Application of the Time-Domain Multichromophoric Fluorescence Resonant Energy Transfer Method in the NISE Programme.

We present the implementation of the time-domain multichromophoric fluorescence resonant energy transfer (TC-MCFRET) approach in the numerical integration of the Schrödinger equation (NISE) program. This method enables the efficient simulation of incoherent energy transfer between distinct segments within large and complex molecular systems, such as photosynthetic complexes. Our approach incorporates a segmentation protocol to divide these systems into manageable components and a modified thermal correction to ensure detailed balance.

ColonNeXt: Fully Convolutional Attention for Polyp Segmentation.

This study introduces ColonNeXt, a novel fully convolutional attention-based model for polyp segmentation from colonoscopy images, aimed at the enhancing early detection of colorectal cancer. Utilizing a purely convolutional neural network (CNN), ColonNeXt integrates an encoder-decoder structure with a hierarchical multi-scale context-aware network (MSCAN) in the encoder and a convolutional block attention module (CBAM) in the decoder. The decoder further includes a proposed CNN-based feature attention mechanism for selective feature enhancement, ensuring precise segmentation.

Examining dimensions of career intentions: insights from medical and nursing students at a private not-for profit university in Vietnam.

Background: Understanding students' career intentions through evidence-based approaches is crucial for developing effective career guidance and intervention strategies. Although there has been considerable attention in this field, research remains limited, particularly in low- and middle-income countries (LMICs) in Asia. These regions have unique socioeconomic conditions and cultural norms that potentially shape decision-making processes.

Financial toxicity in patients with cancer: a cross-sectional study at an oncology hospital in central Vietnam.

Purpose: Cancer imposes a substantial financial burden on patients because of the high out-of-pocket expenses and the significant hardships. Financial toxicity describes the impact of cancer care costs at the patient level. Although the financial impact of cancer has been recognized, understanding the extent and determinants of financial toxicity in specific contexts is crucial.

Variation in Consult and Referral Patterns for Facial Lacerations by Emergency Department Provider Type: A Retrospective Cohort Study.

Introduction: Facial lacerations are a common reason for emergency department (ED) visits in the U.S. Proper laceration repair is imperative as poor wound management can lead to functional and aesthetic impairment and significantly impact patient quality of life.

Neuropilin-1 Protein May Serve as a Receptor for SARS-CoV-2 Infection: Evidence from Molecular Dynamics Simulations.

The binding of the virus to host cells is the first step in viral infection. Human cell angiotensin converting enzyme 2 (ACE2) is the most popular receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), while other receptors have recently been observed in experiments. Neuropilin-1 protein (NRP1) is one of them, but the mechanism of its binding to the wild type (WT) and different variants of the virus remain unclear at the atomic level.

Coarse-Grained Approach to Simulate Signatures of Excitation Energy Transfer in Two-Dimensional Electronic Spectroscopy of Large Molecular Systems.

Two-dimensional electronic spectroscopy (2DES) has proven to be a highly effective technique in studying the properties of excited states and the process of excitation energy transfer in complex molecular assemblies, particularly in biological light-harvesting systems. However, the accurate simulation of 2DES for large systems still poses a challenge because of the heavy computational demands it entails. In an effort to overcome this limitation, we devised a coarse-grained 2DES method.

SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study.

The emergence of the variant of concern Omicron (B.1.1.

Inter-subunit energy transfer processes in a minimal plant photosystem II supercomplex.

Photosystem II (PSII) is an integral part of the photosynthesis machinery, in which several light-harvesting complexes rely on inter-complex excitonic energy transfer (EET) processes to channel energy to the reaction center. In this paper, we report on a direct observation of the inter-complex EET in a minimal PSII supercomplex from plants, containing the trimeric light-harvesting complex II (LHCII), the monomeric light-harvesting complex CP26, and the monomeric PSII core complex. Using two-dimensional (2D) electronic spectroscopy, we measure an inter-complex EET timescale of 50 picoseconds for excitations from the LHCII-CP26 peripheral antenna to the PSII core.

RNA therapeutics for the treatment of blood disorders.

Blood disorders are defined as diseases related to the structure, function, and formation of blood cells. These diseases lead to increased years of life loss, reduced quality of life, and increased financial burden for social security systems around the world. Common blood disorder treatments such as using chemical drugs, organ transplants, or stem cell therapy have not yet approached the best goals, and treatment costs are also very high.

Pro-Resolving Mediators in Rotator Cuff Disease: How Is the Bursa Involved?

So far, tendon regeneration has mainly been analyzed independent from its adjacent tissues. However, the subacromial bursa in particular appears to influence the local inflammatory milieu in the shoulder. The resolution of local inflammation in the shoulder tissues is essential for tendon regeneration, and specialized pro-resolving mediators (SPMs) play a key role in regulating the resolution of inflammation.

Theoretical insights into the HO-induced oxidation of chlorpyrifos pesticide: Mechanism, kinetics, ecotoxicity, and cholinesterase inhibition of degradants.

The oxidation of the common pesticide chlorpyrifos (CPF) initiated by HO radical and the risks of its degradation products were studied in the gaseous and aqueous phases via computational approaches. Oxidation mechanisms were investigated, including H-, Cl-, CH- abstraction, HO-addition, and single electron transfer. In both phases, HO-addition at the C of the pyridyl ring is the most energetically favorable and spontaneous reaction, followed by H-abstraction reactions at methylene groups (i.

An efficient time-domain implementation of the multichromophoric Förster resonant energy transfer method.

The excitation energy transfer (EET) process for photosynthetic antenna complexes consisting of subunits, each comprised of multiple chromophores, remains challenging to describe. The multichromophoric Förster resonance energy transfer theory is a popular method to describe the EET process in such systems. This paper presents a new time-domain method for calculating energy transfer based on the combination of multichromophoric Förster resonance energy transfer theory and the Numerical Integration of the Schrödinger Equation method.

Measuring the Ultrafast Spectral Diffusion and Vibronic Coupling Dynamics in CdSe Colloidal Quantum Wells using Two-Dimensional Electronic Spectroscopy.

We measure the ultrafast spectral diffusion, vibronic dynamics, and energy relaxation of a CdSe colloidal quantum wells (CQWs) system at room temperature using two-dimensional electronic spectroscopy (2DES). The energy relaxation of light-hole (LH) excitons and hot carriers to heavy-hole (HH) excitons is resolved with a time scale of ∼210 fs. We observe the equilibration dynamics between the spectroscopically accessible HH excitonic state and a dark state with a time scale of ∼160 fs.

Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases.

The COVID-19 pandemic, which has already claimed millions of lives, continues to pose a serious threat to human health, requiring the development of new effective drugs. Non-structural proteins of SARS-CoV-2 play an important role in viral replication and infection. Among them, NSP16 (non-structured protein 16) and its cofactor NSP10 (non-structured protein 10) perform C2'-O methylation at the 5' end of the viral RNA, which promotes efficient virus replication.

SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation.

The emergence of the variant of concern Omicron (B.1.1.

Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity.

The amyloid cascade hypothesis states that senile plaques, composed of amyloid β (Aβ) fibrils, play a key role in Alzheimer's disease (AD). However, recent experiments have shown that Aβ oligomers are more toxic to neurons than highly ordered fibrils. The molecular mechanism underlying this observation remains largely unknown.

Ultrafast Excitation Energy Transfer Dynamics in the LHCII-CP29-CP24 Subdomain of Plant Photosystem II.

We measure the two-dimensional electronic spectra of the LHCII(M)-CP29-CP24 complex in photosystem II (PSII) and provide the first study of the ultrafast excitation energy transfer (EET) processes of an asymmetric and native light-harvesting assembly of the antenna of PSII. With comparisons to LHCII, we observe faster energy equilibrations in the intermediate levels of the LHCII(M)-CP29-CP24 complex at 662 and 670 nm. Notably, the putative "bottleneck" states in LHCII exhibit faster effective dynamics in the LHCII(M)-CP24-CP29 complex, with the average lifetime shortening from 2.

Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution.

Steered molecular dynamics (SMD) simulation is a powerful method in computer-aided drug design as it can be used to access the relative binding affinity with high precision but with low computational cost. The success of SMD depends on the choice of the direction along which the ligand is pulled from the receptor-binding site. In most simulations, the unidirectional pathway was used, but in some cases, this choice resulted in the ligand colliding with the complex surface of the exit tunnel.

Two-dimensional electronic spectroscopy of the Q to Q relaxation of chlorophylls a in photosystem II core complex.

Using two-dimensional electronic spectroscopy, we measured the Q to Q transfer dynamics of the chlorophyll a (Chl a) manifold in the photosystem II (PSII) monomeric core complex from Arabidopsis thaliana. A PSII monomeric core consists of 35 Chls a and no Chl b, thus allowing for a clear window to study Chl a Q dynamics in a large pigment-protein complex. Initial excitation in the Q band results in a transfer to the Q band in less than 60 fs.

Elastic moduli of normal and cancer cell membranes revealed by molecular dynamics simulations.

Recent studies indicate that there are mechanical differences between normal cells and cancer cells. Because the cell membrane takes part in a variety of vital processes, we test the hypothesis of whether or not two fundamental alterations in the cell membrane, , the overexpression of phosphatidylserine lipids in the outer leaflet and a reduction in cholesterol concentration, could cause the softening in cancer cells. Adopting ten models of normal and cancer cell membranes, we carry out 1 μs all-atom molecular dynamics simulations to compare the structural properties and elasticity properties of two membrane types.

Electron Transfer Quenching of Rhodamine 6G by -Methylpyrrole Is an Unproductive Process in the Photocatalytic Heterobiaryl Cross-Coupling Reaction.

In the heterobiaryl cross-coupling reaction between aryl halides (Ar-X) and -methylpyrrole (-MP) catalyzed by rhodamine 6G (Rh6G) under irradiation with visible light, a highly active and long-lived (millisecond time range) rhodamine 6G radical (Rh6G) is formed upon electron transfer from ,-diisopropylethylamine (DIPEA) to Rh6G. In this study, we utilized steady-state and time-resolved spectroscopy techniques to demonstrate the existence of another electron-transfer process occurring from the relatively electron-rich -MP to photoexcited Rh6G that was neglected in the previous reports. In this case, the radical Rh6G formed is short-lived and undergoes rapid recombination (nanosecond time-range), rendering it ineffective in reducing Ar-X to aryl radicals Ar that can subsequently be trapped by -MP.

Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations.

Alzheimer's disease (AD) is a neurodegenerative disorder and one of the main causes of dementia. The disease is associated with amyloid beta (Aβ) peptide aggregation forming initial clusters and then fibril structure and plaques. Other neurodegenerative diseases such as type 2 diabetes, amyotrophic lateral sclerosis, and Parkinson's disease follow a similar mechanism.