Classical Mapping Research Articles

Linked candidate genes of different functions for white mold resistance in common bean (Phaseolus vulgaris L) are identified by multiple QTL mapping approaches.

White mold (WM) is a major disease in common bean (Phaseolus vulgaris L.), and its complex quantitative genetic control limits the development of WM resistant cultivars. WM2.2, one of the nine meta-QTL with a major effect on WM tolerance, explains up to 35% of the phenotypic variation and was previously mapped to a large genomic interval on Pv02. Our objective was to narrow the interval of this QTL using combined approach of classic QTL mapping and QTL-based bulk segregant analysis (BSA), and confirming those results with Khufu de novo QTL-seq. The phenotypic and genotypic data from two RIL populations, 'Raven'/I9365-31 (R31) and 'AN-37'/PS02-029C-20 (Z0726-9), were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing. The QTL physical interval was determined by considering overlapping interval of the identified QTL or peak region in both populations by three independent QTL mapping analyses. Our findings revealed that meta-QTL WM2.2 consists of three regions, WM2.2a (4.27-5.76 Mb; euchromatic), WM 2.2b (12.19 to 17.61 Mb; heterochromatic), and WM2.2c (23.01-25.74 Mb; heterochromatic) found in both populations. Gene models encoding for gibberellin 2-oxidase 8, pentatricopeptide repeat, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein (Phvul.002G09200) and LRR domain containing family proteins are potential candidate genes associated with WM2.2b resistance. Nine gene models encoding disease resistance protein [pathogenesis-related thaumatin superfamily protein and disease resistance-responsive (dirigent-like protein) family protein etc] found within the WM2.2c QTL interval are putative candidate genes. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b and WM2.2c regions trigger physiological resistance based on putative candidate genes.

A hesitant approach to sustainable supply chain risk assessment

Supply chains (SCs) are increasingly vulnerable to disruptive events, posing risks to all involved parties. Managing and mitigating these risks is crucial for resilient and sustainable SC, aligned with global sustainability goals. This study proposes a new hesitant approach to classical fuzzy cognitive mapping (FCM) to examine the underlying structure of sustainable supply chain risks (SCRs) and their long-term impact on SC performance. By handling the uncertainty caused by human doubt, the proposed approach captures both interpersonal and intrapersonal hesitancy in complex SC systems with negative and positive causalities. The applicability of the proposed approach is demonstrated through an application for a generic SC. The findings reveal that risk events linked to the economic, social, and environmental dimensions of sustainability have a negative impact on SC performance. Supplier-related risks are identified as the most critical risks in sustainable SC systems, followed by operational risks and demand-side risks. The proposed approach enhances risk assessment accuracy and robustness, providing SC managers with reliable insights for effective risk mitigation strategies, and offering valuable guidance in managing SCRs in a sustainable manner. It highlights the significance of a holistic approach to supply chain management (SCM) by identifying critical concepts related to sustainable SCRs.

Extension of value stream mapping 4.0 for comprehensive identification of data and information flows within the manufacturing domain

The main driver of industry 4.0 is data and information for realizing resilient manufacturing systems through data-based decision-making. This requires the data flow from different machinery and its processing. Therefore, a methodical survey on the logical and technical requirements for enabling an efficient data flow can be beneficial since it fastens the process of establishing the data flow and gives production and software engineers a common understanding of the data’s meaning. Hence, data, related metadata like the unit or the frequency of recordings, and technical information, e.g., the machine’s interface or the communication protocol, are necessary. Based on the classical value stream mapping (VSM) as a lean management tool, the first approach for a methodical gathering of data, value stream mapping 4.0, was established in 2016. Since VSM 4.0 provides technical properties for specifying the data flow, some shortcomings were identified, particularly related to technical information. This contribution introduces the VSM 4.0 plus that solved the identified shortcomings by adding new properties. Compared to VSM 4.0, VSM 4.0 plus offers detailed specifications of data points, includes technical information, e.g., used communication protocols, adds information regarding data processing, and enhances the storage and usage dimension by providing more details. Through the added properties, VSM 4.0 plus allows domain and software engineers more efficient collaboration since all required information for establishing the data flow and its processing are united in one methodology. To verify the practicability, the VSM 4.0 plus was applied within several manufacturing-related use cases.

Predicting Crop Growth Patterns with Spatial–Temporal Deep Feature Exploration for Early Mapping

The timely and accurate mapping of crops over large areas is essential for alleviating food crises and formulating agricultural policies. However, most existing classical crop mapping methods usually require the whole-year historical time-series data that cannot respond quickly to the current planting information, let alone for future prediction. To address this issue, we propose a novel spatial–temporal feature and deep integration strategy for crop growth pattern prediction and early mapping (STPM). Specifically, the STPM first learns crop spatial–temporal evolving patterns from historical data to generate future remote sensing images based on the current observations. Then, a robust crop type recognition model is applied by combining the current early data with the predicted images for early crop mapping. Compared to existing spatial–temporal prediction models, our proposed model integrates local, global, and temporal multi-modal features comprehensively. Not only does it achieve the capability to predict longer sequence lengths (exceeding 100 days), but it also demonstrates a significant improvement in prediction accuracy for each time step. In addition, this paper analyses the impact of feature dimensionality and initial data length on prediction and early crop mapping accuracy, demonstrating the necessity of multi-modal feature fusion for spatial–temporal prediction of high-resolution remote sensing data and the benefits of longer initial time-series (i.e., longer crop planting time) for crop identification. In general, our method has the potential to carry out early crop mapping on a large scale and provide information to formulate changes in agricultural conditions promptly.

A unified bit-to-symbol mapping for generalized constellation modulation

Gray mapping is a well-known way to improve the performance of regular constellation modulation, but it is challenging to be applied directly for irregular alternative. To address this issue, in this paper, a unified bit-to-symbol mapping method is designed for generalized constellation modulation (i.e., regular and irregular shaping). The objective of the proposed approach is to minimize the average bit error probability by reducing the hamming distance (HD) of symbols with larger values of pairwise error probability. Simulation results show that the conventional constellation modulation(i.e., phase shift keying and quadrature amplitude modulation (QAM) with the proposed mapping rule yield the same performance as that of classical gray mapping. Moreover, the recently developed golden angle modulation (GAM) with the proposed mapping method is capable of providing around 1 dB gain over the conventional mapping counterpart and offers comparable performance to QAM with Gray mapping.

Long-term success of a multi-electrode substrate mapping and ablation strategy versus a classic single tip mapping and ablation strategy for ventricular tachycardia ablation in patients with ischemic cardiomyopathy.

Over the past years, mapping and ablation techniques for the treatment of ventricular tachycardia (VT) have evolved rapidly. High Density (HD) substrate mapping is now routine and pre-procedural imaging is increasingly used. The additional value of these techniques for long-term VT-free survival is not clear. We compared baseline and procedural characteristics, procedural success, safety and outcome of mapping and ablation of ventricular tachycardia in patients with ischemic heart disease between two groups. (1) Low Density (LD) group: VT mapping and ablation with a 4mm single tip catheter (2) HD group: HD substrate mapping with the Pentaray (Biosense Webster, USA) or HD Grid (Abbott, USA) catheter and ablation with a 4mm single tip catheter. VT ablation was performed in 133 patients (71 patients in LD group and 62 patients in HD group). The median follow-up was 5.0 years in LD group and 2.0 years in HD group. One-, two-, and five-year VT recurrence rates were 47%, 56%, and 65% in the LD group versus 39%, 50%, and 55% in the HD group (log-rank test for VT recurrence p=.70). One-, two-, and five-year ICD shock recurrence rates were 14%, 18%, and 24% in the LD group versus 8%, 15%, and 19% in the HD group (log-rank test for ICD-shock p=.79). All-cause mortality, cardiac (non-arrhythmic), and arrhythmic death, were similar in both groups. Severe procedural complications (tamponade, stroke, or procedural death) occurred in four patients (5%, 1 vascular, 3 tamponade) in the LD group versus two patients (3%, both tamponade) in the HD group (NS). In univariate and multivariable analysis, only a higher LVEF was significantly associated with VT-free survival. HD mapping was not significantly associated with VT-free survival. Anterior infarct location and age were significantly associated with ICD recurrent shock in both univariate and multivariable analyses. In patients with ischemic cardiomyopathy, a HD substrate mapping, and ablation strategy did not lead to higher VT-free survival and shock-free survival compared to a single tip mapping and ablation strategy. In this study, only LVF is an independent predictor for VT recurrence. Anterior infarct location and age predict recurrent ICD shocks.

Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.).

We developed a new method phenotypic recombination BSA/BSR (PR-BSA/BSR), which could simultaneously identify the candidate genomic regions associated with two traits in a segregating population. Bulked segregant analysis sequencing (BSA-seq) has been widely used for identifying the genomic regions affecting a certain trait. In this study, we developed a modified BSA/bulked segregant RNA-sequencing (BSR-seq) method, which we named phenotypic recombination BSA/BSR (PR-BSA/BSR), to simultaneously identify candidate genomic regions associated with two traits in a segregating population. Lateral branch angle (LBA) and flower-branch pattern (FBP) are two important traits associated with the peanut plant architecture because they affect the planting density and light use efficiency. We generated an F6 population (with two segregating traits) derived from a cross between the inbred lines Pingdu9616 (erect and sequential; ES-type) and Florunner (spreading and alternating; SA-type). The selection of bulks with extreme phenotypes was a key step in this study. Specifically, 30 individuals with recombinant phenotypes [i.e., spreading and sequential (SS-type) and erect and alternating (EA-type)] were selected to generate two bulks. The transcriptomes of individuals were sequenced and then the loci related to LBA and FBP were simultaneously detected via a ΔSNP-index strategy, which involved the direction of positive and negative peaks in the ∆SNP-index plot. The LBA-related locus was mapped to a 6.82Mb region (101,743,223-108,564,267bp) on chromosome 15, whereas the FBP-related locus was mapped to a 2.16Mb region (117,682,534-119,846,824bp) on chromosome 12. Furthermore, the marker-based classical QTL mapping method was used to analyze the PF-F6 population, which confirmed our PR-BSA/BSR results. Therefore, the PR-BSA/BSR method produces accurate and reliable data.

Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region.

Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo-assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades.

Constitutive recasting of macromolecular-based thermoviscoplasticity as yield function-based formulation

The rate- and temperature-dependent “macromolecular” polymer plasticity relies on a thermally-activated model of the non-linear strain measure, and is thus deficient in an explicit definition of the yield surface. Such an approach, typically written in the rate-form, is only suitable for the explicit finite element solver where the consistent tangent modulus and the return mapping process are unnecessary. This paper presents a procedure to deduce the pressure-dependent yield function of the rate- and thermal-based plastic constitutive models in the continuum thermodynamics. The recasted yield model aids in deriving its consistent elasto-thermoviscoplastic tangent modulus and implementing it in the implicit finite element solver. The recasted expressions are suitable for incremental formulation using the classical radial return mapping algorithm, regardless of the complexities of the original macromolecular expression. Four viscoplastic macromolecular models are used to illustrate the recasting process: three of them are based on the classical Boyce-Parks-Argon model and one on the Bergström-Boyce model. Numerical simulations are performed on real-sized specimen geometries to establish the functionality and capabilities of the methodology. The practical advantage of the implicit-oriented forms is studied in comparison to the explicit-based implementation under quasi-static and isothermal conditions.

Efficient geomorphological mapping based on geographic information systems and remote sensing data: an example from Jena, Germany

ABSTRACT We present a detailed geomorphological map (1:5000-scale) of a middle mountainous area in Jena, Germany. To overcome limitations and to extend the possibility of manually digital mapping in a structural way, we propose an approach using geographic information systems (GIS) and high-resolution digital data. The geomorphological map features were extracted by manually interpreting and analyzing the combination of different data sources using light detection and ranging (LiDAR) data. A combination of topographic and geological maps, digital orthophotos (DOPs), Google Earth images, field investigations, and derivatives from digital terrain models (DTMs) revealed that it is possible to generate the geomorphologic features involved in classical mapping approaches. LiDAR-DTM and land surface parameters (LSPs) can provide better results when incorporating the visual interpretation of multidirectional hillshade and LSP composite maps.Findings enabled us to systematically delineate landforms and geomorphological process domains. We suggest that further use of digital data should be undertaken to support analysis and applications.

Versatile mapping-by-sequencing with Easymap v.2.

Mapping-by-sequencing combines Next Generation Sequencing (NGS) with classical genetic mapping by linkage analysis to establish gene-to-phenotype relationships. Although numerous tools have been developed to analyze NGS datasets, only a few are available for mapping-by-sequencing. One such tool is Easymap, a versatile, easy-to-use package that performs automated mapping of point mutations and large DNA insertions. Here, we describe Easymap v.2, which also maps small insertion/deletions (InDels), and includes workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F2, M2, and M3 mapping populations, chemically induced mutation and natural variant mapping, input files containing single-end or paired-end reads of genomic or complementary DNA sequences, and alternative control sample files in FASTQ and VCF formats. Easymap v.2 can also be used as a variant analyzer in the absence of a mapping algorithm and includes a multi-threading option.

Simulation of quantum shortcuts to adiabaticity by classical oscillators

It is known that the dynamics and geometric phase of a quantum system can be simulated by classical coupled oscillators using the quantum−classical mapping method without loss of physics. In this work, we show that this method can also be used to simulate the schemes of quantum shortcuts to adiabaticity, which can quickly achieve the adiabatic effect through a non-adiabatic process. By mapping quantum systems by classical oscillators, two schemes, Berry’s “transitionless quantum driving” and the Lewis−Riesenfeld invariant method, are simulated by a corresponding transitionless classical driving method, which keeps adiabatic phase trajectories and acquires Hannay’s angle and the classical Lewis−Riesenfeld invariant method by manipulating the configurations of classical coupled oscillators. The classical shortcuts to adiabaticity for the two coupled classical oscillators, which is the classical version of a spin-1/2 in a magnetic field, is employed to illustrate our results and compared with quantum shortcuts-to-adiabaticity methods.

Semi-Direct Multimap SLAM System for Real-Time Sparse 3-D Map Reconstruction

The lack of a sufficient number of reliable corners in low-textured environments is a big challenge for classical visual simultaneous localization and mapping (SLAM), especially for point feature-based methods. Many other features (i.e., line and plane segments) are often combined with points to restore an environmental structure. However, using such features requires much computational time. This work focuses on the reliable and high-performance real-time operation of a SLAM system in low-textured scenarios. It proposes a semi-direct multi-map monocular SLAM system (SM-SLAM) that combines direct tracking and feature-based map maintenance with point features and line segments. The proposed system tracks non-keyframes based on a sparse image alignment method for fast tracking, extracts and matches point features and line segments in keyframes for high-quality environment structure and motion optimization. We present an extensive evaluation on two widely-used public datasets and some challenging real-world scenarios. Experimental results show that SM-SLAM can well reconstruct a sparse 3D map with geometrical structure information in 30-40 Hz. Notably, SM-SLAM shows an accuracy improvement of more than 20% than the Oriented FAST and Rotated BRIEF feature-based SLAM (ORB-SLAM) on some low-speed, small-range camera motion datasets and performs well in low-texture scenarios.

Identification of quantitative trait loci of agronomic traits in bread wheat using a Pamyati Azieva×Paragon mapping population harvested in three regions of Kazakhstan.

Although genome-wide association studies (GWAS) are an increasingly informative tool in the mining of new quantitative trait loci (QTLs), a classical biparental mapping approach is still a powerful, widely used method to search the unique genetic factors associated with important agronomic traits in bread wheat. In this study, a newly constructed mapping population of Pamyati Azieva (Russian Federation)×Paragon (UK), consisting of 94 recombinant inbred lines (RILs), was tested in three different regions of Kazakhstan with the purpose of QTL identification for key agronomic traits. The RILs were tested in 11 environments of two northern breeding stations (Petropavlovsk, North Kazakhstan region, and Shortandy, Aqmola region) and one southeastern station (Almalybak, Almaty region). The following eight agronomic traits were studied: heading days, seed maturation days, plant height, spike length, number of productive spikes, number of kernels per spike, thousand kernel weight, and yield per square meter. The 94 RILs of the PAxP cross were genotyped using Illumina's iSelect 20K single nucleotide polymorphism (SNP) array and resulted in the identification of 4595 polymorphic SNP markers. The application of the QTL Cartographer statistical package allowed the identification of 53 stable QTLs for the studied traits. A survey of published studies related to common wheat QTL identification suggested that 28 of those 53 QTLs were presumably novel genetic factors. The SNP markers for the identified QTLs of the analyzed agronomic traits of common wheat can be efficiently applied in ongoing breeding activities in the wheat breeding community using a marker-assisted selection approach.

Abstract 15544: Electrographic Flow Mapping Improves Outcome of Catheter Ablation Procedures for Persistent Atrial Fibrillation

Introduction: Catheter ablation (CA) has been proven to be the most effective treatment strategy in paroxysmal atrial fibrillation (AF), however, it remains challenging due to suboptimal success rates in persistent AF. Existing mapping technologies cannot reliably distinguish active sources in this patient population. Recently, a novel mapping system (electrographic flow mapping, EGF) was developed, using computer vision and optical flow smoothing algorithms to detect and quantify patterns of electrical wavefront propagation in the atria. Hypothesis: We hypothesised that EGF mapping is superior to classical three-dimensional electroanatomic mapping (CARTO) in one-year outcomes of CA for persistent AF. We assessed procedural safety and efficiency too. Methods: The study group included patients with persistent AF undergoing CA using EGF combined with CARTO (group1). Data of group 1 patients were compared with data from pulmonary vein isolation (PVI)-only procedures (group 2) and PVI plus additional empiric substrate ablation procedures (group 3) using CARTO. 12-months outcome as freedom from AF and atrial tachycardia/atrial flutter (AT/AFL), procedural safety and efficiency were analysed too. Results: A total number of 70 consecutive patients were included (mean age 63.9±7.8 years). Thirty-nine patients were included in group 1, 16 patients in group 2) and 15 patients in group 3). Patients in group 1 had fewer AF recurrences compared to group 2 and group 3 at 12 months (23.1% vs. 62.5% vs. 46.7%, p=0.01). There were no differences in AT/AFL recurrence between the study groups (12.8% vs. 18.8% vs. 16.7%, p=0.84). Procedure-related complications were documented in none of the study groups. Procedure times were longer in group 1 (187.2±51.6 vs. 136.3±55.4 vs. 139.6±48.6 min, p<0.01). There were no differences in fluoroscopy use (275.8±172.8 vs. 321.4±254.8 vs. 212.3±127.8 mGy, p=0.27), RF application number (p=0.24) and application duration (p=0.77) between the study groups. Conclusions: Our data suggest that patients treated with combined EGF and CARTO mapping-based CA have less AF recurrences at one-year. The procedure is safe and seems to be a promising treatment alternative for this complex group of patients.

Mapping Mountain Landforms and Its Dynamics: Study Cases in Tropical Environments

High mountain areas are critical for water security and natural hazard dynamics, as well as glacier and ecosystem conservation in a warming world. We present a brief account of the methodological steps for geomorphological mapping in mountain areas, including the required scale, the legends, technology, and software. We analyze the best imagery sources and their combination with fieldwork and geographical information systems (GIS), in performing accurate cartography. In addition, we present two case studies in which we apply several methods described previously. Firstly, we carried out a classical and digital geomorphological mapping of Cerro Chirripó (Talamanca Range). Secondly, we studied the Reserva Biológica Alberto Manuel Brenes (Central Volcanic Range), where we used UAVs to map high-resolution fluvial geomorphology. This methodological framework is suitable for future geomorphological surveys in mountain areas worldwide. Moreover, the case studies can give ideas on the application of these approaches to different mountainous environments.

Global rigidity of the period mapping

Let M g , n {\mathcal M}_{g,n} denote the moduli space of smooth, genus g ≥ 1 g\geq 1 curves with n ≥ 0 n\geq 0 marked points. Let A h {\mathcal A}_h denote the moduli space of h h -dimensional, principally polarized abelian varieties. Let g ≥ 3 g\geq 3 and h ≤ g h\leq g . If F : M g , n → A H F:{\mathcal M}_{g,n} \to {\mathcal A}_H is a nonholomorphic map, then h = g h=g and F F is the classical period mapping, assigning to a Riemann surface X X its Jacobian.

TB-NUCA: A Temperature-Balanced 3D NUCA Based on Bayesian Optimization

Three-dimensional network-on-chip (NoC) is the primary interconnection method for 3D-stacked multicore processors due to their excellent scalability and interconnect flexibility. With the support of 3D NoC, 3D non-uniform cache architecture (NUCA) is commonly used to organize the last-level cache (LLC) due to its high capacity and fast access latency. However, owing to the layered structure that leads to longer heat dissipation paths and variable inter-layer cooling efficiency, 3D NoC experiences a severe thermal problem that has a big impact on the reliability and performance of the chip. In traditional memory-to-LLC mapping in 3D NUCA, the traffic load in each node is inconsistent with its heat dissipation capability, causing thermal hotspots. To solve the above problem, we propose a temperature-balanced NUCA mapping mechanism named TB-NUCA. First, the Bayesian optimization algorithm is used to calculate the probability distribution of cache blocks in each node in order to equalize the node temperature. Secondly, the structure of TB-NUCA is designed. Finally, comparative experiments were conducted under random, transpose-2, and shuffle traffic patterns. The experimental results reveal that, compared with the classical NUCA mapping mechanism (S-NUCA), TB-NUCA can increase the mean-time-to-failure (MTTF) of routers by up to 28.13% while reducing the maximum temperature, average temperature, and standard deviation of temperature by a maximum of 4.92%, 4.48%, and 20.46%, respectively.

All-Atom Nonadiabatic Semiclassical Mapping Dynamics for Photoinduced Charge Transfer of Organic Photovoltaic Molecules in Explicit Solvents.

Direct all-atom simulation of nonadiabatic dynamics in disordered condensed phases like liquid solutions and amorphous solids has been challenging. The first all-atom simulation of the photoinduced charge-transfer dynamics of a prototypical organic photovoltaic carotenoid-porphyrin-C60 molecular triad in explicit tetrahydrofuran is presented. Based on the Meyer-Miller mapping Hamiltonian, various semiclassical and mixed quantum-classical dynamics are employed, including the linearized semiclassical, symmetrical quasiclassical, mean-field Ehrenfest, classical mapping model, and spin-mapping model approaches. The all-atom nonadiabatic dynamics were compared to multi-state harmonic models with a globally shared bath, and the models built using the ensemble averages on the initial electronic state could reproduce the all-atom results. The solvent effect was found to be critical for the photoinduced charge transfer, and the time-dependent solute-solvent radial distribution functions revealed that only the nonadiabatic dynamics started with the effective forces on the initial electronic state could capture the correct nuclear dynamics. The proposed strategy for modeling condensed-phase nonadiabatic dynamics with atomistic details is readily applied to complex condensed-phase systems.

Karyotype conservation and genomic organization of repetitive sequences in the leaf-cutting ant Atta cephalotes (Linnaeus, 1758) (Formicidae: Myrmicinae).

Leaf-cutting ants are among the New World's most conspicuous and studied ant species due to their notable ecological and economic roles. Cytogenetic studies carried out in Atta show remarkable karyotype conservation among the species. We performed classical cytogenetics and physical mapping of repetitive sequences in the leaf-cutting ant Atta cephalotes (Linnaeus, 1758), the type species of the genus. Our goal was to test the karyotype conservation in Atta and to understand the genomic organization and diversity regarding repetitive sequences in leaf-cutting ants. Atta cephalotes showed 2n = 22 (18m + 2sm + 2st) chromosomes. The heterochromatin followed a centromeric pattern, and the GC-rich regions and 18S rDNA clusters were co-located interstitially in the 4th metacentric pair. These cytogenetic characteristics were observed in other Atta species that had previously been studied, confirming the karyotype conservation in Atta. Evolutionary implications regarding the conservation of the chromosome number in leaf-cutting ants are discussed. Telomeric motif (TTAGG)n was detected in A. cephalotes as observed in other ants. Five out of the 11 microsatellites showed a scattered distribution exclusively on euchromatic areas of the chromosomes. Repetitive sequences mapped on the chromosomes of A. cephalotes are the first insights into genomic organization and diversity in leaf-cutting ants, useful in further comparative studies.