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We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
In this letter, we present anti-cancer drug delivery strategies using knowledges obtained from our recent studies. We have conducted inverse analyses of "density distributions of colloidal particles near a focused surface" and "pair…
A computational model is proposed to investigate drug delivery systems in which erosion and diffusion mechanisms are participating in the drug release process. Our approach allowed us to analytically estimate the crossover point between…
We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogenous biological datasets, which can be challenging without sophisticated tools. We developed COMO, a user-friendly…
Acidosis in tumors arises from reprogrammed metabolism and compromised vasculature, creating a harsh, acidic microenvironment that drives the evolutionary selection of acid-resistant cell phenotypes. A mathematical model is proposed to…
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…
The transport of nanoparticles (NPs) in polymer networks, as a typical simplified model describing various structures in living systems, is profoundly important in biomedical engineering and nanotechnology. Predicting the effective…
Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first…
This paper presents a stochastic analysis of the time-variant channel impulse response (CIR) of a three dimensional diffusive mobile molecular communication (MC) system where the transmitter, the absorbing receiver, and the molecules can…
Hydrophobically modified magnetic nanoparticles (MNPs) were encapsulated within the membrane of poly(trimethylene carbonate)-b-poly(L-glutamic acid) (PTMC-b-PGA) block copolymer vesicles using a nanoprecipitation process. This formulation…
The dynamics of polymer-nanoparticle (NP) mixtures, which involves multiple scales and system-specific variables, has posed a long-standing challenge on its theoretical description. In this paper, we construct a microscopic theory for…
Polymer solutions subject to pressure driven flow and in nanoscale slit pores are systematically investigated using the dissipative particle dynamics approach. We investigated the effect of molecular weight, polymer concentration and flow…
In this paper, we design a drug release mechanism for dynamic time division multiple access (TDMA)-based molecular communication via diffusion (MCvD). In the proposed scheme, the communication frame is divided into several time slots over…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
Hypoxia-activated prodrugs offer a promising strategy for targeting oxygen-deficient regions in solid tumors, which are often resistant to conventional therapies. However, modeling their behavior is challenging because of the complex…
Accurate modeling of drug release is essential for designing and developing controlled-release systems. Classical models (Fick, Higuchi, Peppas) rely on simplifying assumptions that limit their accuracy in complex geometries and release…
New generation in vitro high-throughput screening (HTS) assays for the assessment of engineered nanomaterials provide an opportunity to learn how these particles interact at the cellular level, particularly in relation to injury pathways.…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…