Cell simulation

Additive Manufacturing (AM) enables the generation of complex geometries and controlled internal cavities that are so interesting for the biomedical industry due to the benefits they provide in terms of osseointegration and bone growth. These technologies enable the manufacturing of the so-called lattice structures that are cells with different geometries and internal pores joint together for the formation of scaffold-type structures. In this context, the present paper analyses the feasibility of using diamond-type lattice structures and topology optimisation for the re-design of a dental implant...

Recent evidence has demonstrated that the transsynaptic nanoscale organization of synaptic proteins plays a crucial role in regulating synaptic strength in excitatory synapses. However, the molecular mechanism underlying this transsynaptic nanostructure in inhibitory synapses still remains unclear and its impact on synapse function in physiological or pathological contexts has not been demonstrated. In this study, we utilized an engineered proteolysis technique to investigate the effects of acute cleavage of neuroligin-2 (NL2) on synaptic transmission...

Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum approximations based on concentrations break down and a particle-based approach is more accurate and more efficient. We describe and validate a new version of the open-source MCell simulation program (MCell4), which supports generalized 3D Monte Carlo modeling of diffusion and chemical reaction of discrete molecules and macromolecular complexes in solution, on surfaces representing membranes, and combinations thereof...

Interlayer engineering is crucial for achieving efficient and stable organic solar cells (OSCs). Herein, by introducing a commercialized brominated quaternary ammonium salt, hexamethonium bromide (HB), into a perylene diimide (PDI)-structured electron transport layer (ETL), a PDINN:HB hybrid ETL with enhanced charge collection ability and environmental/operational stability is realized. Molecular dynamics simulations and Kelvin probe force microscopy indicate that strong polar bromine and amine groups can form extra interfacial dipoles in the hybrid interlayer, while X-ray photoelectron spectroscopy and electron paramagnetic resonance suggest the hybrid ETL can interact with the Ag cathode, thereby regulating the energy level arrangement at the interface...

The Dielectrically Modulated Full Gate Tunnel Field Effect Transistor (FET) with dual nanocavities, as described in the paper, is a novel device designed as a label-free biosensor for detecting cancer cell biomolecules. This biosensor utilizes the principles of field-effect transistors and incorporates nanocavities to enhance the detection sensitivity. The simulations are conducted using the Silvaco Atlas model, which allowed for the analysis of the device's electrical characteristics in the presence of various cancer cell biomolecules...

Nuclear compartments form via biomolecular phase separation, mediated through multivalent properties of biomolecules concentrated within condensates. Certain compartments are associated with specific chromatin regions, including transcriptional initiation condensates, which are composed of transcription factors and transcriptional machinery, and form at acetylated regions including enhancer and promoter loci. While protein self-interactions, especially within low-complexity and intrinsically disordered regions, are known to mediate condensation, the role of substrate-binding interactions in regulating the formation and function of biomolecular condensates is under-explored...

Gastrulation is the first major differentiation process in animal embryos. However, the dynamics of human gastrulation remain mostly unknown owing to the ethical limitations. We studied the dynamics of the mesoderm and endoderm cell differentiation from human pluripotent stem cells for insight into the cellular dynamics of human gastrulation. Human pluripotent stem cells have properties similar to those of the epiblast, which gives rise to the three germ layers. The mesoderm and endoderm were induced with more than 75% purity from human induced pluripotent stem cells...

The combination of shikonin (SKN) and gefitinib (GFB) can reverse the drug resistance of lung cancer cells by affecting energy metabolism. However, the poor solubility of SKN and GFB limits their clinical application because of low bioavailability. Wheat germ agglutinin (WGA) can selectively bind to sialic acid and N-acetylglucosamine on the surfaces of microfold cells and enterocytes, and is a targeted biocompatible material. Therefore, we created a co-delivery micelle system called SKN/GFB@WGA-micelles with the intestinal targeting functions to enhance the oral absorption of SKN and GFB by promoting mucus penetration for nanoparticles via oral administration...

We recorded current-time ( i - t ) profiles for oxidizing ferrocyanide (FCN) while spherical yeast cells of radius ( r c ≈ 2 μm) collided with disk ultramicroelectrodes (UMEs) of increasing radius ( r e ≈ 12-45 μm). Collision signals appear as minority steps and majority blips of decreased current overlayed on the i - t baseline when cells block ferrocyanide flux ( J FCN ). We assigned steps to adsorption events and blips to bouncing collisions or contactless passages. Yeast cells exhibit impact signals of long duration (Δ t ≈ 15-40 s) likely due to sedimentation...

BACKGROUND: The availability of genes and protein sequences for parasites has provided valuable information for drug target identification and vaccine development. One such parasite is Bartonella quintana, a Gram-negative, intracellular pathogen that causes bartonellosis in mammalian hosts. OBJECTIVE: Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to B. quintana. METHODS AND FINDINGS: To explore these aspects, we have adopted a subtractive proteomics approach to analyse the proteome of B...

Mutations in the human PURA gene cause the neurodevelopmental PURA syndrome. In contrast to several other monogenetic disorders, almost all reported mutations in this nucleic acid-binding protein result in the full disease penetrance. In this study, we observed that patient mutations across PURA impair its previously reported co-localization with processing bodies. These mutations either destroyed the folding integrity, RNA binding, or dimerization of PURA. We also solved the crystal structures of the N- and C-terminal PUR domains of human PURA and combined them with molecular dynamics simulations and nuclear magnetic resonance measurements...

The development and characterization of materials for solid oxide fuel cells (SOFC) is an important step towards sustainable energy technologies. This present study models cubic CeO2 , Gd2 O3 , and gadolinium-doped ceria (GDC) using newly constructed interaction potentials based on a partial atom charge framework. The interaction model was validated by comparing the structural properties with experimental reference data, which were found to be in good agreement. Validation of the potential model was conducted considering the surface stability of CeO2 and Gd2 O3 ...

Photovoltaic technology has been widely recognized as a means to advance green energy solutions in the sub-Saharan region. In the real-time operation of solar modules, temperature plays a crucial role, making it necessary to evaluate the thermal impact on the performance of the solar devices, especially in high-insolation environments. Hence, this paper investigates the effect of operating temperature on the performance of two types of organometallic halide perovskites (OHP) - formamidinium tin iodide (FASnI3 ) and methylammonium lead iodide (MAPbI3 )...

ConspectusBuckminsterfullerene, C60 , was discovered through a prominent mass peak containing 60 atoms produced from laser vaporization of graphite, driven by Kroto's interest in understanding the formation mechanisms of carbon-containing molecules in space. Inspired by the geodesic dome-shaped architecture designed by Richard Buckminster Fuller, after whom the particle was named, C60 was found to have a football-shaped structure comprising 20 hexagons and 12 pentagons. It sparked worldwide interest in understanding this new carbon allotrope, resulting in the awarding of the Noble Prize in Chemistry to Smalley, Kroto, and Curl in 1996...

Developing unique mechanisms of action are essential to combat the growing issue of antimicrobial resistance. Supramolecular assemblies combining the improved biostability of non-natural compounds with the complex membrane-attacking mechanisms of natural peptides are promising alternatives to conventional antibiotics. However, for such compounds the direct visual insight on antibacterial action is still lacking. Here we employ a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular structures of lysine-rich heterochiral β3 -peptides, termed lamellin-2K and lamellin-3K, triggered by bacterial cell surface lipopolysaccharides...

Discovering effective anti-cancer agents poses a formidable challenge given the limited efficacy of current therapeutic modalities against various cancer types due to intrinsic resistance mechanisms. Cancer immunochemotherapy is an alternative strategy for breast cancer treatment and overcoming cancer resistance. Human Indoleamine 2,3-dioxygenase (hIDO1) and human Tryptophan 2,3-dioxygenase 2 (hTDO2) play pivotal roles in tryptophan metabolism, leading to the generation of kynurenine and other bioactive metabolites...

Coronavirus disease (COVID-19) and pulmonary hypertension (PH) are closely correlated. However, the mechanism is still poorly understood. In this article, we analyzed the molecular action network driving the emergence of this event. Two datasets (GSE113439 and GSE147507) from the GEO database were used for the identification of differentially expressed genes (DEGs).Common DEGs were selected by VennDiagram and their enrichment in biological pathways was analyzed. Candidate gene biomarkers were selected using three different machine-learning algorithms (SVM-RFE, LASSO, RF)...

New drugs and technologies are continuously developed to improve the efficacy and minimize the critical side effects of cancer treatments. The present investigation focuses on the development of a liposomal formulation for Idelalisib, a small-molecule kinase inhibitor approved for the treatment of lymphoid malignancies. Idelalisib is a potent and selective antitumor agent, but it is not indicated nor recommended for first-line treatment due to fatal and serious toxicities. Herein, liposomes are proposed as a delivery tool to improve the therapeutic profile of Idelalisib...

The escalating prevalence of Alzheimer's disease (AD) has prompted extensive research into potential therapeutic interventions, with a specific focus on molecular targets such as amyloid beta (Aβ) and tau protein aggregation. In this study, a series of α-ketoamide derivatives was synthesized from β,γ-unsaturated α-keto thioesters, achieving high purity and good yield. Thioflavin T based Aβ aggregation assay identified four promising compounds (BD19, BD23, BD24, and BD27) that demonstrated significant inhibitory effects on Aβ aggregation...

Airway epithelium is extraordinary vulnerable to damage owning to continuous environment exposure. Subsequent repair is therefore essential to restore the homeostasis of respiratory system. Disruptions in respiratory epithelial repair caused by nanoparticles exposure have been linked to various human diseases, yet implications in repair process remain incompletely elucidated. This study aims to elucidate the key stage in epithelial repair disturbed by carbon black (CB) nanoparticles, highlighting the pivotal role of ΔNp63 in mediating the epithelium repair...