Multiscale, Multiresolution Coarse-Grained Model via a Hybrid Approach: Solvation, Structure, and Self-Assembly of Aromatic Tripeptides.

Short aromatic peptides have been observed to assemble into diverse nanostructures, including fibers, tubes, and vesicles, using computational techniques. However, the computational studies have employed top-down coarse-grained (CG) models, which are unable to capture the assembly along with the conformation, packing, and organization of the peptides within the aggregates in a manner that is consistent with the all atom (AA) representation of the molecules. In this study, a hybrid structure- and force-based approach is adapted to develop a bottom-up CG force field of triphenylalanine using reference data from AA trajectories.

A coarse-grained Molecular Dynamics study of phase behavior in Co-assembled lipomimetic oligopeptides.

Multicomponent biomolecular aggregates, i.e., systems consisting of more than one type of biomolecular component co-assembling into one aggregate, provide an interesting design space for engineering unique biomaterials.

A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly.

Protein mimics such as peptoids form self-assembled nanostructures whose shape and function are governed by the side chain chemistry and secondary structure. Experiments have shown that a peptoid sequence with a helical secondary structure assembles into microspheres that are stable under various conditions. The conformation and organization of the peptoids within the assemblies remains unknown and is elucidated in this study via a hybrid, bottom-up coarse-graining approach.

Self-Organization of Mobile, Polyelectrolytic Dendrons on Stable, Amphiphile-Based Spherical Surfaces.

Spherical surfaces bearing mobile, solvophilic chains are ubiquitous. These systems are found in nature in the form of biological cells bearing carbohydrate chains, or glycans, or in drug delivery systems such as vesicles bearing polyethylene glycol chains and carrying therapeutic molecules. The self-organization of the chains on the spherical surface dictates the stability and functionality of the latter and is determined by key factors such as the interchain, chain-surface interactions, excluded volume, concentration of the chains, and external environment.

Symmetry-specific orientational order parameters for complex structures.

A comprehensive framework of characterizing complex self-assembled structures with a set of orientational order parameters is presented. It is especially relevant in the context of using anisotropic building blocks with various symmetries. Two classes of tensor order parameters are associated with polyhedral nematic and bond orientational order.

Controlling morphology in hybrid isotropic/patchy particle assemblies.

Brownian dynamics is used to study self-assembly in a hybrid system of isotropic particles (IPs), combined with anisotropic building blocks that represent special "designer particles." Those are modeled as spherical patchy particles (PPs) with binding only allowed between their patches and IPs. In this study, two types of PPs are considered: Octahedral PPs (Oh-PPs) and Square PPs (Sq-PPs), with octahedral and square arrangements of patches, respectively.

A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides.

Reconstituted photosynthetic proteins which are activated upon exposure to solar energy hold enormous potential for powering future solid state devices and solar cells. The functionality and integration of these proteins into such devices has been successfully enabled by lipid-like peptides. Yet, a fundamental understanding of the organization of these peptides with respect to the photosynthetic proteins and themselves remains unknown and is critical for guiding the design of such light-activated devices.

Dendronized vesicles: formation, self-organization of dendron-grafted amphiphiles and stability.

Fundamental bacterial functions like quorum sensing can be targeted to replace conventional antibiotic therapies. Nanoparticles or vesicles that bind interfacially to charged biomolecules could be used to block quorum sensing pathways in bacteria. Towards this goal, dendronized vesicles (DVs) encompassing polyamidoamine dendron-grafted amphiphiles (PDAs) and dipalmitoyl--3-phosphocholine lipids are investigated using the molecular dynamics simulation technique in conjunction with an explicit solvent coarse-grained force field.

Peptide-based vesicles and droplets: a review.

Peptide assembly is an increasingly important field of study due to the versatility, tunability and vast design space of amino acid based biomolecular assemblies. Peptides can be precisely engineered to possess various useful properties such as the ability to form supramolecular assemblies, desired response to pH, or thermal stability. These peptide supramolecular assemblies have diverse morphologies including vesicles, nanotubes, nanorods and ribbons.

Mechanisms underlying interactions between PAMAM dendron-grafted surfaces with DPPC membranes.

Biofouling is a pervasive problem which demands the creation of smart, antifouling surfaces. Towards this end, we examine the interactions between a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer and a polyamidoamine (PAMAM) dendron-grafted surface. In addition, we investigate the impact of dendron generation on the system behavior.

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition.

Harnessing the self-assembly of peptide sequences has demonstrated great promise in the domain of creating high precision shape-tunable biomaterials. The unique properties of peptides allow for a building block approach to material design. In this study, self-assembly of mixed systems encompassing two peptide sequences with identical hydrophobic regions and distinct polar segments is investigated.

Degree of Unsaturation and Backbone Orientation of Amphiphilic Macromolecules Influence Local Lipid Properties in Large Unilamellar Vesicles.

Liposomes have become increasingly common in the delivery of bioactive agents due to their ability to encapsulate hydrophobic and hydrophilic drugs with excellent biocompatibility. While commercial liposome formulations improve bioavailability of otherwise quickly eliminated or insoluble drugs, tailoring formulation properties for specific uses has become a focus of liposome research. Here, we report the design, synthesis, and characterization of two series of amphiphilic macromolecules (AMs), consisting of acylated polyol backbones conjugated to poly(ethylene glycol) (PEG) that can serve as the sole additives to stabilize and control hydrophilic molecule release rates from distearoylphosphatidylcholine (DSPC)-based liposomes.

Flow-Induced Shape Reconfiguration, Phase Separation, and Rupture of Bio-Inspired Vesicles.

The structural integrity of red blood cells and drug delivery carriers through blood vessels is dependent upon their ability to adapt their shape during their transportation. Our goal is to examine the role of the composition of bio-inspired multicomponent and hairy vesicles on their shape during their transport through in a channel. Through the dissipative particle dynamics simulation technique, we apply Poiseuille flow in a cylindrical channel.

Modeling Interactions between Multicomponent Vesicles and Antimicrobial Peptide-Inspired Nanoparticles.

We examine the interaction between peptide-inspired nanoparticles, or nanopins, and multicomponent vesicles using the dissipative particle dynamics simulation technique. We study the role of nanopin architecture and cholesterol concentration on the binding of the nanopins to the lipid bilayer, their insertion, and postembedding self-organization. We find the insertion to be triggered by enthalpically unfavorable interactions between the hydrophilic solvent and the lipophilic components of the nanopins.

Surface Reconfiguration of Binary Lipid Vesicles via Electrostatically Induced Nanoparticle Adsorption.

We demonstrate the adsorption of nanoparticles (NPs) with charged patches onto a binary vesicle encompassing polar neutral and polar zwitterionic lipids via an implicit solvent coarse-grained model and molecular dynamics simulations. Our investigations on the interactions between NPs and a binary vesicle demonstrate that the adsorption of charged NPs onto a binary vesicle surface can induce structural reorganization of the lipid bilayer. The approach of the NP to the vesicle surface is accompanied by spatial reorganization of the zwitterionic lipids, and the degree of reorganization is found to depend on the NP patch size.

Self-Assembly and Critical Aggregation Concentration Measurements of ABA Triblock Copolymers with Varying B Block Types: Model Development, Prediction, and Validation.

The dissipative particle dynamics (DPD) simulation technique is a coarse-grained (CG) molecular dynamics-based approach that can effectively capture the hydrodynamics of complex systems while retaining essential information about the structural properties of the molecular species. An advantageous feature of DPD is that it utilizes soft repulsive interactions between the beads, which are CG representation of groups of atoms or molecules. In this study, we used the DPD simulation technique to study the aggregation characteristics of ABA triblock copolymers in aqueous medium.

Harnessing steric hindrance to control interfacial adsorption of patchy nanoparticles onto hairy vesicles.

Via the Dissipative Particle Dynamics simulation technique we investigate the interfacial adsorption of nanoparticles with a binding site onto a hairy vesicle encompassing phospholipids and lipids functionalized with oligo ethylene glycol (OEG) chain. The functionalized nanoparticles are modeled as patchy spherical particles. We examine the relation between the relative concentration and size of the OEG chains, the adsorption kinetics, life-time and post-adsorption dynamics of the nanoparticles.

Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH.

Highly branched polymers such as polyamidoamine (PAMAM) dendrimers are promising macromolecules in the realm of nanobiotechnology due to their high surface coverage of tunable functional groups. Modeling efforts of PAMAM can provide structural and morphological properties, but the inclusion of solvents and the exponential growth of atoms with generations make atomistic simulations computationally expensive. We apply an implicit solvent coarse-grained model, called the Dry Martini force field, to PAMAM dendrimers.

Harnessing Nanoscale Confinement to Design Sterically Stable Vesicles of Specific Shapes via Self-Assembly.

We design sterically stable biocompatible vehicles with tunable shapes through the self-assembly of a binary mixture composed of amphiphilic molecular species, such as PEGylated lipids, and phospholipids under volumetric confinement. We use a molecular dynamics-based mesoscopic simulation technique called dissipative particle dynamics to resolve the aggregation dynamics, structure, and morphology of the hybrid aggregate. We examine the effect of confinement on the growth dynamics and shape of the hybrid aggregate, and demonstrate the formation of different morphologies, such as oblate and prolate shaped vesicles and bicelles.

Design of PAMAM-COO dendron-grafted surfaces to promote Pb(II) ion adsorption.

An expanding area of green technology is the wastewater treatment of heavy metal ions. As the adsorption of cations onto solid surfaces has been proven to be successful, recent research has demonstrated enhanced adsorption profiles by grafting dendron brushes onto a solid support. Via the molecular dynamics technique, we examine the adsorption of Pb(II) ions onto polyamidoamine (PAMAM) with carboxylate terminal groups through a coarse-grained implicit solvent model.

The design of shape-tunable hairy vesicles.

Via the use of a mesoscopic simulation technique called dissipative particle dynamics, we design sterically stable biocompatible vehicles through the self-assembly of a binary mixture composed of amphiphilic molecular species, such as PEGylated lipids, and phospholipids. We examine the factors controlling the shape of the hairy vesicle, and report the shape to change with molecular stiffness, and dissimilarity in the hydrocarbon tail groups, along with the relative concentration of the species, and the functional group length. We also draw correspondence with experimental studies on the shape transformations of the hairy vesicles through phase diagrams of the reduced volume, the ratio of the minimum and maximum radii, and the interfacial line tension, as a function of the concentration of the hairy lipids and the hydrocarbon tail molecular chain stiffness.

Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species.

Our aim is to investigate the phase segregation and the structure of multi-component bio-inspired phospholipid vesicles via dissipative particle dynamics. The chemical distinction in the phospholipid species arises due to different head and tail group moieties, and molecular stiffness of the hydrocarbon tails. The individual amphiphilic phospholipid molecular species are represented by a hydrophilic head group and two hydrophobic tails.

Bioinspired vesicles encompassing two-tail phospholipids: self-assembly and phase segregation via implicit solvent coarse-grained molecular dynamics.

Via implicit solvent molecular dynamics simulations, we demonstrate the self-assembly of stable single and binary vesicles composed of two-tail phospholipid molecules. The amphiphilic lipid molecules are composed of a hydrophilic headgroup and two hydrophobic tails and are represented by a reduced coarse-grained model which effectively captures the key chemical and geometric attributes of phospholipid molecules. We report our measurements of the bilayer thickness to be consistent with experimental values reported in the literature.

Nano-pipette directed transport of nanotube transmembrane channels and hybrid vesicles.

Using computational modeling, we simulate the interactions between a nanopipette and transmembrane, end-functionalized nanotubes that are localized within flat bilayers or nanoscopic vesicles. The functional groups (hairs) provide a "handle" for the moving pipette to controllably pick up and move the nanotubes to specific locations in the flat membrane, or the hybrid vesicle to specified regions on a surface. The ability to localize these hybrid vesicles on surfaces paves the way for creating nanoreactor arrays in fluidic devices.

Modeling the self-assembly of lipids and nanotubes in solution: forming vesicles and bicelles with transmembrane nanotube channels.

Via dissipative particle dynamics (DPD), we simulate the self-assembly of end-functionalized, amphiphilic nanotubes and lipids in a hydrophilic solvent. Each nanotube encompasses a hydrophobic stalk and two hydrophilic ends, which are functionalized with end-tethered chains. With a relatively low number of the nanotubes in solution, the components self-assemble into stable lipid-nanotube vesicles.