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Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
This paper introduces a novel optically controllable molecular communication (MC) transmitter (TX) design based on vesicular nanodevices (NDs). The NDs are functionalized for the controlled release of signaling molecules (SMs) via…
We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…
Nucleic acids such as mRNA have emerged as a promising therapeutic modality with the capability of addressing a wide range of diseases. Lipid nanoparticles (LNPs) as a delivery platform for nucleic acids were used in the COVID-19 vaccines…
This work presents a new multi-chemical experimental platform for molecular communication where the transmitter can release different chemicals. This platform is designed to be inexpensive and accessible, and it can be expanded to simulate…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
Evolutionary algorithms have long been used for optimization problems where the appropriate size of solutions is unclear a priori. The applicability of this methodology is here investigated on the problem of designing a nano-particle (NP)…
Recently there has been an increase in demand for soft and biocompatible electronic devices capable of withstanding large stretch. Ionically conductive polymers present a promising class of soft materials for these emerging applications due…
Peptide nucleic acids (PNAs) are artificial nucleic acids with a peptide backbone instead of sugar phosphate backbone of DNA or RNA. Their resistance to degradation, selectivity and greater binding affinity in comparison to usual nucleic…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Field-theoretical method is efficient in predicting the assembling structures of polymeric systems. However, for the polymer/nanoparticle mixture, the continuous density description is not suitable to capture the realistic assembly of…
Practically, all chemotherapeutic agents lead to drug resistance. Clinically, it is a challenge to determine whether resistance arises prior to, or as a result of, cancer therapy. Further, a number of different intracellular and…
Polymer electrolytes are critical for safe, high-energy-density solid-state batteries, yet discovering candidates that balance high ionic conductivity with high transference numbers remains a significant challenge. In this work, we develop…
This paper presents a modeling framework---mathematical model and computational framework---to study the response of a plastic material due to the presence and transport of a chemical species in the host material. Such a modeling framework…
With the goal of determining strategies to maximise drug delivery to a specific site in the body, we developed a mathematical model for the transport of drug nanocarriers (nanoparticles) in the bloodstream under the influence of an external…
Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in…
Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
We present a general mechanistic model of mass diffusion for a composite sphere placed in a large ambient medium. The multi-layer problem is described by a system of diffusion equations coupled via interlayer boundary conditions such as…
Diffusion models have emerged as powerful tools for molecular generation, particularly in the context of 3D molecular structures. Inspired by non-equilibrium statistical physics, these models can generate 3D molecular structures with…