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Nonadiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the Born-Oppenheimer approximation, and the accuracy of the results heavily depends on the electronic structure theory employed. Sophisticated electronic methods, however, make these techniques computationally expensive, even for medium size systems. Consequently, simulations are often performed on simplified models to interpret the experimental results. In this context, a variety of techniques have been developed to perform NAMD using approximate methods, particularly density functional tight binding (DFTB). Despite the use of these techniques on large systems, where ab initio methods are computationally prohibitive, a comprehensive validation has been lacking. In this work, we present a new implementation of trajectory surface hopping combined with DFTB, utilizing nonadiabatic coupling vectors. We selected the methaniminium cation and furan systems for validation, providing an exhaustive comparison with the higher-level electronic structure methods. As a case study, we simulated a system from the class of molecular motors, which has been extensively studied experimentally but remains challenging to simulate with ab initio methods due to its inherent complexity. Our approach effectively captures the key photophysical mechanism of dihedral rotation after the absorption of light. Additionally, we successfully reproduced the transition from the bright to dark states observed in the time-dependent fluorescence experiments, providing valuable insights into this critical part of the photophysical behavior in molecular motors.
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http://dx.doi.org/10.1021/acs.jctc.4c01263 | DOI Listing |
Eur J Neurosci
September 2025
Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, California, USA.
Voltage-gated K channels of the Kv2 family coassemble with electrically silent KvS subunits in specific subpopulations of brain neurons, forming heteromeric Kv2/KvS channels with distinct functional properties. Little is known about the composition and function of Kv2 channels in spinal cord neurons, however. Here, we show that while Kv2.
View Article and Find Full Text PDFFront Immunol
September 2025
College of Physical Education, Yangzhou University, Yangzhou, Jiangsu, China.
Traumatic spinal cord injury (TSCI) is a devastating neurological condition with limited therapeutic options and a high likelihood of permanent disability. Among the multifaceted secondary injury mechanisms triggered by TSCI, pyroptosis-an inflammatory form of programmed cell death-has emerged as a key pathological process. In particular, microglial pyroptosis plays a pivotal role in exacerbating neuroinflammation and disrupting tissue homeostasis, thereby amplifying the secondary injury cascade.
View Article and Find Full Text PDFNan Fang Yi Ke Da Xue Xue Bao
August 2025
School of Sports Medicine, Wuhan Sports University, Wuhan 430079, China.
Objectives: To investigate the effects of formulated granules of (TGY) on motor deficits in a mouse model of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced subacute Parkinson's disease (PD) and explore the possible molecular mechanisms.
Methods: Ninety C57BL/6 mice were randomized equally into 6 groups, including a control group, a PD model group, a NEC-1 (6.5 mg/kg) treatment group, two TGY treatment groups at 5 and 2.
Brain
September 2025
State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, Guangdong Provincial Key Laboratory of Non-human Primate Research, Guangdong-Hong Kong-Macau Institute of CNS Rege
Abnormal accumulation of TAR DNA-binding protein-43 (TDP-43) is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Small interfering RNAs (siRNAs) targeting TDP-43 offer potential therapeutic strategies for these diseases. However, efficient and safe delivery of siRNAs to the central nervous system (CNS) remains a critical challenge.
View Article and Find Full Text PDFEur J Pharmacol
September 2025
Faculty of Medicine, Department of Histology and Embryology, İzmir Katip Çelebi University, İzmir, Turkiye.
Age is the most significant risk factor for Parkinson's disease, a common and progressive neurodegenerative disorder; however, exposure to toxic substances is also strongly implicated. Rotenone, an organic pesticide, induces neuropathological features of Parkinson's disease, and is widely used to create rodent models of the condition. Although the molecular mechanisms involved in the onset and progression of the disease are still unknown, neurodegenerative diseases due to protein accumulation in certain areas of the brain, have been associated with endoplasmic reticulum stress.
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