Study Of Dynamics Research Articles

Modeling absorbed alpha particle dose from diffusing alpha-emitters radiation therapy in changing tissue volumes.

Diffusing alpha-emitters Radiation Therapy ("Alpha DaRT") is a promising new radiation therapy modality for treating bulky tumors. 224Ra-carrying sources are inserted intratumorally, producing a therapeutic alpha-dose region with a total size of a few millimeter via the diffusive motion of 224Ra's alpha-emitting daughters. Clinical studies of Alpha DaRT have reported 100% positive response (30%-100% shrinkage within several weeks), with post-insertion swelling in close to half of the cases. While dosimetry recommendations informed by the effects of edema are standard in some radiation therapy modalities, the effect of edema and tumor shrinkage on the absorbed dose delivered by Alpha DaRT is stillunknown. The aim of this work is to develop a simple model for Alpha-DaRT dose deposition in a time-dependent tissue volume in order to study the effect of geometrical changes in source location due to edema and tumor shrinkage on the delivered alpha particledose. We perform FEM-based dose deposition modeling for a single Alpha-DaRT source inside shrinking and swelling tissues. Gradual volume change models were used for shrinkage and swelling, and an additional immediate volume gain model was also used for "worst case" swelling. Volume change rates were estimated from source location data from serial scans acquired at time of insertion and removal for seven patients treated using Alpha DaRT. We calculate absorbed dose profiles under both the high- and low-diffusion regimes described by the Diffusion-Leakagemodel. Changes in tissue volume can lead to over- or underestimation of the calculated absorbed dose. In the low-diffusion regime, gradual tissue shrinkage can result in an increase of 100% and gradual swelling can result in a 35% decrease in absorbed dose compared to a calculation in static tissue. Although immediate post-insertion swelling can reduce the absorbed dose by close to 65% for very closely spaced sources, in all cases analyzed the final absorbed dose continues to exceed the 10Gy target. These effects are less severe in the high-diffusionregime. These results indicate that tissue swelling and shrinkage can have a non-negligible effect on the tumor absorbed dose. Further study of tissue dynamics during Alpha-DaRT treatment will be necessary for improvements in dosimetrypractice.

Epidemiology of Xylella fastidiosa in Ibiza and Formentera: A Comprehensive Study of Insect Vectors and Transmission Dynamics

Xylella fastidiosa (XF) is a Gram-negative bacterium responsible for severe plant diseases affecting a wide range of host plants, some of them important crops. Since 2017, only the pauca subspecies (ST80) have been identified in Ibiza. XF is naturally transmitted by xylem sap-feeding insects; among them, only Philaenus spumarius (PS) and Neophilaenus campestris Fallén (NC) have been reported as potential insect vectors for XF in Ibiza. This study aims to investigate the dissemination of XF and to propose effective control strategies. The crops and the surrounding vegetation were sampled for potential vectors. DNA from insects was extracted and amplified by three qPCR methods, allowing subspecies identification. The results confirmed the continuous presence of adults of PS and NC in Ibiza and Formentera from May to December with important populations. During the summer period, PS captures predominantly took place within the surrounding woody vegetation adjacent to the plots. The main host plant for PS was Pinus halepensis Miller in Ibiza and Juniperus phoenicea subsp. turbinata (Guss.) Nyman in Formentera. In Ibiza, off the total PS captures, 4.47% tested positive for XF. These results confirm that PS is the main vector of XF on these islands, both in terms of captures and the percentage of positive insects for XF. In Formentera, despite the presence of potential vectors and the proximity and contact with Ibiza, no XF-positive insects were found, confirming the absence of the bacterium on the island.

Sensitivity of coronary hemodynamics to vascular structure variations in health and disease

Local hemodynamics play an essential role in the initiation and progression of coronary artery disease. While vascular geometry alters local hemodynamics, the relationship between vascular structure and hemodynamics is poorly understood. Previous computational fluid dynamics (CFD) studies have explored how anatomy influences plaque-promoting hemodynamics. For example, areas exposed to low wall shear stress (ALWSS) can indicate regions of plaque growth. However, small sample sizes, idealized geometries, and simplified boundary conditions have limited their scope. We generated 230 synthetic models of left coronary arteries and simulated coronary hemodynamics with physiologically realistic boundary conditions. We measured the sensitivity of hemodynamic metrics to changes in bifurcation angles, positions, diameter ratios, tortuosity, and plaque topology. Our results suggest that the diameter ratio between left coronary branches plays a substantial role in generating adverse hemodynamic phenotypes and can amplify the effect of other geometric features such as bifurcation position and angle, and vessel tortuosity. Introducing mild plaque in the models did not change correlations between structure and hemodynamics. However, certain vascular structures can induce ALWSS at the trailing edge of the plaque. Our analysis demonstrates that coronary artery vascular structure can provide key insight into the hemodynamic environments conducive to plaque formation and growth.

Efficacy of dynamic MRI sleep study in the management of obstructive sleep apnea: an observational study

Background: Obstructive sleep apnea has become a more common health problem owing to a more sedentary lifestyle and work culture. Dynamic MRI in the preoperative evaluation of these patients aims at diagnosing the actual cause, level and pattern of obstruction and guides the surgeon in decision making among the various treatment options established. Methods: In this retrospective study, Dynamic MRI was performed in 66 patients who were previously diagnosed with polysomnography. The levels and pattern of obstruction were analysed with the severity of AHI grading and their significance in planning the treatment protocol is discussed. Results: 62 patients had significant retropalatal collapse and 53 had lateral pharyngeal wall collapse in the Dynamic MRI. Retroglossal collapse is usually presenting with the retropalatal collapse and are found in six patients. Collapse at all three levels namely retropalatal, retroglossal and hypopharyngeal are present in three patients. 48 patients were advised for surgical management after pre-operative evaluation with MRI and 30 patients who underwent surgery had promising results at the six month follow up visit. Conclusion: This study shows that lateral pharyngeal wall collapse is majorly contributory to the AHI severity although multilevel collapse is seen in both mild and severe OSA patients. Hence, Dynamic MRI is suggested before proceeding with the management of the OSA patients.

Thermal properties and non-bonded interactions in human PMP2 variants: A molecular dynamics study

Charcot-Marie-Tooth disease has been known for a long time, affecting population worldwide. Many studies on this disease have been conducted, including clinical as well as computational, but no effective medical cure has yet been found. This disease is caused due to mutation in the human peripheral myelin protein 2 (PMP2) responsible for myelin formation and maintenance. In this research work, we have done a comparative molecular dynamics study on the PMP2 protein and its M114T mutant variant, focusing on non-bonded interactions and thermal properties in a biologically relevant environment. The primary objective was to explore the structural differences between the two proteins at temperatures of 305 K, 310 K, and 315 K. Using the NAMD software for molecular dynamics simulations, various analyses were performed, including RMSD estimation, counting number of hydrogen bond formation, salt bridge occupancy assessment, estimation of vdW and electrostatic interaction energies in the system, and estimation of thermal diffusivity of the proteins as well as specific heat capacity (Cv) of the system. The results suggested slight difference between the structure of the two proteins. In the mutant, a slight increase in RMSD values was observed, suggesting a minor reduction in structural stability compared to the wild-type protein. The number of hydrogen bonds formed was generally higher in the wild-type protein, with slightly more differences observed at 305 K and 315 K than at 310 K. Analysis of salt bridge occupancy revealed notable differences in the formation patterns between the two proteins. The mutation was found to have a greater impact on salt bridge formation. In addition to this, the vdW and electrostatic interaction energies were found to be lower in the system with mutant variant, with both energies decreasing gradually as temperature increased, indicating a more robust interaction profile in the system with wild-type protein. Also, the estimated value of thermal diffusivity indicated that the mutant was slightly more efficient at conducting heat than the wild-type protein; the thermal diffusivity of both proteins was much lower than that of water. Finally, a non-linear (concave nature) change in Cv with temperature was observed in both protein systems. The work was further extended to verify the Maxwell-Boltzmann distribution law which confirmed the proper distribution of kinetic energy among particles, and the temperature fluctuation was found to follow a Gaussian distribution during the NVE simulation, which was as expected.

Molecular Dynamics Study of Carbon Dioxide Gas Within Ice XVII Structure

We conducted a molecular dynamics study on CO2 hydrate within the ice XVII structure to examine the molecular diffusion of CO2 molecules, as it is essential to the hydrate potential as a carbon capture. The simulated CO2 hydrate system used 324 water molecules and 90 CO2 molecules. We used the TIP4P/Ice model for water molecules, and the CO2 molecules were treated as united atom. The simulations were carried out at 273,15 K under various pressures of 200 MPa, 500 MPa, and 1000 MPa for 1,50 ns, with a step size of 1 fs. The results showed that the CO2 molecules were confined and freely moved inside the cage-like chiral tube along the c-axis of the ice XVII structure. No significant inter-cage hopping was observed during the evolution of all simulated systems. The diffusion coefficient values for CO2 molecules within the ice XVII structure were 5.03 × 10-8 cm2s-1, 2.45 × 10-8 cm2s-1, and 8.86 × 10-8 cm2s-1 for the respective pressure variations of 200 MPa, 500 MPa, and 1000 MPa, resulting in an inverse proportional with the system's pressure. A higher diffusion coefficient facilitates a faster the mass transfer and adsorption rate of CO2 in formation build up of the CO2 hydrate system.

Anemia Across Lifespans in Rural South India: A Comprehensive Study of Age and Gender Dynamics From the Field Practice Area of Centre for Rural Health (CRHA), Nutakki, Andhra Pradesh

Anemia Across Lifespans in Rural South India: A Comprehensive Study of Age and Gender Dynamics From the Field Practice Area of Centre for Rural Health (CRHA), Nutakki, Andhra Pradesh

Computational Design of a Multi-Epitope Vaccine against Prevotella copri: Molecular Dynamics and Immunoinformatics Study

Prevotella copri is a prominent constituent of the human gastrointestinal microbiome, and its fluctuating abundance has been linked with positive and negative influences on diseases such as Parkinson’s disease and rheumatoid arthritis. Prevotella copri demonstrates flexibility against drugs. There is presently no vaccine approved by the FDA against prevotella copri,and treatment options are restricted. Hence, this research work was designed to create an in silico-based vaccine for prevotella copri.The protein sequences of two distinct strains ofprevotella copriwere retrieved from NCBI. The T-cell and B-cell epitopes were obtained and then analyzed for antigenicity, allergenicity, docking and simulation. The peptide comprises linear B-cell and T-cell epitopes from proteins identified as potential novel vaccine candidates. The molecular dynamics (MD) simulations and protein-protein docking results revealed that the vaccine exhibits strong and Sustained interaction with Toll-like receptor 4 (TLR4). The constructed sequence was integrated into the pET-30a (+) biological vehicle (vector) for subsequent analysis expression in E. coli through the SnapGene server. The constructed multi-epitopic vaccine candidate was assessed for its structural, physicochemical and immunological properties. The results demonstrated solubility, stability, antigenicity and nonallergenicity and showed a strong affinity for its target receptors. The in silico study represents a significant step forward in designing a vaccine that could effectively eliminate Prevotella copri globally.

Shear behavior of CoCrNi medium-entropy alloy bicrystals with symmetric tilt grain boundaries: a molecular dynamics study

Shear behavior of CoCrNi medium-entropy alloy bicrystals with symmetric tilt grain boundaries: a molecular dynamics study

Multi-SpinX: An advanced framework for automated tracking of mitotic spindles and kinetochores in multicellular environments.

SpinX, an AI-guided spindle tracking software, allows the 3-dimensional (3D) tracking of metaphase spindle movements in mammalian cells. Using over 900 images of dividing cells, we create the Multi-SpinX framework to significantly expand SpinX's applications: a) to track spindles and cell cortex in multicellular environments, b) to combine two object tracking (spindle with kinetochores marked by centromeric probes) and c) to extend spindle tracking beyond metaphase to prometaphase and anaphase stages where spindle morphology is different. We have used a human-in-the-loop approach to assess our optimisation steps, to manually identify challenges and to build a robust computational pipeline for segmenting kinetochore pairs and spindles. Spindles of both H1299 and RPE1 cells have been assessed and validated for use through Multi-SpinX, and we expect the tool to be versatile in enabling quantitative studies of mitotic subcellular dynamics.

PD-1 cis-targeted IL-2v in combination with radiotherapy inhibits lung cancer growth and remodels the immune microenvironment

BackgroundMore efficient therapeutic options for non-small cell lung cancer (NSCLC) are needed as the survival at 5 years of metastatic disease is near zero. In this regard, we used a...

HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting.

The exploration of the 3D organization of DNA within the nucleus in relation to various stages of cellular development has led to experiments generating spatiotemporal Hi-C data. However, there is limited spatiotemporal Hi-C data for many organisms, impeding the study of 3D genome dynamics. To overcome this limitation and advance our understanding of genome organization, it is crucial to develop methods for forecasting Hi-C data at future time points from existing timeseries Hi-C data. In this work, we designed a novel framework named HiCForecast, adopting a dynamic voxel flow algorithm to forecast future spatiotemporal Hi-C data. We evaluated how well our method generalizes forecasting data across different species and systems, ensuring performance in homogeneous, heterogeneous, and general contexts. Using both computational and biological evaluation metrics, our results show that HiCForecast outperforms the current state-of-the-art algorithm, emerging as an efficient and powerful tool for forecasting future spatiotemporal Hi-C datasets. HiCForecast is publicly available at https://github.com/OluwadareLab/HiCForecast.

In-depth study of emission dynamics in (Dy,Tb):LuAG transparent ceramics

In-depth study of emission dynamics in (Dy,Tb):LuAG transparent ceramics

Wearless-nanofrictional law regarding sliding-speed thresholds elucidated by elaborate nonequilibrium molecular dynamics study

ABSTRACT This investigation explored universal features of sustained dynamic friction between atomically flat surfaces (hereinafter referred to simply as ‘nanofriction’). The sliding-speed dependence of the wearless-nanofrictional force density is predicted to be characterised by the threshold phenomenon originating from the spatial translational symmetry of the interfacial atomic configuration along the sliding direction. Molecular dynamics (MD) simulations were performed for steady wearless nanofriction between nonmetallic crystals. In the present study, accurate ensemble-averaged data on the sliding-speed dependence were obtained comprehensively for various lattice-constant pairs (i.e. combinations of the lattice constants of the two crystals along the sliding direction) and interfacial temperatures. Analyses of these accurate results revealed an unambiguous, simple relationship holding between the sliding-speed threshold and the lattice-constant pair. This article organises the fundamental aspects of the threshold phenomenon and the phononic energy-dissipation mechanisms underlying these aspects to conclude the MD investigation concerning nanofriction between two basic-structure lattices. Understanding the universal features of the accurate sliding-speed dependence is expected to aid in developing artificial materials for the sliding parts of nanoelectromechanical systems (NEMSs).

Design Rule of Tetradentate Ligand-Based Pt(II) Complex for Efficient Singlet Exciton Harvesting in Fluorescent Organic Light-Emitting Diodes.

Controlling intermolecular interactions, such as triplet-triplet annihilation (TTA) and triplet-polaron annihilation (TPA), is crucial for achieving high quantum efficiency in organic light-emitting diodes (OLEDs) by suppressing exciton loss. This study investigates the molecular design of tetradentate Pt(II) complexes used for singlet exciton harvesting in fluorescent OLEDs to elucidate the relationship between the chemical structure of the ligands and exciton quenching mechanisms. It was discovered that the bulkiness of substituents is pivotal for maximizing quantum efficiency in these devices. An exciton dynamics study conducted during device operation quantitatively analyzed the contribution of substituents to the OLED operation mechanism, demonstrating that complexes with bulky 2,6-diisopropylphenyl and tert-butyl substituents enhance singlet exciton harvesting by suppressing TTA and TPA, thereby facilitating Förster energy transfer.

Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study.

Metal flux methods are excellent for synthesizing high-quality hexagonal boron nitride (hBN) crystals, but the atomic mechanisms of hBN nucleation and growth in these systems are poorly understood and difficult to probe experimentally. Here, we harness classical reactive molecular dynamics (ReaxFF) to unravel the mechanisms of hBN synthesis from liquid nickel solvent over time scales up to 30 ns. These simulations mimic experimental conditions by including relatively large liquid nickel slabs containing dissolved boron and a molecular nitrogen gas phase. Overall, the reaction takes place almost exclusively on the surface of the liquid nickel, owing to the low solubility of nitrogen in bulk nickel and the intermediate species' preference for the metal-gas interface. The formation of hBN invariably begins by reaction of dinitrogen with nickel-solvated boron atoms at the surface, forming intermediate N-N-B species, which typically evolve into B-N-B units through a short-lived intermediate where a single nitrogen atom is coordinated by one nitrogen and two boron atoms. The resulting B-N-B units, in turn, coalesce with growing hBN nuclei and carry nitrogen between hBN nanocrystals in an Ostwald ripening process. The amount of hBN produced on the tens of nanosecond time scale depends critically on the boron concentration, while having a much weaker dependence on the N2 pressure for the regime considered (N2 pressures of 2.5-10 MPa, Ni-B solutions with 6-12% boron by atom fraction). The highest rate of hBN formation occurs at the lowest temperature considered (1750 K, just above the melting point of nickel), while no hBN sheets are formed at 2000 K or above. An analysis of the transition pathways for nitrogen atoms shows that the final step, incorporation of small B-N motifs into larger hBN sheets, is the rate-limiting step in the regimes considered. While raising the temperature from 1750 to 2000 K has little effect on the formation of intermediates (N-N-B, B-N-B, etc.), the lack of large hBN sheets at temperatures >1900 K is explained by decreased probability of the final step and increased probability of breakup of hBN into B-N motifs.

Data-driven Dynamics with Orbital Torus Imaging: A Flexible Model of the Vertical Phase Space of the Galaxy

Abstract The vertical kinematics of stars near the Sun can be used to measure the total mass distribution near the Galactic disk and to study out-of-equilibrium dynamics. With contemporary stellar surveys, the tracers of vertical dynamics are so numerous and so well measured that the shapes of underlying orbits are almost directly visible in the data through element abundances or even stellar density. These orbits can be used to infer a mass model for the Milky Way, enabling constraints on the dark matter distribution in the inner galaxy. Here, we present a flexible model for foliating the vertical position–velocity phase space with orbits for use in data-driven studies of dynamics. The vertical acceleration profile in the vicinity of the disk, along with the orbital actions, angles, and frequencies for individual stars, can all be derived from that orbit foliation. We show that this framework—“orbital torus imaging” (OTI)—is rigorously justified in the context of dynamical theory, and does a good job of fitting orbits to simulated stellar abundance data with varying degrees of realism. OTI (1) does not require a global model for the Milky Way mass distribution, and (2) does not require detailed modeling of the selection function of the input survey data. We discuss the approximations and limitations of the OTI framework, which currently trades dynamical interpretability for flexibility in representing the data in some regimes, and which also presently separates the vertical and radial dynamics. We release an open-source tool, torusimaging, to accompany this article.

Melt pond CO2 dynamics and fluxes with the atmosphere in the central Arctic Ocean during the summer-to-autumn transition

Melt ponds are a common feature of the Arctic sea-ice environment during summer, and they play an important role in the exchange of heat and water vapor between the ocean and the atmosphere. We report the results of a time-series study of the CO2 dynamics within melt ponds (and nearby lead) and related fluxes with the atmosphere during the summer-to-autumn transition in the central Arctic Ocean during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. In late summer 2020, low-salinity meltwater was distributed throughout the melt ponds, and undersaturation of pCO2 in the meltwater drove a net influx of CO2 from the atmosphere. The meltwater layer subsequently thinned due to seawater influx, and a strong gradient in salinity and low-pCO2 water was observed at the interface between meltwater and seawater at the beginning of September. Mixing between meltwater and underlying seawater drives a significant drawdown of pCO2 as a result of the non-linearities in carbonate chemistry. By the middle of September, the strong stratification within the meltwater had dissipated. Subsequent freezing then began, and cooling and wind-induced drifting of ice floes caused mixing and an influx of seawater through the bottom of the melt pond. The pCO2 in the melt pond reached 300 µatm as a result of exchanging melt pond water with the underlying seawater. However, gas exchange was impeded by the formation of impermeable freshwater ice on the surface of the melt pond, and the net flux of CO2 was nearly zero into the pond, which was no longer a sink for atmospheric CO2. Overall, the melt ponds in this Arctic sea-ice area (both melt ponds and lead water) act as moderate sinks for atmospheric CO2.

Assessment of FOXP3+ Expression in Endometrial Precancerous and Neoplastic Lesions: A Comparative Study of Immune Microenvironment Dynamics

Assessment of FOXP3+ Expression in Endometrial Precancerous and Neoplastic Lesions: A Comparative Study of Immune Microenvironment Dynamics

Dynamic response study of curved polymer sandwich panels under contact explosion load

Dynamic response study of curved polymer sandwich panels under contact explosion load