Coarse-Grained Simulation of Polycation/DNA-Like Complexes: Role of Neutral Block

Predicting Adhesive Free Energies of Polymer-Surface Interactions with Machine Learning

Polymer-surface interactions are crucial to many biological processes and industrial applications. Here we propose a machine learning method to connect a model polymer's sequence with its adhesion to decorated surfaces. We simulate the adhesive free energies of 20000 unique coarse-grained one-dimensional polymer sequences interacting with functionalized surfaces and build support vector regression models that demonstrate inexpensive and reliable prediction of the adhesive free energy as a function of sequence. Our work highlights the promising integration of coarse-grained simulation with data-driven machine learning methods for the design of functional polymers and represents an important step toward linking polymer compositions with polymer-surface interactions.

Protection of Double-Stranded RNA via Complexation with Double Hydrophilic Block Copolymers: Influence of Neutral Block Length in Biologically Relevant Environments

Interaction between the anionic phosphodiester backbone of DNA/RNA and polycations can be exploited as a means of delivering genetic material for therapeutic and agrochemical applications. In this work, quaternized poly(2-(dimethylamino)ethyl methacrylate)-block-poly(N,N-dimethylacrylamide) (PQDMAEMA-b-PDMAm) double hydrophilic block copolymers (DHBCs) were synthesized via reversible addition-fragmentation chain-transfer (RAFT) polymerization as nonviral delivery vehicles for double-stranded RNA. The assembly of DHBCs and dsRNA forms distinct polyplexes that were thoroughly characterized to establish a relationship between the length of the uncharged poly(N,N-dimethylacrylamide) (PDMA) block and the polyplex size, complexation efficiency, and colloidal stability. Dynamic light scattering reveals the formation of smaller polyplexes with increasing PDMA lengths, while gel electrophoresis confirms that these polyplexes require higher N/P ratio for full complexation. DHBC polyplexes exhibit enhanced stability in low ionic strength environments in comparison to homopolymer-based polyplexes. In vitro enzymatic degradation assays demonstrate that both homopolymer and DHBC polymers efficiently protect dsRNA from degradation by RNase A enzyme.

Coarse-Grained Modeling of Ion-Containing Polymers

Ion-containing polymers have continued to be an important research focus for several decades due to their use as an electrolyte in energy storage and conversion devices. Elucidation of connections between the mesoscopic structure and multiscale dynamics of the ions and solvent remains incompletely understood. Coarse-grained modeling provides an efficient approach for exploring the structural and dynamical properties of these soft materials. The unique physicochemical properties of such polymers are of broad interest. In this review, we summarize the current development and understanding of the structure-property relationship of ion-containing polymers and provide insights into the design of such materials determined from coarse-grained modeling and simulations accompanying significant advances in experimental strategies. We specifically concentrate on three types of ion-containing polymers: proton exchange membranes (PEMs), anion exchange membranes (AEMs), and polymerized ionic liquids (polyILs). We posit that insight into the similarities and differences in these materials will lead to guidance in the rational design of high-performance novel materials with improved properties for various power source technologies.

Efficient Molecular Approach to Quantifying Solvent-Mediated Interactions

The solvent-mediated interaction, or equivalently the depletion force, play a pivotal role in the processes, by which two objects in solution such as lock and key particles, antibody and antigen, macromolecule and substrate, are attracted to each other. The quantification of this interaction is important yet challenging since it depends on the microscopic solvent structure in the surrounding. Here, we report an efficient molecular approach for predicting the solvent-mediated interaction by combining the classical density functional theory with a reversible solvation thermodynamic circle. For demonstration, the solvent-mediated interactions between two nanoparticles and between a nanoparticle and a rough wall are examined, and good agreements compared with the simulation results are illustrated. This approach is thereafter employed to interpret the reported self-assembly phenomena of lock and key colloidal particles. We show that the binding probability between the lock and key colloids can be successfully characterized at different depletant concentrations and system temperatures. This approach provides a potential route for identifying the coarse-graining interaction between two objects in fluid systems.

Molecular dynamics study on the mechanism of polynucleotide encapsulation by chitosan

The safe and effective delivery of therapeutic genes into target cell interiors is of great importance in gene therapy. Chitosan has been extensively studied as a gene delivery carrier due to its good biocompatibility and biodegradability. Understanding the atomic interaction mechanism between chitosan and DNA is important in the design and application of chitosan-based drug and gene delivery systems. In this work, the interactions between single-stranded polynucleotides and different types of chitosan were systematically investigated by using molecular dynamics (MD) simulation. Our results demonstrate that the functional groups of chitosan, the types of base and length of polynucleotides regulate the interaction behavior between chitosan and polynucleotides. The encapsulation capacity of polynucleotide by chitosan is mainly balanced by two factors: the strength of polynucleotide binding to chitosan and the tendency of self-aggregation of polynucleotide in the solution. For -NH3+ chitosan, due to the strong electrostatic interaction, especially the H-bond between -NH3+ groups in chitosan and phosphate groups in polynucleotide, the aggregation effect could be partially eliminated. The good dispersal capacity of polynucleotides may improve the encapsulation of polynucleotides by chitosan, and hence increase the delivery and transfection efficiency of chitosan-based gene carrier.

Polymer-Nucleic Acid Interactions

Gene therapy is an important therapeutic strategy in the treatment of a wide range of genetic disorders. Polymers forming stable complexes with nucleic acids (NAs) are non-viral gene carriers. The self-assembly of polymers and nucleic acids is typically a complex process that involves many types of interaction at different scales. Electrostatic interaction, hydrophobic interaction, and hydrogen bonds are three important and prevalent interactions in the polymer/nucleic acid system. Electrostatic interactions and hydrogen bonds are the main driving forces for the condensation of nucleic acids, while hydrophobic interactions play a significant role in the cellular uptake and endosomal escape of polymer-nucleic acid complexes. To design high-efficiency polymer candidates for the DNA and siRNA delivery, it is necessary to have a detailed understanding of the interactions between them in solution. In this chapter, we survey the roles of the three important interactions between polymers and nucleic acids during the formation of polyplexes and summarize recent understandings of the linear polyelectrolyte-NA interactions and dendrimer-NA interactions. We also review recent progress optimizing the gene delivery system by tuning these interactions.

Mesoscopic Simulations of Adsorption and Association of PEO-PPO-PEO Triblock Copolymers on a Hydrophobic Surface: From Mushroom Hemisphere to Rectangle Brush

The dissipative particle dynamics (DPD) method is used to investigate the adsorption behavior of PEO-PPO-PEO triblock copolymers at the liquid/solid interface. The effect of molecular architecture on the self-assembled monolayer adsorption of PEO-PPO-PEO triblock copolymers on hydrophobic surfaces is elucidated by the adsorption process, film properties, and adsorption morphologies. The adsorption thicknesses on hydrophobic surfaces and the diffusion coefficient as well as the aggregation number of Pluronic copolymers in aqueous solution observed in our simulations agree well with previous experimental and numerical observations. The radial distribution function revealed that the ability of self-assembly on hydrophobic surfaces is P123 > P84 > L64 > P105 > F127, which increased with the EO ratio of the Pluronic copolymers. Moreover, the shape parameter and the degree of anisotropy increase with increasing molecular weight and mole ratio of PO of the Pluronic copolymers. Depending on the conformation of different Pluronic copolymers, the morphology transition of three regimes on hydrophobic surfaces is present: mushroom or hemisphere, progressively semiellipsoid, and rectangle brush regimes induced by decreasing molecular weight and mole ratio of EO of Pluronic copolymers.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems

Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.