Deltin 7

Journal: Journal of Biological Research, Publisher: ACS

Abstract: Transient pore formation in lipid membranes plays a critical role in diverse biological and synthetic processes. Understanding the molecular transport mechanism through these membrane pores is a key step in the optimization of drug release and membrane integrity regulation. In this study, we investigated molecular transport through nanopores formed in the membrane of Giant Unilamellar Vesicles (GUVs) using finite element simulation in COMSOL Multiphysics. We explored the impact of nanopore diameter (16–60 nm) and fluorescent probe size (RSE 0.74–5.00 nm) on molecular transport. Using Fick's law of diffusion and the Stokes-Einstein equation, we calculated leakage rate constants (kleak) for various fluorescent probe sizes. Simulations revealed that larger nanopores significantly increased leakage rates, whereas increasing probe size led to slower leakage. Additionally, larger suspension areas accelerated molecular clearance from the vesicle, amplifying overall flux. The model was validated against experimental data on magainin 2-induced pores, showing strong agreement and confirming the accuracy of our approach. These findings provide insight into nanopore-mediated transport and offer a predictive framework for designing membrane-permeabilizing systems in synthetic biology and drug delivery applications.

Journal: Journal of Bangladesh Chemical Society

Journal: European Biophysics Journal, Publisher: Springer Link, Rank = Q2,  IF= 2.2

Abstract: Biomembranes regulate molecular transport essential to cellular function and numerous biomedical applications, such as drug delivery and gene therapy. This study simulates molecular transport through nano-sized multipores in Giant Unilamellar Vesicles (GUVs) using COMSOL Multiphysics. We analyzed the diffusion dynamics of fluorescent probes—including Calcein, Texas-red dextran 3000 (TRD- 3k), TRD- 10k, and Alexa Fluor-labeled soybean trypsin inhibitor (AF-SBTI)—across different pore sizes, and derived rate constants using curve fitting that closely align with experimental data. Additionally, an analytical model based on Fick’s law of diffusion provides further insight into transport efficiency. This approach offers a novel perspective by examining simultaneous transport through multiple nanopores, which better mimics realistic biological environments compared to traditional single-pore studies. We used COMSOL for efficiently simulating large-scale, multi-nanopore systems, particularly in biomedical applications where modeling of complex transport phenomena is essential. This work provides new insights into multipore-mediated transport, critical for optimizing nanopore-based drug delivery and advancing the understanding of cellular transport mechanisms.

Journal: Journal of Biological Physics, Publisher: Springer Link, Rank = Q2, IF=2.2

Abstract: Electroporation, a widely used physical method for transiently increasing cell permeability, facilitates molecular delivery for therapeutic and research applications. While electroporation proves to be a useful process, the mechanisms of pore formation and molecular transport remain incompletely understood. This study investigates the dynamics of electropore formation in lipid bilayers using molecular dynamics (MD) simulations and subsequent molecular transport by quantitative diffusion modeling. MD simulations reveal different stages of pore formation under applied electric fields, focusing on the lipid headgroup realignment and the hydration process of the pores. An FDM (Finite Difference Method)-based transport model quantifies the transport of molecules, such as glucose, calcein and bleomycin, using pore dimensions obtained from MD simulations. The results demonstrate a size-dependent transport efficiency, with smaller molecules diffusing more rapidly than larger ones. This work underscores the synergy between atomistic simulations and macroscopic transport modeling. Also, the findings offer valuable insights for optimizing electroporation protocols and developing targeted delivery systems for drugs and genetic material.

Journal: MRS Communications, Publisher: Springer Link, IF=2.3  Rank= Q2

Abstract: We investigated CO coverage (θCO) on Pt2Ru3 nanoparticle with various morphologies in H2/CO mixture gas atmosphere at 333 K by grand canonical ensemble Monte Carlo (GCMC) combined with quantitative structure–property relationship. In nanoparticles enclosed by (111) facets, θCO was significantly reduced when the surface and the subsurface were composed of Pt and Ru, respectively. The nanoparticles with homogeneously mixed surface showed low θCO, while the Janus-type showed high θCO. A similar tendency was obtained in the (100)-enclosed nanoparticle. These results revealed that the homogeneous mixing of Pt and Ru on the surface is essential to increase the CO tolerance.

Journal: IEEE Explore, Publisher: IEEE, IF =3.4

Abstract: Dielectrophoresis is the motion produced by non-uniform electric field on a non-electrolytic cell to study intracellular organism. In this work numerical analysis was used to modeling the electric field due to two nickel electrodes and calculating the intracellular transport of various macromolecules from outside to inside in the giant unilamellar vesicle (GUV) using COMSOL simulation. Here we have considered single-cell level technology to reveal transfer rate to make the cell concentration the highest it could be (0.99768432928 mol/m3), The molecular transport is measured for specific direction of fluid flow from outside of the cell membrane to inside for same direction of applied electric field. This simulation results suggests that developing electroporation technologies that simultaneously combine electroporation and dielectrophoresis technique could play a crucial role in the field of intra-cellular delivery also it may allow its wider application in both biomedical research and clinical therapy.

Journal: IEEE Explore, Publisher: IEEE    IF= 3.4 

Abstract: Microfluidic electroporation, or electro-permeabilization is the short, high-voltage pulses produced by an external electric field on a non-electrolytic cell to study intramolecular organisms. This is a sophisticated and newly established substantial molecular transport technique for gene transfection, cancer and tumor treatment, transdermal drug delivery, and so on. In this study, a dysregulated cell is used to simulate the molecular transport from the exterior of the cell to the interior of the cell and analyze the molecular transport with respect to time for direct clinical use. We have developed a non-electrolytic microelectroporation electrode surface, on which metal electrodes are coated with a dielectric. A COMSOL-based numerical analysis was used to calculate the molecular transport and dielectric material properties dependent electric field produced in the dielectric, fluid flow, electroporation, or electro-permeabilization field and Clausius-Mossotti factor for a 

Journal: IEEE Explore,  Publisher: IEEE

Abstract:Electroporation, or electropermeabilization, in the context of bioinformatics, refers to a simulation-based or laboratory-based technique used to introduce foreign genetic material, such as DNA, RNA, or plasmids into cells after creating reversible pores in the bilayer surface of the cells with the help of short-timed, high-voltage pulses produced by an external electric field. This transport technique is used for gene transfection, transdermal drug delivery, cancer chemotherapy, tumor treatment, and even in the Cancer Genome Atlas (TCGA). In this technique, an electric field is used to reduce the cell viability for some seconds to transport the molecules from the cell’s interior to the exterior and vice versa due to the concentration gradient in the cell itself and the suspension area. In this research work, we’ve demonstrated a model of post-electroporation molecular transport from the inner side of the different unilamellar vesicles to the outer side of the different unilamellar vesicles by COMSOL Multiphysics. The model determines transmembrane potential, multiple nanopores of multiple Giant Unilamellar Vesicles (GUV), multiple Large Unilamellar Vesicles (LUV), and distribution of pores radii as functions of position and time of the surfaces of the vesicles. At the outset, reversible electroporation is conducted, and then molecular transport is calculated for different points within the surface. The molecular transport graphs (concentration vs. time) are found steeper for large unilamellar vesicles which mean more transport happened within a short time from the starting moment and finally got saturated. In the same way, the transport rates of the giant unilamellar vesicles were found.

Journal: DIU Science and Technology

Abstract: The adsorption of carbon monoxide (CO) on nanoscale clusters is a topic of significant interest for catalytic and gas sensing applications. Quantum mechanical density functional theory (DFT) and molecular mechanics (MM) simulations were employed to investigate the interactions between carbon monoxide (CO) and Pt3, Pd3, Pd-doped Pt2, and Pt-doped Pd2 clusters. The aim of this research was to study the adsorption of CO on these clusters and understand the resulting changes in geometric and electronic properties. Our methodology involved performing DFT calculations to determine the adsorption energies, examining the bond lengths and binding energies of CO, and analyzing the electronic properties of the clusters. The key findings of our study revealed favorable adsorption of CO on all clusters, with notable modifications in bond lengths and binding energies. Among the clusters, Pt-doped Pd2 exhibited the highest adsorption energy, suggesting its potential as an efficient catalyst for CO removal and oxidation. Furthermore, the electronic properties of the clusters provided insights into their suitability for CO sensing applications. Overall, our research contributes to the understanding of CO adsorption behavior on nanoscale clusters and highlights the significance of Pt-doped Pd2 in CO-related applications, such as catalysis and gas sensing.

Journal: Bangladesh Journal of Physics, Publisher: Bangladesh Physical Society

Abstract: The controlled transport of molecules through cell membrane nanopores holds significant promise for various biomedical applications, ranging from gene transfection and cancer chemotherapy to transdermal drug delivery. Among the diverse array of membrane-active agents, antimicrobial peptides (AMPs) have garnered substantial interest due to their antibacterial and antifungal properties. Magainin 2, initially uncovered within the African clawed frog Xenopus laevis, is one such AMP known to interact with lipid bilayers that lead pore formation induced by membrane-active agents like magainin-2. In this study, we employed simulation techniques using COMSOL Multiphysics to investigate molecular transport of Calcein, Texas-Red Dextran 3000 (TRD-3k), TRD-10k, and AF-SBTI through nanoscale multipores of varying sizes, assessing the impact of both pore diameter and molecular size. Our simulations reveal that the rate constant of molecular transport decreases with increasing fluorescent probe size and pore diameter which comply with experimental observations of inside-to-outside probe leakage.