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Search Results (116)

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Keywords = population relaxation time

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16 pages, 2568 KiB  
Article
Nonadiabatic Surface Hopping Dynamics of Photocatalytic Water Splitting Process with Heptazine–(H2O)4 Chromophore
by Xiaojuan Pang, Chenghao Yang, Ningbo Zhang and Chenwei Jiang
Int. J. Mol. Sci. 2025, 26(10), 4549; https://doi.org/10.3390/ijms26104549 - 9 May 2025
Viewed by 350
Abstract
Recent research on the use of heptazine-based polymeric carbon nitride materials as potential photocatalysts for hydrogen evolution has made significant progress. However, the impact of the water cluster’s size on the time-dependent photochemical mechanisms during the water splitting process of heptazine–water clusters remains [...] Read more.
Recent research on the use of heptazine-based polymeric carbon nitride materials as potential photocatalysts for hydrogen evolution has made significant progress. However, the impact of the water cluster’s size on the time-dependent photochemical mechanisms during the water splitting process of heptazine–water clusters remains largely unexplored. Here, we present a Landau–Zener trajectory surface hopping dynamics calculation for heptazine–(H2O)4 clusters at the ADC(2) level. The electron-driven proton transfer (EDPT) mechanism reaction from water to hydrogen-bonded heptazine–water clusters was confirmed using this method, yielding a heptazinyl radical and an OH biradical as products. The calculated quantum yield of the EDPT for the heptazine–(H2O)4 complex was 6.5%, which was slightly lower than that of the heptazine–H2O complex (9%), suggesting that increasing the water cluster size does not significantly enhance the efficiency of hydrogen transfer. Interestingly, our results show that the de-excitation of the heptazine–water complex from the excited state to the ground state via the EDPT process follows both fast and slow decay modes, which govern population relaxation and facilitate the photochemical water splitting reaction. This newly identified differential decay behavior offers valuable insights that could help deepen our understanding of the EDPT process, potentially improving the efficiency of water splitting under sunlight. Full article
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12 pages, 940 KiB  
Case Report
A Rare Homozygous AP4S1 Variant in Rwandan Siblings with Autosomal Recessive Hereditary Spastic Paraplegia Type 52 (SPG52)
by Sylvine Niyoyita, Esther Uwibambe, Janvier Ndinkabandi, Placide Sesonga, Josse Belladone Niyongere, Benjamin Tuyishimire, Adelaide Urugwiro, Alype Rwamatwara, Gisèle Isingizwe, Janvière Mutamuliza, Christian Nsanzabaganwa, John Bukuru, Florent Rutagarama, Agnès Mukaruziga, Osée Karangwa, Augustin Ndatinya, Maurice Nsanzabera, Norbert Dukuze and Léon Mutesa
Genes 2025, 16(5), 542; https://doi.org/10.3390/genes16050542 - 30 Apr 2025
Viewed by 664
Abstract
Background/Objectives: Hereditary spastic paraplegia type 52 (SPG52) is a rare, inherited neurodevelopmental condition passed down in an autosomal recessive pattern. In this report, we describe two siblings from Rwanda who exhibited classic signs of the disorder, including progressive lower-limb spasticity, significant delays [...] Read more.
Background/Objectives: Hereditary spastic paraplegia type 52 (SPG52) is a rare, inherited neurodevelopmental condition passed down in an autosomal recessive pattern. In this report, we describe two siblings from Rwanda who exhibited classic signs of the disorder, including progressive lower-limb spasticity, significant delays in motor development, and exaggerated deep tendon reflexes. Methods: Genetic testing through Whole-Exome Sequencing (WES) reveals a rare homozygous splice-site variant (NM_001128126.3:c.295-3C>A) in the AP4S1 gene. Results: Despite the severity of symptoms, both children responded positively to treatment with muscle relaxants and regular physiotherapy. Notably, MRI scans of the brain and spine showed no structural abnormalities. Conclusions: By documenting this case, we add to the growing understanding of SPG52, particularly within under-represented Sub-Saharan African populations, and underscore the critical role of early genetic testing in guiding timely diagnosis and intervention. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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13 pages, 1139 KiB  
Article
A Crossover Study of Virtual Reality Exposure for Emotional and Physiological Regulation in Mild Dementia
by Paula Latorre, Cleiton Pons Ferreira and Francisco Nieto-Escamez
Brain Sci. 2025, 15(5), 470; https://doi.org/10.3390/brainsci15050470 - 28 Apr 2025
Viewed by 594
Abstract
(1) Background: Immersive virtual reality (IVR) has emerged as a promising non-pharmacological intervention to promote relaxation and improve emotional well-being in this population. (2) Methods: This crossover study evaluated the effects of IVR on anxiety and psychological well-being in a sample of eight [...] Read more.
(1) Background: Immersive virtual reality (IVR) has emerged as a promising non-pharmacological intervention to promote relaxation and improve emotional well-being in this population. (2) Methods: This crossover study evaluated the effects of IVR on anxiety and psychological well-being in a sample of eight participants with mild dementia attending a day-care center. Participants underwent two conditions: an experimental condition involving relaxing nature-based VR scenarios (Nature Treks VR) and a control condition using personalized YouTube videos on a tablet. Each condition lasted 12 sessions. Assessments included heart rate (HR), the I-PANAS-SF, the reduced State–Trait Anxiety Inventory (STAI-r), behavioral observations, and a subjective response questionnaire. (3) Results: A significant reduction in HR over time was found during IVR exposure, suggesting a calming physiological effect not observed in the control condition. While changes in PANAS and STAI-r scores were not statistically significant, the PANAS score improvement in the experimental condition approached statistical significance (p = 0.054) and was just below the minimal clinically important difference (MCID), suggesting a potentially meaningful trend. Behavioral responses were higher during YouTube sessions, likely due to personalized content. All participants rated the IVR experience positively on the subjective questionnaire, indicating high acceptability, though social desirability bias cannot be excluded. (4) Conclusions: IVR appears to be a feasible and acceptable intervention for individuals with dementia, warranting further investigation. Full article
(This article belongs to the Special Issue The Rehabilitation of Neurologic Disorders)
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14 pages, 2283 KiB  
Article
Molecular Phylogeny and Evolutionary History of the Genus Cyprinus (Teleostei: Cypriniformes)
by Yanyan Chen, Heng Xiao, Zhaoping Yue, Xiaoyun Wu, Ruiguang Zan and Shanyuan Chen
Fishes 2025, 10(3), 121; https://doi.org/10.3390/fishes10030121 - 10 Mar 2025
Viewed by 940
Abstract
The genus Cyprinus encompasses economically vital freshwater fish species; yet the phylogenetic relationships and evolutionary history of many taxa within this genus remain unresolved. To address this knowledge gap, we reconstructed the molecular phylogenetic and estimated divergence times using complete mitochondrial cytochrome b [...] Read more.
The genus Cyprinus encompasses economically vital freshwater fish species; yet the phylogenetic relationships and evolutionary history of many taxa within this genus remain unresolved. To address this knowledge gap, we reconstructed the molecular phylogenetic and estimated divergence times using complete mitochondrial cytochrome b (CYTB) sequences of 76 Cyprinidae specimens, within Cyprinidae, including 4 outgroup species. Phylogenetic trees were reconstructed using maximum likelihood (ML) and Bayesian inference (BI) methods, while divergence times were estimated using a Bayesian relaxed molecular clock approach. The results confirmed the monophyly of the genus Cyprinus. The relationships among C. (Cyprinus) multitaeniata, C. (C.) pellegrini, C. (C.) acutidorsalis, and three Erhai Lake species (C. (C.) longipectoralis, C. (C.) barbatus, and C. (C.) chilia) were resolved with strong support. Cyprinus (C.) multitaeniata is basal. The species in Erhai Lake form a monophyletic group, and C. (C.) acutidorsalis is at the top of the phylogenetic tree. The taxonomic delineation within the genus Cyprinus remains controversial, particularly regarding the proposed division into two subgenera (Cyprinus and Mesocyprinus), which has been historically constrained by limited specimen availability for Mesocyprinus. Our comprehensive phylogenetic analysis reveals significant evolutionary divergence patterns: The genus Cyprinus diverged from Carassius during the 56.9 Mya. Notably, the Erhai Lake radiation species (C. (C.) longipectoralis, C. (C.) barbatus, and C. (C.) chilia) originated during 2.03 Mya, while the Lake Biwa endemic C. (C.) haematopterus demonstrates 8.7 Mya. We identified a late Pleistocene speciation event (0.75 Mya) in C. (C.) acutidorsalis, coinciding with its adaptation to brackish water ecosystems. The native C. (C.) pellegrini of Xingyun Lake and Chilu Lake may have originated 4.8 Mya, when the ancient lake that its ancestral population inhabited became isolated. These findings provide robust molecular evidence supporting the recognition of two evolutionary distinct subgenera within Cyprinus. Full article
(This article belongs to the Section Taxonomy, Evolution, and Biogeography)
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13 pages, 263 KiB  
Article
Alcohol-Exposed Pregnancy Risk, Mental Health, Self-Understanding, and Relational Connections Among Urban Native American Young Women During the COVID-19 Pandemic
by Sara M. London, Caitlin T. Howley, Michelle Sarche and Carol E. Kaufman
Int. J. Environ. Res. Public Health 2025, 22(3), 358; https://doi.org/10.3390/ijerph22030358 - 28 Feb 2025
Viewed by 657
Abstract
The COVID-19 pandemic had a disproportionate impact on American Indian and Alaska Native (“Native”) communities, including factors impacting alcohol-exposed pregnancy (AEP) risk. This is especially true for young Native women in urban settings, where over 70% of the population resides, yet their experiences [...] Read more.
The COVID-19 pandemic had a disproportionate impact on American Indian and Alaska Native (“Native”) communities, including factors impacting alcohol-exposed pregnancy (AEP) risk. This is especially true for young Native women in urban settings, where over 70% of the population resides, yet their experiences are rarely accounted for in research. We conducted remote in-depth interviews from March to May 2022, roughly concurrent with the Omicron surge and relaxed lockdown measures, with a subsample of 15 urban Native young women ages 16–20 who were participating in a national randomized controlled trial of an AEP preventive intervention. Participants were asked how the pandemic affected their use of alcohol, sexual health, mental health, and relationships. A qualitative analysis revealed diverse experiences during the pandemic. While some participants experienced greater risks for AEP due to increased alcohol use and reduced access to birth control, other participants drank less alcohol and had greater access to birth control. Additionally, while some participants faced mental health challenges due to isolation and relational strains that emerged during the pandemic, others found the pandemic to be a time that afforded self-reflection, self-development, and a deepening of relationships. Full article
9 pages, 1487 KiB  
Article
Kinetic Laser Absorption Spectroscopy of Vibrationally Excited Hydroxyl Radicals on Infrared Transitions ν = 3 ← 1 and ν = 4 ← 2
by Daria M. Plastinina, Evgeni N. Chesnokov, Pavel V. Koshlyakov and Lev N. Krasnoperov
Molecules 2025, 30(3), 540; https://doi.org/10.3390/molecules30030540 - 24 Jan 2025
Viewed by 677
Abstract
The kinetics of vibrationally excited OH(ν = 1) and OH(ν = 2) radicals was studied by time-resolved laser absorption in the overtone IR region. Two DFB laser diodes, 1509.3 and 1589 nm, were used. The technique allowed for the reliable study of the [...] Read more.
The kinetics of vibrationally excited OH(ν = 1) and OH(ν = 2) radicals was studied by time-resolved laser absorption in the overtone IR region. Two DFB laser diodes, 1509.3 and 1589 nm, were used. The technique allowed for the reliable study of the vibrational relaxation kinetics as well as the relative populations of the vibrationally excited states. The yields of OH(ν = 1) and OH(ν = 2) in the reaction O(1D) + H2O were determined. The rate constant of OH(ν = 1) relaxation in collision with water molecules was obtained ((9.2 ± 2.0) × 10−12 cm3/s). The dynamics of OH(ν = 1) and OH(ν = 2) populations were analyzed in detail, which made it possible to separately determine the relative contribution of the vibrational ladder relaxation channels OH(ν = 2) → OH(ν = 1) → OH(ν = 0) and the direct relaxation OH(ν = 2) → OH(ν = 0). Full article
(This article belongs to the Section Physical Chemistry)
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19 pages, 4390 KiB  
Article
Evaluating Biomechanical and Viscoelastic Properties of Masticatory Muscles in Temporomandibular Disorders: A Patient-Centric Approach Using MyotonPRO Measurements
by Daniele Della Posta, Ferdinando Paternostro, Nicola Costa, Jacopo J. V. Branca, Giulia Guarnieri, Annamaria Morelli, Alessandra Pacini and Gaetano Campi
Bioengineering 2025, 12(2), 97; https://doi.org/10.3390/bioengineering12020097 - 22 Jan 2025
Cited by 2 | Viewed by 1412
Abstract
The temporomandibular joint (TMJ) is essential for chewing and speaking functions, as well as for making facial expressions. However, this joint can be affected by disorders, known as temporomandibular disorders (TMDs), induced by complex causes that lead to limitations in daily activities. Building [...] Read more.
The temporomandibular joint (TMJ) is essential for chewing and speaking functions, as well as for making facial expressions. However, this joint can be affected by disorders, known as temporomandibular disorders (TMDs), induced by complex causes that lead to limitations in daily activities. Building on the methodology and findings from our previous study on TMJ function, our research aims to apply the established criteria and norms to patients with TMDs. The primary goal is to evaluate the applicability and clinical relevance of these reference norms in predicting the severity and progression of TMJ disorders within a clinical population. Using non-invasive myotonic measurements, we evaluated 157 subjects, including both non-TMD-affected and TMD-affected individuals. To achieve optimal results, five primary parameters (frequency, stiffness, decrement, relaxation time, and creep) were analyzed using statistical–physical tools, providing quantitative functionality degrees across different previously examined clinical groups. The obtained results identified significant quantitative markers for early diagnosis and personalized treatment of TMJ disorders. This interdisciplinary approach leads to a deeper understanding of TMJ dysfunctions and makes a meaningful contribution to clinical practice, providing more precise tools for managing and treating this complex condition. Full article
(This article belongs to the Section Biomechanics and Sports Medicine)
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14 pages, 705 KiB  
Article
Postprandial Vascular Effects of a High Potassium Meal in Patients with Treated Hypertension
by Daniela Malta, Sam Esfandiari, Livia A. Goldraich, Johane P. Allard and Gary E. Newton
Nutrients 2025, 17(1), 45; https://doi.org/10.3390/nu17010045 - 27 Dec 2024
Viewed by 1309
Abstract
Background: There is compelling evidence of an inverse association between potassium intake and blood pressure (BP). A potential mechanism for this effect may be dietary potassium-mediated augmentation of endothelium-dependent relaxation. To date, studies have investigated potassium intake supplementation over several weeks in healthy [...] Read more.
Background: There is compelling evidence of an inverse association between potassium intake and blood pressure (BP). A potential mechanism for this effect may be dietary potassium-mediated augmentation of endothelium-dependent relaxation. To date, studies have investigated potassium intake supplementation over several weeks in healthy volunteers with variable results on vascular function. There is no assessment of the acute vascular effects of potassium supplementation achieved by the ingestion of potassium-rich food in a hypertensive population. Objective: The purpose of this study was to investigate the effect of a high potassium meal on postprandial endothelial function as measured by flow-mediated dilatation (FMD). Methods: We performed an investigator-blinded randomized crossover trial in 33 treated hypertensive individuals. Participants consumed both a high (~2400 mg) and low (~543 mg) K+ meal, separated by a one-week washout period. The primary endpoint was endothelial function as assessed by FMD pre-meal and postprandially at 60 and 120 min. Meals were compared at each time point using the Hills–Armitage approach. Results: 33 individuals were included in the study (48% male, mean age 68). In the fasting state (Baseline), and at 60 min postprandial, radial artery FMD was not significantly different between the participants after consumption of either meal (baseline: high K+ 4.2 ± 2% versus Low K+ 2.6 ± 3%, p = 0.93; 60 min: high K+ 3.8 ± 4% versus Low K+ 4.1 ± 3%, p = 0.69). However, at 120 min, FMD tended to be higher in participants after the high K+ meal (5.2 ± 4.1%) than after the low K+ meal (3.9 ± 4.1%) (p = 0.07). There were no differences in participants’ radial artery diameter and blood flow between meals. Conclusions: This study does not support our hypothesis that a single high K+ meal improves vascular function in individuals with treated hypertension. This does not contradict the clinical evidence relating greater K+ intake with lower BP, but suggests that mechanistic investigations of increased K+ intake through diet alone and its impact on endothelial function as a mediator to reducing BP are complex and not simply due to single nutrient-mediated improvement in vascular function. Full article
(This article belongs to the Special Issue Salt and Cardiovascular Health)
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9 pages, 1924 KiB  
Article
Vortex–Swirl Flow Results in Microbubble-Enhanced Transient Water Properties: A Time-Resolved Analysis from Fine-Bubble Engineering
by Niall J. English and Cees M. B. Kamp
Water 2024, 16(24), 3565; https://doi.org/10.3390/w16243565 - 11 Dec 2024
Viewed by 1278
Abstract
The inward vortex–swirl-type motion of convective, rectilinear water flow has been studied vis-à-vis its propensity for bubble formation, with a particular focus on the microbubble region. It has been found that a large population of smaller microbubbles, around 1 μm in diameter, is [...] Read more.
The inward vortex–swirl-type motion of convective, rectilinear water flow has been studied vis-à-vis its propensity for bubble formation, with a particular focus on the microbubble region. It has been found that a large population of smaller microbubbles, around 1 μm in diameter, is created in the process of these types of motions, and the time-dependent behaviour of this “micro-bubbly” water is analysed as Stokes’ law for microbubble dissipation occurs, such as bubble population, dissolved oxygen, pH, etc. Exponential decay analysis on the DLS-measured microbubble populations gave relaxation times τ of ~2.4 h and 3.6 h in exp(−t/τ) fits for DI and filtered tap water, respectively. The downward shift in pH was about 0.08 ± 0.016 and 0.11 ± 0.018 for DI and filtered tap water, respectively. For DI water, the level of dissolved oxygen (DO) at room temperature of 19 °C was ~102% at “t = 0”, and it declined to ~87% within 3 h (with the unprocessed background sample being about 84 ± 1.1%). The respective DO decay results in the case of the filtered tap water (at 19 °C) were ~105% at “t = 0”, declining to 91% within 3 h (background = 86 ± 1.2%). This allows for the dynamic properties to be understood in the context of how microbubbles determine the observed properties of post-flow water, including rationalising the observations of its time-transient properties. Naturally, this may well be of interest in gas transfer optimisation in the growing field of “fine-bubble engineering”. Full article
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17 pages, 2772 KiB  
Article
Factors Affecting the Population of Excited Charge Transfer States in Adenine/Guanine Dinucleotides: A Joint Computational and Transient Absorption Study
by Vasilis Petropoulos, Lara Martinez-Fernandez, Lorenzo Uboldi, Margherita Maiuri, Giulio Cerullo, Evangelos Balanikas and Dimitra Markovitsi
Biomolecules 2024, 14(12), 1548; https://doi.org/10.3390/biom14121548 - 3 Dec 2024
Cited by 1 | Viewed by 1260
Abstract
There is compelling evidence that the absorption of low-energy UV radiation directly by DNA in solution generates guanine radicals with quantum yields that are strongly dependent on the secondary structure. Key players in this unexpected phenomenon are the photo-induced charge transfer (CT [...] Read more.
There is compelling evidence that the absorption of low-energy UV radiation directly by DNA in solution generates guanine radicals with quantum yields that are strongly dependent on the secondary structure. Key players in this unexpected phenomenon are the photo-induced charge transfer (CT) states, in which an electric charge has been transferred from one nucleobase to another. The present work examines the factors affecting the population of these states during electronic relaxation. It focuses on two dinucleotides with opposite orientation: 5′-dApdG-3′ (AG) and 5′-dGpdA-3′ (GA). Quantum chemistry calculations determine their ground state geometry and the associated Franck–Condon states, map their relaxation pathways leading to excited state minima, and compute their absorption spectra. It has been shown that the most stable conformer is anti-syn for AG and anti-anti for GA. The ground state geometry governs both the excited states populated upon UV photon absorption and the type of excited state minima reached during their relaxation. Their fingerprints are detected in the transient absorption spectra recorded with excitation at 266 nm and a time resolution of 30 fs. Our measurements reveal that in the large majority of dinucleotides, chromophore coupling is already operative in the ground state and that the charge transfer process occurs within ~120 fs. The competition among various relaxation pathways affects the quantum yields of the CT state formation in each dinucleotide, which are estimated to be 0.18 and 0.32 for AG and GA, respectively. Full article
(This article belongs to the Special Issue Molecular Mechanisms in DNA and RNA Damage and Repair)
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10 pages, 636 KiB  
Article
Fitness Costs in Diamondback Moth Plutella xylostella (L.) (Lepidoptera: Plutellidae) Resistant to Lufenuron, A Chitin-Synthesis Inhibitor Insecticide
by Natalia C. Bermúdez, Nataly de la Pava, Deividy V. Nascimento, Lilian M. S. Ribeiro, Herbert A. A. Siqueira and Jorge B. Torres
Insects 2024, 15(11), 856; https://doi.org/10.3390/insects15110856 - 2 Nov 2024
Viewed by 1531
Abstract
The diamondback moth (DBM), Plutella xylostella, is the main pest of Brassicas crops worldwide, and its recorded resistance to 101 active ingredients indicates it is difficult to control. The purpose of this study was to investigate the hypothesis that P. xylostella has fitness [...] Read more.
The diamondback moth (DBM), Plutella xylostella, is the main pest of Brassicas crops worldwide, and its recorded resistance to 101 active ingredients indicates it is difficult to control. The purpose of this study was to investigate the hypothesis that P. xylostella has fitness costs associated with its resistance to lufenuron, a chitin-synthesis inhibitor insecticide. Thus, concentration–mortality bioassays were performed for susceptible (REC-S), resistant (BZR-R) populations, their progenies F1 and F1′, and one established population without selection pressure (BZR-Rns) after four generations. A fertility life table was used to assess the biological performance of the REC-S and BZR-R. BZR-Rns of P. xylostella. The larval stage, longevity, and survival differed between populations. The reproductive rate (R0) was significantly lower in the F1 (♀R × ♂S) (28.19) and F1′ (♀S × ♂R) (34.06) progenies compared with their parents, but not with the relaxed BZR-Rns (39.39). The mean generation time (T), intrinsic rate of population growth (rm), and doubling time (DT) differed between REC-S and progenies, with fitness of 0.52 and 0.64 for F1 and F1′, respectively. Overall, the results suggest that the resistance of P. xylostella to lufenuron is stable and that low fitness costs appear to be associated with resistance to lufenuron, although heterozygotes showed lower fitness than their parents. Strategies such as preserving refuge areas, rotation of modes of action, etc., are essential for resistance management and prolonging the efficacy of control agents; this highlights the importance of integrated insecticide resistance management. Full article
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27 pages, 1446 KiB  
Article
A Graph-Refinement Algorithm to Minimize Squared Delivery Delays Using Parcel Robots
by Fabian Gnegel, Stefan Schaudt, Uwe Clausen and Armin Fügenschuh
Mathematics 2024, 12(20), 3201; https://doi.org/10.3390/math12203201 - 12 Oct 2024
Viewed by 1152
Abstract
In recent years, parcel volumes have reached record highs, prompting the logistics industry to explore innovative solutions to meet growing demand. In densely populated areas, delivery robots offer a promising alternative to traditional truck-based delivery systems. These autonomous electric robots operate on sidewalks [...] Read more.
In recent years, parcel volumes have reached record highs, prompting the logistics industry to explore innovative solutions to meet growing demand. In densely populated areas, delivery robots offer a promising alternative to traditional truck-based delivery systems. These autonomous electric robots operate on sidewalks and deliver time-sensitive goods, such as express parcels, medicine and meals. However, their limited cargo capacity and battery life require a return to a depot after each delivery. This challenge can be modeled as an electric vehicle-routing problem with soft time windows and single-unit capacity constraints. The objective is to serve all customers while minimizing the quadratic sum of delivery delays and ensuring each vehicle operates within its battery limitations. To address this problem, we propose a mixed-integer quadratic programming model and introduce an enhanced formulation using a layered graph structure. For this layered graph, we present two solution approaches based on relaxations that reduce the number of nodes and arcs compared to the expanded formulation. The first approach, Iterative Refinement, solves the current relaxation to optimality and refines the graph when the solution is infeasible for the expanded formulation. This process continues until a proven optimal solution is obtained. The second approach, Branch and Refine, integrates graph refinement into a branch-and-bound framework, eliminating the need for restarts. Computational experiments on modified Solomon instances demonstrate the effectiveness of our solution approaches, with Branch and Refine consistently outperforming Iterative Refinement across all tested parameter configurations. Full article
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12 pages, 930 KiB  
Article
Purifying Selection Influences the Comparison of Heterozygosities between Populations
by Sankar Subramanian
Biology 2024, 13(10), 810; https://doi.org/10.3390/biology13100810 - 10 Oct 2024
Viewed by 1242
Abstract
Heterozygosity is a fundamental measure routinely used to compare between populations to infer the level of genetic variation and their relative effective population sizes. However, such comparison is highly influenced by the magnitude of selection pressure on the genomic regions used. Using over [...] Read more.
Heterozygosity is a fundamental measure routinely used to compare between populations to infer the level of genetic variation and their relative effective population sizes. However, such comparison is highly influenced by the magnitude of selection pressure on the genomic regions used. Using over 2 million Single Nucleotide Variants (SNVs) from chimpanzee and mouse populations, this study shows that the heterozygosities estimated using neutrally evolving sites of large populations were two times higher than those of small populations. However, this difference was only ~1.6 times for the heterozygosities estimated using nonsynonymous sites. This suggests an excess in the nonsynonymous heterozygosities due to the segregation of deleterious variants in small populations. This excess in the nonsynonymous heterozygosities of the small populations was estimated to be 23–31%. Further analysis revealed that the magnitude of the excess is modulated by effective population size (Ne) and selection intensity (s). Using chimpanzee populations, this investigation found that the excess in nonsynonymous diversity in the small population was little (6%) when the difference between the Ne values of large and small populations was small (2.4 times). Conversely, this was high (23%) when the difference in Ne was large (5.9 times). Analysis using mouse populations showed that the excess in the nonsynonymous diversity of highly constrained genes of the small population was much higher (38%) than that observed for the genes under relaxed selective constraints (21%). Similar results were observed when the expression levels of genes were used as a proxy for selection intensity. These results emphasize the use of neutral regions, less constrained genes, or lowly expressed genes when comparing the heterozygosities between populations. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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24 pages, 2214 KiB  
Article
Adaptive Constraint Relaxation-Based Evolutionary Algorithm for Constrained Multi-Objective Optimization
by Junming Chen, Kai Zhang, Hui Zeng, Jin Yan, Jin Dai and Zhidong Dai
Mathematics 2024, 12(19), 3075; https://doi.org/10.3390/math12193075 - 30 Sep 2024
Cited by 2 | Viewed by 1577
Abstract
The key problem to solving constrained multi-objective optimization problems (CMOPs) is how to achieve a balance between objectives and constraints. Unfortunately, most existing methods for CMOPs still cannot achieve the above balance. To this end, this paper proposes an adaptive constraint relaxation-based evolutionary [...] Read more.
The key problem to solving constrained multi-objective optimization problems (CMOPs) is how to achieve a balance between objectives and constraints. Unfortunately, most existing methods for CMOPs still cannot achieve the above balance. To this end, this paper proposes an adaptive constraint relaxation-based evolutionary algorithm (ACREA) for CMOPs. ACREA adaptively relaxes the constraints according to the iteration information of population, whose purpose is to induce infeasible solutions to transform into feasible ones and thus improve the ability to explore the unknown regions. Completely ignoring constraints can cause the population to waste significant resources searching for infeasible solutions, while excessively satisfying constraints can trap the population in local optima. Therefore, balancing constraints and objectives is a crucial approach to improving algorithm performance. By appropriately relaxing the constraints, it induces infeasible solutions to be transformed into feasible ones, thus obtaining more information from infeasible solutions. At the same time, it also establishes an archive for the storage and update of solutions. In the archive update process, a diversity-based ranking is proposed to improve the convergence speed of the algorithm. In the selection process of the mating pool, common density selection metrics are incorporated to enable the algorithm to obtain higher-quality solutions. The experimental results show that the proposed ACREA algorithm not only achieved the best Inverse Generation Distance (IGD) value in 54.6% of the 44 benchmark test problems and the best Hyper Volume (HV) value in 50% of them, but also obtained the best results in seven out of nine real-world problems. Clearly, CP-TSEA outperforms its competitors. Full article
(This article belongs to the Special Issue Advance in Control Theory and Optimization)
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33 pages, 14062 KiB  
Article
Parametric Characterization of Nonlinear Optical Susceptibilities in Four-Wave Mixing: Solvent and Molecular Structure Effects
by José L. Paz, Alberto Garrido-Schaeffer, Marcos A. Loroño, Lenin González-Paz, Edgar Márquez, José R. Mora and Ysaias J. Alvarado
Symmetry 2024, 16(10), 1263; https://doi.org/10.3390/sym16101263 - 25 Sep 2024
Viewed by 1275
Abstract
We study the nonlinear absorptive and dispersive optical properties of molecular systems immersed in a thermal reservoir interacting with a four-wave mixing (FWM) signal. Residual spin-orbit Hamiltonians are considered in order to take into account the internal structure of the molecule. As system [...] Read more.
We study the nonlinear absorptive and dispersive optical properties of molecular systems immersed in a thermal reservoir interacting with a four-wave mixing (FWM) signal. Residual spin-orbit Hamiltonians are considered in order to take into account the internal structure of the molecule. As system parameters in the dissipation processes, transverse and longitudinal relaxation times are considered for stochastic solute–solvent interaction processes. The intramolecular coupling effects on the optical responses are studied using a molecule model consisting of two coupled harmonic curves of electronic energies with displaced minima in nuclear energies and positions. In this study, the complete frequency space is considered through the pump–probe detuning, without restricting the derivations to only maximums of population oscillations. This approach opens the possibility of studying the behavior of optical responses, which is very useful in experimental design. Our results indicate the sensitivity of the optical responses to parameters of the molecular structure as well as to those derived from the photonic process of FWM signal generation. Full article
(This article belongs to the Section Physics)
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