Analyzing mechanisms and microscopic reversibility of self-assembly

We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements of dynamical activity and assembly progress to compare their propensities for kinetic trapping. We use the analytic solution of a simple minimal model to illustrate the key features associated with such trapping, paying particular attention to the number of ways that particles can misbind. We discuss the relevance of our results for the design and control of self-assembly in general.     

Polynucleotides in cellular mimics: Coacervates and lipid vesicles

In this review, we examine the interaction of nucleic acids with cell-like structures based on liquid–liquid phase separation of charged molecules (complex coacervation) and amphiphilic self-assembly (lipid vesicles). We discuss the mechanisms of their assembly and describe how they can be used as models for origin of life studies and for understanding two recently-described phenomena in modern cells: membrane-free organelles and exosomes. Hybrid cells with increased structural complexity are highlighted and we then briefly explore how strategies based on electrostatic and hydrophobic assembly can be used for designing and synthesizing delivery agents for therapeutic nucleic acids. While the physical mechanisms of self-assembly vary, both strategies provide viable routes for generating minimal compartmentalized systems, modeling cellular pathways, and for rational design of new synthetic cells for technological applications.     

Lyotropic liquid crystal engineering-ordered nanostructured small molecule amphiphile self-assembly materials by design

Future nanoscale soft matter design will be guided to a large extent by the teachings of amphiphile (lipid or surfactant) self-assembly. Ordered nanostructured lyotropic liquid crystalline mesophases may form in select mixtures of amphiphile and solvent. To reproducibly engineer the low energy amphiphile self-assembly of materials for the future, we must first learn the design principles. In this critical review we discuss the evolution of these design rules and in particular discuss recent key findings regarding (i) what drives amphiphile self-assembly, (ii) what governs the self-assembly structures that are formed, and (iii) how can amphiphile self-assembly materials be used to enhance product formulations, including drug delivery vehicles, medical imaging contrast agents, and integral membrane protein crystallisation media. We focus upon the generation of 'dilutable' lyotropic liquid crystal phases with two- and three-dimensional geometries from amphiphilic small molecules (225 references).     

Forces,stresses and the (thermo?) dynamics of active matter

The statistical mechanics and microhydrodynamics of active matter systems have been studied intensively during the past several years, by various soft matter physicists, chemists, engineers, and biologists around the world. Recent attention has focused on the fascinating nonequilibrium behaviors of active matter that cannot be observed in equilibrium thermodynamic systems, such as spontaneous collective motion and swarming. Even minimal kinetic models of active Brownian particles exhibit self-assembly that resembles a gas–liquid phase separation from classical equilibrium systems. Self-propulsion allows active systems to generate internal stresses that enable them to control and direct their own behavior and that of their surroundings. In this review, we discuss the forces that govern the motion of active Brownian microswimmers, the stress (or pressure) they generate, and the implication of these concepts on their collective behavior. We focus on recent work involving the unique “swim pressure” exerted by active systems and discuss how this perspective may be the basic underlying physical mechanism responsible for self-assembly and pattern formation in all active matter. We discuss the utility of the swim pressure concept to quantify the forces, stresses, and the (thermo?) dynamics of active matter.     

Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions

The E. coli chaperone trigger factor (TF) interacts directly with nascent polypeptide chains as they emerge from the ribosome exit tunnel. Small protein domains can fold under the cradle created by TF, but the co-translational folding of larger proteins is slowed down by its presence. Because of the great experimental challenges in achieving high spatial and time resolution, it is not yet known whether or not TF alters the folding properties of small proteins and if the reduced rate of folding of larger proteins is the result of kinetic or thermodynamic effects. We show, by molecular simulations employing a coarse-grained model of a series of ribosome nascent-chain complexes, that TF does not alter significantly the co-translational folding process of a small protein G domain but delays that of a large β-galactosidase domain as a result of kinetic trapping of its unfolded ensemble. We demonstrate that this trapping occurs through a combination of three distinct mechanisms: a decrease in the rate of structural rearrangements within the nascent chain, an increase in the effective exit tunnel length due to folding outside the cradle, and entanglement of the nascent chain with TF. We present evidence that this TF-induced trapping represents a trade-off between promoting co-translational folding and sterically shielding the nascent chain from aberrant cytosolic interactions that could lead to its aggregation or degradation.     

Kinetic Delay in Cooperative Supramolecular Polymerization by Redefining the Trade-Off Relationship between H-Bonds and Van der Waals/π–π Stacking Interactions

We here present how rebalancing the interplay between H-bonds and dispersive forces (Van der Waals/π–π stacking) may induce or not the generation of kinetic metastable states. In particular, we show that extending the aromatic content and favouring the interchain VdW interactions causes a delay into the cooperative supramolecular polymerization of a new family of toluene bis-amide derivatives by trapping the metastable inactive state.     

Insertion and assembly of membrane proteins via simulation

Interactions of lipids are central to the folding and stability of membrane proteins. Coarse-grained molecular dynamics simulations have been used to reveal the mechanisms of self-assembly of protein/membrane and protein/detergent complexes for representatives of two classes of membrane protein, namely, glycophorin (a simple alpha-helical bundle) and OmpA (a beta-barrel). The accuracy of the coarse-grained simulations is established via comparison with the equivalent atomistic simulations of self-assembly of protein/detergent micelles. The simulation of OmpA/bilayer self-assembly reveals how a folded outer membrane protein can be inserted in a bilayer. The glycophorin/bilayer simulation supports the two-state model of membrane folding, in which transmembrane helix insertion precedes dimer self-assembly within a bilayer. The simulations also suggest that a dynamic equilibrium exists between the glycophorin helix monomer and dimer within a bilayer. The simulated glycophorin helix dimer is remarkably close in structure to that revealed by NMR. Thus, coarse-grained methods may help to define mechanisms of membrane protein (re)folding and will prove suitable for simulation of larger scale dynamic rearrangements of biological membranes.     

Hyperthermal organic thin film growth on surfaces terminated with self-assembled monolayers. I. The dynamics of trapping

We have examined the initial stages of growth of a crystalline small molecule organic thin film, diindenoperylene (DIP), on SiO(2) surfaces terminated with a series of self-assembled monolayers (SAMs). In this study we make use of supersonic molecular beam techniques to vary the incident kinetic energy of the DIP molecules, and we use in situ, real time synchrotron x-ray scattering to monitor the buildup of each molecular layer in the growing thin film. We find that the effects of the SAMs are most apparent concerning growth in the sub-monolayer regime, before the substrate is entirely covered by the DIP thin film. In this coverage regime on bare SiO(2), and SiO(2) terminated with either hexamethyldisilazane or perflurooctyltrichlorosilane the adsorption dynamics are consistent with trapping-mediated adsorption as observed in more simple systems, where the probability of adsorption decreases significantly with increasing kinetic energy. Once these surfaces are covered with DIP, however, the adsorption probability increases, particularly at the highest incident kinetic energy, and the probability of adsorption exhibits only a weak dependence on the incident kinetic energy. In contrast, on surfaces terminated by octyl- (OTS) and octadecyltrichlorosilane (ODTS) the trapping probability is high and exhibits little dependence on the incident kinetic energy, essentially the same as what is observed on these same surfaces covered by DIP. We postulate, which is backed by the results of molecular dynamics simulations, that direct molecular insertion into the OTS and ODTS layers is a primary explanation for efficient trapping on these surfaces.     

Segregation of Dispersed Silica Nanoparticles in Microfluidic Water-in-Oil Droplets: A Kinetic Study

Dispersed negatively charged silica nanoparticles segregate inside microfluidic water-in-oil (W/O) droplets that are coated with a positively charged lipid shell. We report a methodology for the quantitative analysis of this self-assembly process. By using real-time fluorescence microscopy and automated analysis of the recorded images, kinetic data are obtained that characterize the electrostatically-driven self-assembly. We demonstrate that the segregation rates can be controlled by the installment of functional moieties on the nanoparticle's surface, such as nucleic acid and protein molecules. We anticipate that our method enables the quantitative and systematic investigation of the segregation of (bio)functionalized nanoparticles in microfluidic droplets. This could lead to complex supramolecular architectures on the inner surface of micrometer-sized hollow spheres, which might be used, for example, as cell containers for applications in the life sciences.     

Preorganization boosts the artificial esterase activity of a self-assembling peptide

The creation of artificial enzymes to mimic natural enzymes remains a great challenge owing to the complexity of the structural arrangement of the essential amino acids in catalytic centers. In this study, we used the phosphatase-based enzyme-instructed self-assembly(EISA) to supervise artificial esterases' final structures and catalytic activities. We reported that peptide precursors containing different phosphorylation sites could preorganize into alternated nanostructures and undergo dephosphorylation in the presence of alkaline phosphatase(ALP) with variation in kinetic and thermodynamic profiles. Although identical self-assembly compositions were formed after dephosphorylation, precursors with more enhanced preorganized states tended to better promote ALP dephosphorylation, facilitate further self-assembly, and strengthen the catalytic activities of the final assemblies. We envisioned that our strategy would be useful for further construction and manipulation of various artificial enzymes with superior catalytic activities.     

Strands, networks, and continents from polystyrene dewetting at the air-water interface: implications for amphiphilic block copolymer self-assembly

We demonstrate that nanoscale aggregates similar to those formed via amphiphilic block copolymer self-assembly at the air-water interface, including strands, networks, and continents, can be generated by the simple spreading of PS homopolymer solutions on water. Two different PS homopolymers of different molecular weight (PS-405k, M(n) = 405?000 g mol(-1) and PS-33k, M(n) = 33?000 g mol(-1)) are spread at the air-water interface at various spreading concentrations ranging from 0.25 to 3.0 mg/mL. Aggregate formation is driven by PS dewetting from water as the spreading solvent evaporates. We propose that a high spreading concentration or a high molecular weight lead to chain entanglements that restrict macromolecular mobility in the solution, enabling the kinetic trapping of nanostructures associated with early and intermediate stages of PS dewetting. Comparison of PS-405k with a mainly hydrophobic PS-b-PEO block copolymer of similar molecular weight (PSEO-392k, M(n) = 392?000 g mol(-1), 2.0 wt % PEO) allows the effect of a relatively short surface active block on aggregate formation to be investigated. We show that whereas the PEO block is not a required component for the formation of strands and other nonglobular aggregates, it does increase the number of these aggregates at a given spreading concentration and decreases the minimum spreading concentration at which these aggregates are observed, along with decreasing the dimensions and polydispersity of specific surface features. The results provide supporting evidence for the role of PS dewetting in the generation of multiple PS-b-PEO aggregate morphologies at the air-water interface, as originally described in earlier paper from our group.     

Physical mechanisms and biological significance of supramolecular protein self-assembly

In living cells, chemical reactions of metabolism, information processing, growth and development are organized in a complex network of interactions. At least in part, the organization of this network is accomplished as a result of physical assembly by supramolecular scaffolds. Indeed, most proteins function in cells within the context of multimeric or supramolecular assemblies. With the increasing availability of atomic structures and molecular thermodynamics, it is possible to recast the problem of non-covalent molecular self-assembly from a unified perspective of structural thermodynamics and kinetics. Here, we present a generalized theory of self-assembly based on Wegner's kinetic model and use it to delineate three physical mechanisms of self-assembly: as limited by association of assembly units (nucleation), by association of monomers (isodesmic), and by conformational reorganization of monomers that is coupled to assembly (conformational). Thus, we discuss actin, tubulin, clathrin, and the capsid of icosahedral cowpea chlorotic mottle virus with respect to assembly of architectural scaffolds that perform largely mechanical functions, and pyruvate dehydrogenase, and RING domain proteins PML, arenaviral Z, and BRCA1:BARD1 with regard to assembly of supramolecular enzymes with metabolic and chemically directive functions. In addition to the biological functions made possible by supramolecular self-assembly, such as mesoscale mechanics of architectural scaffolds and metabolic coupling of supramolecular enzymes, we show that the physical mechanisms of self-assembly and their structural bases are biologically significant as well, having regulatory roles in both formation and function of the assembled structures in health and disease.     

Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments

Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.     

Database of atomistic reaction mechanisms with application to kinetic Monte Carlo

Kinetic Monte Carlo is a method used to model the state-to-state kinetics of atomic systems when all reaction mechanisms and rates are known a priori. Adaptive versions of this algorithm use saddle searches from each visited state so that unexpected and complex reaction mechanisms can also be included. Here, we describe how calculated reaction mechanisms can be stored concisely in a kinetic database and subsequently reused to reduce the computational cost of such simulations. As all accessible reaction mechanisms available in a system are contained in the database, the cost of the adaptive algorithm is reduced towards that of standard kinetic Monte Carlo.     

Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami‐induced local destruction of silicon dioxide

DNA origami is a widely used method for fabrication of custom‐shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick‐like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved “C”‐shaped and angular “L”‐shaped origamis were trapped with nanoscale precision and single‐structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol‐linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single‐structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick‐like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol‐linkers tended to induce an etched “nanocanyon” in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP‐trapped origami. The results show that the demonstrated DEP‐trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP‐assisted deformation of the substrates onto which they are attached.     

Nonuniform electro-osmotic flow on charged strips and its use in particle trapping

In this article, we investigate theoretically electro-osmotic flow set up by charged strips on an otherwise uncharged surface. Starting with a single-strip problem we demonstrate that for simple polynomial surface charge distributions several basic solutions can be derived in closed forms constituted by the analogous idea-flow solutions, which provide a more lucid way of revealing the flow features. These solutions reveal two types of flow topology: simple draining-in/pumping-out streaming and a pair of microvortices for symmetric and antisymmetric surface charge distributions, respectively. For an arbitrary surface charge distribution, more complicated flow structures can be found by the superposition of these basic solutions. We further extend the analysis to two uniformly charged strips and show how the flow characteristics vary with the strips' dimensions and surface zeta potentials. The far-field velocity behavior is also asymptotically identified and indicates that the hydrodynamic nature of the flow is typically long-range. An application to particle trapping with electro-osmotic vortices is also investigated theoretically for the first time. We show that in collaboration with short-range attraction effects the trapping can be facilitated by symmetric vortices with a converging stagnation point, but not by asymmetric vortices.     

Synthesis, self-assembly, and characterization of supramolecular polymers from electroactive dendron rodcoil molecules

We report here the synthesis and self-assembly of a series of three molecules with dendron rodcoil architecture that contain conjugated segments of oligo(thiophene), oligo(phenylene-vinylene), and oligo(phenylene). Despite their structural differences, all three molecules yield similar self-assembled structures. Electron and atomic force microscopy reveals the self-assembly of the molecules into high aspect ratio ribbon-like nanostructures which at low concentrations induce gelation in nonpolar solvent. Self-assembly results in a blue-shifted absorption spectrum and a red-shifted, quenched fluorescence spectrum, indicating aggregation of the conjugated segments within the ribbon-like structures. The assembly of these molecules into one-dimensional nanostructures is a route to pi-pi stacked supramolecular polymers for organic electronic functions. In the oligo(thiophene) derivative, self-assembly leads to a 3 orders of magnitude increase in the conductivity of iodine-doped films due to self-assembly. We also found that electric field alignment of these supramolecular assemblies can be used to create arrays of self-assembled nanowires on a device substrate.     

Multiple morphologies of amphiphilic diblock copolymer micelles in two and three dimensions

We show that in aqueous solution, diblock copolymers, where one block is hydrophobic and the other hydrophilic can undergo self-assembly in three dimensions in a manner similar to small molecule amphiphiles. In addition, two dimensional self-assembly has been studied at the air-water interface. We describe the various morphologies which have been observed in these systems and the parameters which we can use to tailor them.     

Self-assembly of amphiphilic molecules: A review on the recent computer simulation results

We provided a short review on the recent progresses in computer simulations of adsorption and self-assembly of amphiphilic molecules. Owing to the extensive applications of amphiphilic molecules, it is very important to understand thoroughly the effects of the detailed chemistry, solid surfaces and the degree of confinement on the aggregate morphologies and kinetics of self-assembly for amphiphilic systems. In this review we paid special attention on (i) morphologies of adsorbed surfactants on solid surfaces, (ii) self-assembly in confined systems, and (iii) kinetic processes involving amphiphilic molecules.     

Interactions,Structure, and Microscopic Response: Complex Fluid Rheology Using Laser Tweezers

Optical trapping techniques are emerging as significant research tools in complex fluids, offering the ability to probe nano‐ and microscopic interactions, structures, and responses that govern the rheology of complex fluids. In combination with real‐space imaging, microstructural response of these fluids can be directly and quantitatively correlated to imposed microscopic stresses and strains. Thus, laser tweezers are enabling us to bridge multiple length scales in colloid and polymer rheology and should be highly useful for investigating the mechanisms of linear and nonlinear rheology. In this article, we briefly review the theory and practice of using optical traps in complex fluids. We discuss the characteristics of the gradient force trap, practical concerns in trapping experiments, and applications, including measurements of micromechanics and microrheology in colloid and polymer gels.