mapping for 2D ion imaging studies. By considering the two-dimensional projection of the ion momenta as recorded by the detector, one opens the door to a complex suite of analysis tools adapted from three-dimensional momentum imaging studies. This includes the use of different frames of reference to unravel the dynamics of fragmentation and the application of fragment momentum constraints to isolate specific fragmentation channels. The technique is demonstrated on data from a two-dimensional ion imaging study of the Coulomb explosion of the cis and trans isomers of 1,2-dichloroethene, following strong-field ionization by an intense near-infrared femtosecond laser pulse. Classical simulations are used to guide the interpretation of projected-momentum covariance maps. The results offer a detailed insight into the distinct Coulomb explosion dynamics for this pair of isomers and lay the groundwork for future time-resolved studies of photoisomerization dynamics in this molecular system.

Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism

This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.

Generalized Born-Huang expansion under macroscopic quantum electrodynamics framework.

Born-Huang expansion is the cornerstone for studying potential energy surfaces and non-adiabatic couplings (NACs) in molecular systems. However, the traditional approach is insufficient to describe the molecular system, which strongly interacts with quantum light. Inspired by the work by Schäfer et al., we develop the generalized Born-Huang expansion theory within a macroscopic quantum electrodynamics (QED) framework. The theory we present allows us to describe electromagnetic vacuum fluctuations in dielectric media and incorporate the effects of dressed photons (or polaritons) into NACs. With the help of the generalized Born-Huang expansion, we clearly classify electronic nuclear NACs, polaritonic nuclear NACs, and polaritonic electronic NACs. Furthermore, to demonstrate the advantage of the macroscopic QED framework, we estimate polaritonic electronic NACs without any free parameter, such as the effective mode volume, and demonstrate the distance dependence of the polaritonic electronic NACs in a silver planar system. In addition, we take a hydrogen atom in free space as an example and derive spontaneous emission rates from photonic electronic NACs (polaritonic electronic NACs are reduced to photonic electronic NACs). We believe that this work not only provides an avenue for the theoretical exploration of NACs in a nucleus-electron-polariton coupled system but also offers a more comprehensive understanding for molecules coupled with quantum light.

Computational Insights into the Interaction of the Conserved Cysteine-Noose Domain of the Human Respiratory Syncytial Virus G Protein with the Canonical Fractalkine Binding site of Transmembrane Receptor CX3CR1 Isoforms

The human Respiratory Syncytial Virus (hRSV) stands as one of the most common causes of acute respiratory diseases. The infectivity of this virus is intricately linked to its membrane proteins, notably the attachment glycoprotein (G protein). The latter plays a key role in facilitating the attachment of hRSV to respiratory tract epithelial cells, thereby initiating the infection process. The present study aimed to characterize the interaction of the conserved cysteine-noose domain of hRSV G protein (cndG) with the transmembrane CX3C motif chemokine receptor 1 (CX3CR1) isoforms using computational tools of molecular modeling, docking, molecular dynamics simulations, and binding free energy calculations. From MD simulations of the molecular system embedded in the POPC lipid bilayer, we showed a stable interaction of cndG with the canonical fractalkine binding site in the N-terminal cavity of the CX3CR1 isoforms and identified that residues in the extracellular loop 2 (ECL2) region and Glu279 of this receptor are pivotal for the stabilization of CX3CR1/cndG binding, corroborating what was reported for the interaction of the chemokine fractalkine with CX3CR1 and its structure homolog US28. Therefore, the results presented here contribute by revealing key structural points for the CX3CR1/G interaction, allowing us to better understand the biology of hRSV from its attachment process and to develop new strategies to combat it.

Involvement of the JAK-STAT pathway in the molecular landscape of tyrosine kinase fusion-negative hypereosinophilic syndromes: A nationwide CEREO study.

We investigated using a custom NGS panel of 149 genes the mutational landscape of 64 consecutive adult patients with tyrosine kinase fusion-negative hypereosinophilia (HE)/hypereosinophilic syndrome (HES) harboring features suggestive of myeloid neoplasm. At least one mutation was reported in 50/64 (78%) patients (compared to 8/44 (18%) patients with idiopathic HE/HES/HEUS used as controls; p < .001). Thirty-five patients (54%) had at least one mutation involving the JAK-STAT pathway, including STAT5B (n = 18, among which the hotspot N642H, n = 13), JAK1 (indels in exon 13, n = 5; V658F/L, n = 2), and JAK2 (V617F, n = 6; indels in exon 13, n = 2). Other previously undescribed somatic mutations were also found in JAK2, JAK1, STAT5B, and STAT5A, including three patients who shared the same STAT5A V707fs mutation and features consistent with primary polycythemia. Nearly all JAK-STAT mutations were preceded by (or associated with) myelodysplasia-related gene mutations, especially in RNA-splicing genes or chromatin modifiers. In multivariate analysis, neurologic involvement (hazard ratio [HR]4.95 [1.87-13.13]; p = .001), anemia (HR 5.50 [2.24-13.49]; p < .001), and the presence of a high-risk mutation (as per the molecular international prognosis scoring system: HR 6.87 [2.39-19.72]; p < .001) were independently associated with impaired overall survival. While corticosteroids were ineffective in all treated JAK-STAT-mutated patients, ruxolitinib showed positive hematological responses including in STAT5A-mutated patients. These findings emphasize the usefulness of NGS for the workup of tyrosine kinase fusion-negative HE/HES patients and support the use of JAK inhibitors in this setting. Updated classifications could consider patients with JAK-STAT mutations and eosinophilia as a new "gene mutated-entity" that could be differentiated from CEL, NOS, and idiopathic HES.

Construction of RNA Methylation Modification-immune-related lncRNA Molecular Subtypes and Prognostic Scoring System in Lung Adenocarcinoma.

RNA methylation modification is not only intimately interrelated with cancer development and progression but also actively influences immune cell infiltration in the tumor microenvironment (TME). RNA methylation modification genes influence the therapeutic progression of lung adenocarcinoma (LUAD), and mining RNA methylation modification prognosis-related markers in LUAD is crucial for its precise prognosis. RNA-Seq data and Gene sets were collected from online databases or published literature. Genomic variation analysis was conducted by the Maftools package. RNA methylation-immune-related lncRNAs were obtained by Pearson correlation analysis. Then, Consistent clustering analysis was performed to obtain RNA methylation modification- immune molecular subtypes (RMM-I Molecular subtypes) in LUAD based on selected lncRNAs. COX and random survival forest analysis were carried out to construct the RMM-I Score. The receiver operating characteristic (ROC) curve and Kaplan Meier survival analysis were used to assess survival differences. Tumor immune microenvironment was assessed through related gene signatures and CIBERSORT algorithm. In addition, drug sensitivity analysis was executed by the pRRophetic package. Four RNA methylation modified-immune molecular subtypes (RMM-I1, RMM- I2, RMM-I3, RMM-I4) were presented in LUAD. Patients in RMM-I4 exhibited excellent survival advantages and immune activity. HAVCR2, CD274, and CTLA-4 expression were activated in RMM-I4, which might be heat tumors and a potential beneficial group for immunotherapy. OGFRP1, LINC01116, DLGAP1-AS2, CRNDE, LINC01137, MIR210HG, and CYP1B1-AS1 comprised the RMM-I Score. The RMM-I Score exhibited excellent accuracy in the prognostic assessment of LUAD, as patients with a low RMM- I Score exhibited remarkable survival advantage. Patients with a low RMM-I score might be more sensitive to treatment with Docetaxel, Vinorelbine, Paclitaxel, Cisplatin, and immunotherapy. The RMM-I molecular subtype constituted the novel molecular characteristic subtype of LUAD, which complemented the existing pathological typing. More refined and accurate molecular subtypes provide help to reveal the mechanism of LUAD development. In addition, the RMM-I score offers a reliable tool for accurate prognosis of LUAD.

(223) - How Well Does the Molecular Microscope Diagnostic System (MMDx) Correlate with Traditional Pathologic Biopsy Interpretation in a Pediatric Heart Transplant Population?

(223) - How Well Does the Molecular Microscope Diagnostic System (MMDx) Correlate with Traditional Pathologic Biopsy Interpretation in a Pediatric Heart Transplant Population?

On Secrecy Performance in D-MoSK-Based 3-D Diffusive Molecular Communication System.

This paper studies the secrecy performance in a 3-D diffusive molecular communication system with the general depleted molecule shift keying (D-MoSK) modulation, where a point transmitter Alice transmits through diffusion multiple types of molecules modulation to a legitimate absorbing receiver Bob, suffering the eavesdropping from an absorbing eavesdropper Eve. We first develop a solid theoretical framework to determine the probabilistic distributions for the number of molecules absorbed by Bob and Eve, respectively. Based on the results, we then derive the average symbol error rate (SER) as well as the mutual information of Alice-Bob and Alice-Eve, and further apply the Shannon theory to determine the secrecy capacity of Alice-Bob transmission. We also develop the closed-form results for the optimal detection threshold at Bob to achieve the secrecy capacity, and thus devise a complete algorithm for secrecy capacity maximization. Finally, we provide numerical results to illustrate the secrecy performance in the concerned system.

(418) - Clinical Utility of Molecular Microscope Diagnostic System (MMDx) in Heart Transplant Recipients: Moving Towards a New Paradigm

(418) - Clinical Utility of Molecular Microscope Diagnostic System (MMDx) in Heart Transplant Recipients: Moving Towards a New Paradigm

Real-time, depth-resolved, in vivo multiphoton fluorescence lifetime imaging microscopy of agricultural herbicide treatments in plants

The development of effective and safe agricultural treatments requires sub-cellular insight of the biochemical effects of treatments in living tissue in real-time. Industry-standard mass spectroscopic imaging lacks real-time in vivo capability. As an alternative, multiphoton fluorescence lifetime imaging microscopy (MPM-FLIM) allows for 3D sub-cellular quantitative metabolic imaging but is often limited to low frame rates. To resolve relatively fast effects (e.g., photosynthesis inhibiting treatments), high-frame-rate MPM-FLIM is needed. In this paper, we demonstrate and evaluate a high-speed MPM-FLIM system, “Instant FLIM”, as a time-resolved 3D sub-cellular molecular imaging system in highly scattering, living plant tissues. We demonstrate simultaneous imaging of cellular autofluorescence and crystalline agrochemical crystals within plant tissues. We further quantitatively investigate the herbicidal effects of two classes of agricultural herbicide treatments, photosystem II inhibiting herbicide (Basagran) and auxin-based herbicide (Arylex), and successfully demonstrate the capability of the MPM-FLIM system to measure biological changes over a short time with enhanced imaging speed. Results indicate that high-frame-rate 3D MPM-FLIM achieves the required fluorescence lifetime resolution, temporal resolution, and spatial resolution to be a useful tool in basic plant cellular biology research and agricultural treatment development.

Comparing Plasma Donor-derived Cell-free DNA to Gene Expression in Endomyocardial Biopsies in the Trifecta-Heart Study.

Plasma donor-derived cell-free DNA (dd-cfDNA) is used to screen for rejection in heart transplants. We launched the Trifecta-Heart study (ClinicalTrials.gov No. NCT04707872), an investigator-initiated, prospective trial, to examine the correlations between genome-wide molecular changes in endomyocardial biopsies (EMBs) and plasma dd-cfDNA. The present report analyzes the correlation of plasma dd-cfDNA with gene expression in EMBs from 4 vanguard centers and compared these correlations with those in 604 kidney transplant biopsies in the Trifecta-Kidney study (ClinicalTrials.gov No. NCT04239703). We analyzed 137 consecutive dd-cfDNA-EMB pairs from 70 patients. Plasma %dd-cfDNA was measured by the Prospera test (Natera Inc), and gene expression in EMBs was assessed by Molecular Microscope Diagnostic System using machine-learning algorithms to interpret rejection and injury states. Top transcripts correlating with dd-cfDNA were related to genes increased in rejection such as interferon gamma-inducible genes (eg, HLA-DMA) but also with genes induced by injury and expressed in macrophages (eg, SERPINA1 and HMOX1). In gene enrichment analysis, the top dd-cfDNA-correlated genes reflected inflammation and rejection pathways. Dd-cfDNA correlations with rejection genes in EMB were similar to those seen in kidney transplant biopsies, with somewhat stronger correlations for TCMR genes in hearts and ABMR genes in kidneys. However, the correlations with parenchymal injury-induced genes and macrophage genes were much stronger in hearts. In this first analysis of Trifecta-Heart study, dd-cfDNA correlates significantly with molecular rejection but also with injury and macrophage infiltration, reflecting the proinflammatory properties of injured cardiomyocytes. The relationship supports the utility of dd-cfDNA in clinical management of heart transplant recipients.

A genetically encoded fluorescent protein sensor for mitochondrial membrane damage detection

Mitochondria are essential cellular organelles; detecting mitochondrial damage is crucial in cellular biology and toxicology. Compared with existing chemical probe detection methods, genetically encoded fluorescent protein sensors can directly indicate cellular and molecular events without involving exogenous reagents. In this study, we introduced a molecular sensor system, MMD-Sensor, for monitoring mitochondrial membrane damage. The sensor consists of two molecular modules. Module I is a fusion structure of the mitochondrial localization sequence (MLS), AIF cleavage site sequence (CSS), nuclear localization sequence (NLS), N-terminus of mNeonGreen and mCherry. Module II is a fusion structure of the C-terminus of mNeonGreen, NLS sequence, and mtagBFP2. Under normal condition, Module I is constrained in the inner mitochondrial membrane anchored by MLS, while Module II is restricted to the nucleus by its NLS fusion component. If the mitochondrial membrane is damaged, CSS is cut from the inner membrane, causing Module I to shift into the nucleus guided by the NLS fusion component. After Module I enters the nucleus, the N- and C-terminus of mNeonGreen meet each other and rebuild its intact 3D structure through fragment complementation and thus generates green fluorescence in the nucleus. Dynamic migration of red fluorescence from mitochondria to the nucleus and generation of green fluorescence in the nucleus indicate mitochondrial membrane damage. Using the MMD-Sensor, mitochondrial membrane damage induced by various reagents, such as uncoupling agents, ATP synthase inhibitors, monovalent cationic carriers, and ROS, in HeLa and 293T cells are directly observed and evaluated.

Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations.

This work reports on new software for automatic conformer energy benchmarking calculations for flexible molecules. The software workflow consists of four parts: conformational search, preoptimization, optimization, and frequency calculations at a higher level and last calculations using several theoretical levels. The software was written to be user-friendly and versatile to be used by nonexperts in computational chemistry. Any theoretical levels available in either Gaussian 16 or ORCA 5 may be applied in the benchmarking study. The workflow will automatically run conformational search calculations and deal with conformers that converge to the same minimum and those that show a negative frequency. At the end of the workflow, the user will have the mean absolute deviations and the most accurate method/DFT functional and basis set in comparison to the benchmark to be applied for the molecular system of interest. Case examples are given at the end of the paper that may help users to get insight into the software's main features.

Interference effects in Compton scattering of keV photons at H 2+ : a nonrelativistic analytical approach

In this paper we study interference effects in Compton scattering at molecule by keV photons. As a test case we investigate the molecular system H 2+ at the equilibrium internuclear distance and in the dissociative channel. The initial molecular wavefunction is described as a linear combination of atomic orbitals centered on each nucleus. The final continuum state is a two-centre continuum Coulomb wavefunction. Using these approximations, we obtain an analytical form for the Compton scattering fully differential cross section. We investigate the molecular effects at various internuclear distance for an incident photon energy close to 2.1 keV. The relative contribution of the A⋅P and A 2 coupling terms in the Compton scattering magnitude is discussed (where P is the electron momentum operator and A the vector potential of the field). We focus on Cohen-Fano type interference effects, as the ones observed in the photoionization of molecules.

Dominance complementation of parental heading date alleles of Hd1, Ghd7, DTH8, and PRR37 confers transgressive late maturation in hybrid rice.

Rice (Oryza sativa L.) is a short-day plant whose heading date is largely determined by photoperiod sensitivity (PS). Many parental lines used in hybrid rice breeding have weak PS, but their F1 progenies have strong PS and exhibit an undesirable transgressive late-maturing phenotype. However, the genetic basis for this phenomenon is unclear. Therefore, effective methods are needed for selecting parents to create F1 hybrid varieties with the desired PS. In this study, we used bulked segregant analysis with F1 Ningyou 1179 (strong PS) and its F2 population, and through analyzing both parental haplotypes and PS data for 918 hybrid rice varieties, to identify the genetic basis of transgressive late maturation which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents rather than from a single parental genotype. We designed a molecular marker-assisted selection system to identify the genotypes of Hd1, Ghd7, DTH8, and PRR37 in parental lines to predict PS in F1 plants prior to crossing. Furthermore, we used CRISPR/Cas9 technique to knock out Hd1 in Ning A (sterile line) and Ning B (maintainer line) and obtained an hd1-NY material with weak PS while retaining the elite agronomic traits of NY. Our findings clarified the genetic basis of transgressive late maturation in hybrid rice and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired PS for improving their adaptability.

Sustained remission after cord blood transplantation for breast cancer with lung metastases and myelodysplastic syndrome.

Allogenic hematopoietic stem cell transplantation (allo-HSCT) is not a standard therapy for solid cancer because of its high toxicity and insufficient evidence levels. However, the potential graft-versus-solid-tumor (GVT) effect of this therapy has been discussed. Many case reports have also described treatment effects of allo-HSCT in patients with hematologic malignancies and active solid tumors. A 38-year-old woman treated with fulvestrant and abemaciclib for recurrent breast cancer with multiple lung metastases was diagnosed with myelodysplastic syndrome (MDS) with increased blasts 2. She was classified as adverse risk by the 2017 European LeukemiaNet risk stratification and as very high risk by the Molecular International Prognostic Scoring System. Breast cancer treatment was interrupted and venetoclax and azacitidine therapy was started. Complete hematologic response was achieved after three cycles. However, multiple lung metastases from the breast cancer remained. The patient then underwent umbilical cord blood transplantation. She has maintained complete remission of MDS as of 1year post-transplantation, without serious complications. Lung metastatic activity on FDG-PET/CT scan also completely disappeared by half a year post-transplantation, and this response has continued as of 1year post-transplantation. This favorable treatment course suggests the existence of a GVT effect.

Harnessing graph neural networks to craft fragrances based on consumer feedback

In this research, we present a comprehensive methodology to categorize perfumes based on their fragrance profiles and subsequently aid in creating innovative odoriferous molecules using advanced neural networks. Drawing from data on Parfumo (2008) and The Good Scents Company (2021) webpage, the study employs web scraping techniques to gather diverse perfume attributes. Following this, a k-means algorithm is applied for perfume clustering, paving the way for recommending similar scents to consumers. The process then bridges customer preferences to molecular design by incorporating their feedback into generating new molecules via graph neural networks (GNNs). Through converting the Simple Molecular Input Line Entry System (SMILES) representation into graph structures, the GNN facilitates the creation of new molecular designs attuned to consumer desires. The proposed approach offers promising avenues for consumers to pinpoint similar perfume choices, incorporating feedback, and for manufacturers to conceptualize new fragrant molecules with a high likelihood of market resonance.

Multifunctional Logic Operations Based Upon Congruent ion Sensing Appended with a Strategic Molecular Device: Spectroscopic Approach

AbstractA multi‐responsive smart molecular system is constructed using a newly synthesized Salen molecule, 1,3‐bis((E)‐2,3,4‐trimethoxy benzylideneamino) propan‐2‐ol (TMBP), to selectively recognize the presence and absence of Cu2+ ions aided by another selective metal ion, Zn2+. The emission efficiency of the non‐emissive probe is selectively and significantly enhanced in presence of Zn2+, while the improved emission of probe‐Zn2+ complex is completely quenched upon interaction with Cu2+. Thus, the probe acts as a reporter molecule for the selective detection of Cu2+ in the co‐presence of Zn2+. Comprehensive spectroscopic studies indicate that Zn2+ ion‐coordination significantly reduces the flexibility of the Schiff base unit and the extent of photoinduced electron transfer which in turn enhance the fluorescence intensity. While Cu2+, a d9 system, induces paramagnetic quenching over the enhanced emission through stable ground‐state complexation and metal‐ligand charge transfer. The spectroscopic results are translated into the designing of a multifunctional smart‐molecular system that could function as YES, NOT, INHIBIT, PASS 0, TRANSFER and NOT TRANSFER logic gates. Finally, a blueprint of a smart molecular device is proposed to present the relay sensing of Zn2+ and Cu2+ through logical outputs that would work in‐sync with the spectroscopic results.