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Journal of Environmental Sciences... Jul 2024Covalent organic frameworks (COFs) are a new kind of crystalline porous materials composed of organic molecules connected by covalent bonds, processes the... (Review)
Review
Covalent organic frameworks (COFs) are a new kind of crystalline porous materials composed of organic molecules connected by covalent bonds, processes the characteristics of low density, large specific surface area, adjustable pore size and structure, and easy to functionalize, which have been widely used in the field of membrane separation technology. Recently, there are more and more researches focusing on the preparation methods, separation application, and mechanism of COF membranes, which need to be further summarized and compared. In this review, we primarily summarized several conventional preparation methods, such as two-phase interfacial polymerization, in-situ growth on substrate, unidirectional diffusion method, layer-by-layer assembly method, mixed matrix membranes, and so on. The advantages and disadvantages of each method are briefly summarized. The application potential of COF membrane in liquid separation are introduced from four aspects: dyeing wastewater treatment, heavy metal removal, seawater desalination and oil-water separation. Then, the mechanisms including pore structure, hydrophilic/hydrophobic, electrostatic repulsion/attraction and Donnan effect are introduced. For the efficient removal of different kind of pollutions, researchers can select different ligands to construct membranes with specific pore size, hydrophily, salt or organic rejection ability and functional group. The ideas for the design and preparation of COF membranes are introduced. Finally, the future direction and challenges of the next generation of COF membranes in the field of separation are prospected.
Topics: Phase Separation; Sodium Chloride; Diffusion; Environmental Pollution; Metal-Organic Frameworks
PubMed: 38408835
DOI: 10.1016/j.jes.2023.06.037 -
AAPS PharmSciTech Jul 2023Since earlier times, dermatological remedies have been utilized to treat diseases associated with pain, irritation, and skin conditions. Compared to other routes of drug... (Review)
Review
Since earlier times, dermatological remedies have been utilized to treat diseases associated with pain, irritation, and skin conditions. Compared to other routes of drug delivery, topical delivery of drugs offers several benefits. Scientists are investigating different alterations in dosage forms in addition to existing topical formulations such as ointments, gels, creams, lotions, and ointments to significantly improve the permeation of drugs and enhance the pharmacological efficacy of medications that are poorly absorbed via the skin. Conventional formulations have a plethora of problems viz. poor absorption, no target specificity, low spreadability, and inadequate bioavailability which leads the researchers toward developing novel formulations like nanoemulsions. The nanoemulsion can enhance the gradient in concentration and thermodynamic movement toward the epidermis and enhance the penetration of its constituents. However, due to its difficult application, nanoemulsion's lower viscosity limited its use in transdermal delivery. Thus, the development of nanoemulsion-based hydrogels has shown to be a successful strategy for removing obstacles from existing drug formulations. The simple application, expedient spreadability, non-stickiness, safety, and effectiveness of nanoemulsion-based hydrogel have led to substantial growth in their research in recent years. This review gives a brief idea about the prevalence of skin diseases, skin as an obstacle for drug delivery, and recent research insights to combat these obstacles. The work highlights the mechanism of drug release via nanoemulsion, hydrogels, and nanoemulsion-based hydrogels with reference to recent research on hydrophobic and hydrophilic drugs.
Topics: Hydrogels; Ointments; Drug Delivery Systems; Diffusion; Biological Availability
PubMed: 37438613
DOI: 10.1208/s12249-023-02611-x -
Journal of Chemical Information and... Apr 2024We present a diffusion-based generative model for conformer generation. Our model is focused on the reproduction of the bonded structure and is constructed from the...
We present a diffusion-based generative model for conformer generation. Our model is focused on the reproduction of the bonded structure and is constructed from the associated terms traditionally found in classical force fields to ensure a physically relevant representation. Techniques in deep learning are used to infer atom typing and geometric parameters from a training set. Conformer sampling is achieved by taking advantage of recent advancements in diffusion-based generation. By training on large, synthetic data sets of diverse, drug-like molecules optimized with the semiempirical GFN2-xTB method, high accuracy is achieved for bonded parameters, exceeding that of conventional, knowledge-based methods. Results are also compared to experimental structures from the Protein Databank and the Cambridge Structural Database.
Topics: Pharmaceutical Preparations; Molecular Conformation; Models, Molecular; Deep Learning; Diffusion
PubMed: 38486425
DOI: 10.1021/acs.jcim.3c01816 -
European Biophysics Journal : EBJ Oct 2023In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover,... (Review)
Review
In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover, formation of a biologically active complex often requires a specific orientation of the ligand relative to the binding site. Before the formation of the initial form of the complex, only long-range, electrostatic and hydrodynamic interactions can act between the ligand approaching the binding site and the receptor. In this context, the question arises whether as a result of these interactions, there is a pre-orientation of the ligand towards the binding site, which to some extent would accelerate the formation of the complex. The role of electrostatic interactions in the orientation of the ligand relative to the binding site of the receptor is well documented. The analogous role of hydrodynamic interactions, although assessed as very significant by Brune and Kim (PNAS 91, 2930-2934, (1994)), is still debatable. In this article, I present the current state of knowledge on this subject and consider the possibilities of demonstrating the orienting effect of hydrodynamic interactions in the processes of receptor-ligand association, in an experimental way supported by computer simulations.
Topics: Ligands; Hydrodynamics; Diffusion; Protein Binding; Computer Simulation; Kinetics; Carrier Proteins
PubMed: 37173574
DOI: 10.1007/s00249-023-01653-0 -
The Journal of Physical Chemistry. B Oct 2023The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated... (Review)
Review
The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the detection, monitoring, and treatment of the disease. Robust surveillance systems have been established to understand the clinical characteristics of new variants, although the unpredictable nature of these variants presents significant challenges. Some variants have shown resistance to current treatments, but innovative technologies like computational protein design (CPD) offer promising solutions and versatile therapeutics against SARS-CoV-2. Advances in computing power, coupled with open-source platforms like AlphaFold and RFdiffusion (employing deep neural network and diffusion generative models), among many others, have accelerated the design of protein therapeutics with precise structures and intended functions. CPD has played a pivotal role in developing peptide inhibitors, mini proteins, protein mimics, decoy receptors, nanobodies, monoclonal antibodies, identifying drug-resistance mutations, and even redesigning native SARS-CoV-2 proteins. Pending regulatory approval, these designed therapies hold the potential for a lasting impact on human health and sustainability. As SARS-CoV-2 continues to evolve, use of such technologies enables the ongoing development of alternative strategies, thus equipping us for the "New Normal".
Topics: Humans; SARS-CoV-2; COVID-19; Antibodies, Monoclonal; Diffusion
PubMed: 37815479
DOI: 10.1021/acs.jpcb.3c04542 -
The Journal of Chemical Physics Aug 2023Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein... (Review)
Review
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
Topics: Single Molecule Imaging; Diffusion; Microscopy, Fluorescence; Photobleaching; Protein Conformation
PubMed: 37589409
DOI: 10.1063/5.0155638 -
Physical Review. E Dec 2023Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial...
Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial ecology. In free space, most microswimmers perform diffusive random walks as a result of the interplay of self-propulsion and orientation decorrelation mechanisms such as run-and-tumble dynamics or rotational diffusion. In an unstructured porous medium, collisions with the microstructure result in a decrease in the effective spatial diffusivity of the particles from its free-space value. Here, we analyze this problem for a simple model system consisting of noninteracting point particles performing run-and-tumble dynamics through a two-dimensional disordered medium composed of a random distribution of circular obstacles, in the absence of Brownian diffusion or hydrodynamic interactions. The particles are assumed to collide with the obstacles as hard spheres and subsequently slide on the obstacle surface with no frictional resistance while maintaining their orientation, until they either escape or tumble. We show that the variations in the long-time diffusivity can be described by a universal dimensionless hindrance function f(ϕ,Pe) of the obstacle area fraction ϕ and Péclet number Pe, or ratio of the swimmer run length to the obstacle size. We analytically derive an asymptotic expression for the hindrance function valid for dilute media (Peϕ≪1), and its extension to denser media is obtained using stochastic simulations. As we explain, the model is also easily generalized to describe dispersion in three dimensions.
PubMed: 38243487
DOI: 10.1103/PhysRevE.108.064608 -
NMR in Biomedicine Aug 2023This work aimed to demonstrate an essential phase shift for better quantifying and in human brain white matter (WM), and to further elucidate its origin related to...
This work aimed to demonstrate an essential phase shift for better quantifying and in human brain white matter (WM), and to further elucidate its origin related to the directional diffusivities from standard diffusion tensor imaging (DTI). was integrated into a proposed generalized transverse relaxation model for characterizing previously published and orientation dependence profiles in brain WM, and then comparisons were made with those without . It was theorized that anisotropic diffusivity direction was collinear with an axon fiber subject to all eigenvalues and eigenvectors from an apparent diffusion tensor. To corroborate the origin of , orientation dependences referenced by were compared with those referenced by the standard principal diffusivity direction at b-values of 1000 and 2500 (s/mm ). These orientation dependences were obtained from -weighted images (b = 0) of ultrahigh-resolution Connectome DTI datasets in the public domain. A normalized root-mean-square error ( ) and an -test were used for evaluating curve-fittings, and statistical significance was considered to be a p of 0.05 or less. A phase-shifted model resulted in significantly reduced compared with that without in quantifying various and profiles, both in vivo and ex vivo at multiple fields. The profiles based on manifested a right-shifted phase ( ) at two b-values, while those based on became free from . For all phase-shifted and profiles, generally depended on the directional diffusivities by , as predicted. In summary, a ubiquitous phase shift has been demonstrated as a prerequisite for better quantifying transverse relaxation orientation dependences in human brain WM. Furthermore, the origin of associated with the directional diffusivities from DTI has been elucidated. These findings could have a significant impact on interpretations of prior and datasets and on future research.
Topics: Humans; White Matter; Diffusion Tensor Imaging; Brain; Diffusion Magnetic Resonance Imaging; Axons; Anisotropy
PubMed: 36908074
DOI: 10.1002/nbm.4925 -
Biotechnology Letters Aug 2024Simultaneous membrane-based feeding and monitoring of the oxygen transfer rate shall be introduced to the newly established perforated ring flask, which consists of a...
PURPOSE
Simultaneous membrane-based feeding and monitoring of the oxygen transfer rate shall be introduced to the newly established perforated ring flask, which consists of a cylindrical glass flask with an additional perforated inner glass ring, for rapid bioprocess development.
METHODS
A 3D-printed adapter was constructed to enable monitoring of the oxygen transfer rate in the perforated ring flasks. Escherichia coli experiments in batch were performed to validate the adapter. Fed-batch experiments with different diffusion rates and feed solutions were performed.
RESULTS
The adapter and the performed experiments allowed a direct comparison of the perforated ring flasks with Erlenmeyer flasks. In batch cultivations, maximum oxygen transfer capacities of 80 mmol L h were reached with perforated ring flasks, corresponding to a 3.5 times higher capacity than in Erlenmeyer flasks. Fed-batch experiments with a feed reservoir concentration of 500 g glucose L were successfully conducted. Based on the oxygen transfer rate, an ammonium limitation could be observed. By adding 40 g ammonium sulfate L to the feed reservoir, the limitation could be prevented.
CONCLUSION
The membrane-based feeding, an online monitoring technique, and the perforated ring flask were successfully combined and offer a new and promising tool for screening and process development in biotechnology.
Topics: Escherichia coli; Oxygen; Fermentation; Bioreactors; Batch Cell Culture Techniques; Glucose; Diffusion; Printing, Three-Dimensional
PubMed: 38758336
DOI: 10.1007/s10529-024-03493-0 -
Journal of Visualized Experiments : JoVE Aug 2023Nanoimpact electrochemistry enables the time-resolved in situ characterization (e.g., size, catalytic activity) of single nanomaterial units, providing a means of...
Nanoimpact electrochemistry enables the time-resolved in situ characterization (e.g., size, catalytic activity) of single nanomaterial units, providing a means of elucidating heterogeneities that would be masked in ensemble studies. To implement this technique with redox inactive particles, a solution-phase redox reaction is used to produce a steady-state background current on a disk ultramicroelectrode. When a particle adsorbs onto the electrode, it produces a stepwise reduction in the exposed electrode area, which produces, in turn, a stepwise decrease in the current commensurate with the size of the adsorbing species. Historically, however, nanoimpact electrochemistry has suffered from "edge effects," in which the radial diffusion layer formed at the circumference of the ultramicroelectrodes renders the step size dependent not only on the size of the particle but also on where it lands on the electrode. The introduction of electrocatalytic current generation, however, mitigates the heterogeneity caused by edge effects, thus improving the measurement precision. In this approach, termed "electrocatalytic interruption," a substrate that regenerates the redox probe at the diffusion layer is introduced. This shifts the rate-limiting step of the current generation from diffusion to the homogeneous reaction rate constant, thus reducing flux heterogeneity and increasing the precision of particle sizing by an order of magnitude. The protocol described here explains the set-up and data collection employed in nanoimpact experiments implementing this effect for improved precision in the sizing of redox in-active materials.
Topics: Data Collection; Diffusion; Electrochemistry; Electrodes; Nanostructures
PubMed: 37590554
DOI: 10.3791/65116