Entropic Confinement Research Articles

Photothermal Transport of DNA in Entropy-Landscape Plasmonic Waveguides.

The ability to handle single, free molecules in lab-on-a-chip systems is key to the development of advanced biotechnologies. Entropic confinement offers passive control of polymers in nanofluidic systems by locally asserting a molecule's number of available conformation states through structured landscapes. Separately, a range of plasmonic configurations have demonstrated active manipulation of nano-objects by harnessing concentrated electric fields. The integration of these two independent techniques promises a range of sophisticated and complementary functions to handle, for example, DNA, but numerous difficulties, in particular, conflicting requirements of channel size, have prevented progress. Here, we show that metallic V-groove waveguides, embedded in fluidic nanoslits, form entropic potentials that trap and guide DNA molecules over well-defined routes while simultaneously promoting photothermal transport of DNA through the losses of plasmonic modes. The propulsive forces, assisted by in-coupling to propagating channel plasmon polaritons, extend along the V-grooves with a directed motion up to ≈0.5 μm·mW-1 away from the input beam and λ-DNA velocities reaching ≈0.2 μm·s-1·mW-1. The entropic trapping enables the V-grooves to be flexibly loaded and unloaded with DNA by variation of transverse fluid flow, a process that is selective to biopolymers versus fixed-shape objects and also allows the technique to address the challenges of nanoscale interaction volumes. Our self-aligning, light-driven actuator provides a convenient platform to filter, route, and manipulate individual molecules and may be realized wholly by wafer-scale fabrication suitable for parallelized investigation.

Entropy-driven segregation of polymer-grafted nanoparticles under confinement

The modification of nanoparticles with polymer ligands has emerged as a versatile approach to control the interactions and organization of nanoparticles in polymer nanocomposite materials. Besides their technological significance, polymer-grafted nanoparticle (PGNP) dispersions have attracted interest as model systems to understand the role of entropy as a driving force for microstructure formation. For instance, densely and sparsely grafted nanoparticles show distinct dispersion and assembly behaviors within polymer matrices due to the entropy variation associated with conformational changes in brush and matrix chains. Here we demonstrate how this entropy change can be harnessed to drive PGNPs into spatially organized domain structures on submicrometer scale within topographically patterned thin films. This selective segregation of PGNPs is induced by the conformational entropy penalty arising from local perturbations of grafted and matrix chains under confinement. The efficiency of this particle segregation process within patterned mesa-trench films can be tuned by changing the relative entropic confinement effects on grafted and matrix chains. The versatility of topographic patterning, combined with the compatibility with a wide range of nanoparticle and polymeric materials, renders SCPINS (soft-confinement pattern-induced nanoparticle segregation) an attractive method for fabricating nanostructured hybrid films with potential applications in nanomaterial-based technologies.

Inversion of Signal Sequence Topology during Membrane Integration

In many cases, the topology of membrane proteins is established during co-translational membrane integration. This process involves the Sec translocon, a heterotrimeric protein-conducting channel that allows for both the translocation of secreted domains across the membrane through the central pore and the integration of membrane domains directly into the lipid bilayer through a lateral opening. For many proteins, the N-terminus is retained on the cytosolic side of the membrane and forms an inverted (type II) topology that threads the C-terminus through the channel. This inverted topology is hypothesized to involve a head-first intermediate which then undergoes a step-wise inversion process to its final topology. We use a newly developed coarse-grained model to simulate the integration of the signal sequence during the elongation of the nascent chain on the minute-long timescales that are relevant to the biological process. This coarse-grained simulation method enables direct comparisons to experimentally measured energetics of ribosome-nascent chain to translocon interactions. We observe a series of pulling and pushing forces on the ribosome-nascent chain as translation proceeds and identify a head-first intermediate whose inversion is driven by the entropic confinement of nascent chain residues in the ribosome-translocon junction.

Design of polymer conjugated 3-helix micelles as nanocarriers with tunable shapes

Amphiphilic peptide-polymer conjugates have the ability to form stable nanoscale micelles, which show great promise for drug delivery and other applications. A recent design has utilized the end-conjugation of alkyl chains to 3-helix coiled coils to achieve amphiphilicity, combined with the side-chain conjugation of polyethylene glycol (PEG) to tune micelle size through entropic confinement forces. Here we investigate this phenomenon in depth, using coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent and micelle theory. We analyze the conformations of PEG chains conjugated to three different positions on 3-helix bundle peptides to ascertain the degree of confinement upon assembly, as well as the ordering of the subunits making up the micelle. We discover that the micelle size and stability is dictated by a competition between the entropy of PEG chain conformations in the assembled state, as well as intermolecular cross-interactions among PEG chains that promote cohesion between neighboring conjugates. Our analyses build on the role of PEG molecular weight and conjugation site and lead to computational phase diagrams that can be used to design 3-helix micelles. This work opens pathways for the design of multifunctional micelles with tunable size, shape and stability.

The Entropic Cost of Polymer Confinement

The confinement of a polymer into a small space is thermodynamically unfavorable because of the reduction in the number of conformational states. The entropic penalty affects a variety of biological processes, and it plays an important role in polymer transport properties and in microfluidic devices. We determine the entropic penalty for the confinement of elastic polymer of persistence length P in the long-chain limit. We examine three geometries: (1) parallel planes separated by a distance d (a slit); (2) a circular tube of diameter d; and (3) a sphere of diameter d. We first consider infinitely thin (ideal) chains. As d/P drops from 100 to 0.01, TΔS rises from ∼5 × 10(-4) kT to ∼30 kT per persistence length for cases (1) and (2), with the entropic penalty for case (2) being consistently about twice that for case (1). TΔS is ∼5 kT per persistence length for confinement to a sphere when d = P, about twice the value predicted by mean field theory. For all three geometries, in the limit d/P ≫ 1, the asymptotic behavior of ΔS vs d is consistent with the d(-2) behavior predicted by theory. In the limit d/P ≪ 1, the scaling of ΔS for slits and tubes is also consistent with earlier predictions (d(-2/3)). Finally, we treat volume exclusion effects, examining chains of diameter D > 0. Confinement to a narrow slit or tube (d/P ≪ 1) has the same entropic penalty as that for an ideal chain in a slit or tube with d' = d - D; in the weak confinement regime (d/P ≫ 1), the entropic penalties are significantly larger than those for infinitely thin chains. When a chain of finite diameter is forced into a sphere or other closed cavity, the entropic confinement penalty rises without limit because there are no configurations available to the chain once its volume exceeds that of the cavity.

Diffusion Resonance of Nanoconfined Polymers

We examine the diffusive behavior of single polymers under spatially varying entropic confinement. A nanofluidic slit embedded with a lattice of pits was used to constrain single DNA molecules to d...

Ethanol Induced Shortening of dsDNA in Nanochannels

The entropic confinement and manipulation of DNA in fabricated nanostructures has facilitated both the study of DNA-protein interactions and the polymer physics of DNA conformations in different solvent conditions and geometries. Moreover, it holds great promise as a powerful tool for rapid genomic sequencing. Ethanol precipitation is a common tool in molecular biology used to purify and concentrate DNA, typically in 70% (or greater) ethanol solutions. Even at lower ethanol concentrations, however, DNA has been shown to undergo a transformation from its physiological B-form to A-form, a shorter yet slightly less twisted molecular conformation. To examine this transition, we isolated individual YOYO-1 labeled λ-DNA molecules in 100nm×100nm nanochannels in 0, 20, 40 and 60% ethanol solutions. We observed a dramatic shortening in the mean measured lengths with increasing ethanol and a broadening of the distribution of measured lengths at the intermediate ethanol concentrations. These observed lengths are less than that of fully A-form λ-DNA, suggesting that other mechanisms are involved in shortening the observed molecules. First, the possible effect of ethanol dislodging of the intercolated fluorophores and subsequent shortening the observed molecule is discussed. Second, the substantial variations in intensity in our observed molecules at the higher ethanol concentrations are (i) suggestive of the higher order DNA conformations such as loops and toroids that have been observed in DNA dried on mica surfaces and (ii) in accord with the observation that the effective persistence length of DNA is reduced in ethanol solutions.

Scaling Theory of Polymer Translocation into Confined Regions

We examine the voltage-driven polymer translocation from a spacious region into a confined region imposed by two parallel planes, so that the entry is impeded by the entropic confinement but aided by the electric field inside the confined region. Two modes of entry are examined: linear translocation where a chain enters the confined region with chain ends, and hairpin translocation where a chain enters the confined region by forming a hairpin. Our calculation shows that translocation time increases with polymer length for linear entries but decreases with polymer length for hairpin entries. Applying to electrophoresis of DNA molecules through periodic spacious and confined regions, our theory shows that the dominance of hairpin translocations leads to the experimentally observed faster migration of longer DNA molecules. Our theory predicts experimental conditions for the validity of this law in terms of polymer length, size of the confined region, and solution conditions.

Brownian Dynamics Simulations of Polyelectrolyte Adsorption onto Topographically Patterned Surfaces

The effect of patterned surface topography on the adsorption of single polyelectrolyte molecules is explored using Brownian dynamics simulations. The polyelectrolyte is modeled as a free-draining, freely jointed bead-rod chain, and electrostatic interactions are incorporated using a screened Coulombic potential with excluded volume interactions accounted for by the repulsive part of a Lennard-Jones potential. Topography consisting of periodically spaced valleys of square cross section separated by flat hills is considered. Chain conformations are characterized for a wide range of valley widths, depths, and spacings as well as for several different types of surface charge distributions. Depending on the parameter values describing the topography, the chains are found to adopt conformations ranging from flat and extended to those associated with bridge-, brush-, or semi-bridge-like structures. The formation of these structures is rationalized on the basis of a free-energy model that takes into account the increase in free energy due to entropic confinement, excluded volume interactions, and chain stretching as well as the decrease in free energy due to bead-surface electrostatic attraction. The results of this work are expected to be useful in designing patterned surface topography to control the conformations of adsorbed polyelectrolyte molecules.

Preparation and Characterization of Confined Atactic Polystyrene in Ordered Silica/Polystyrene Composites

Ordered silica/polystyrene composites were prepared via radical polymerization in silica colloidal crystal templates, and ordered macroporous polymers were accordingly obtained after removing the silica templates. The confinement effect of the templates on the polymers in the composites was investigated. NMR results indicated that the polystyrenes formed both inside and outside the template were atactic. The polystyrene inside the template possessed a higher molecular weight and a narrower molecular weight distribution than the bulk one outside the template. The glass transition temperature of the confined polystyrene increased significantly with decreasing silica sphere size of the templates, and so did the contraction of polymer pores. The smaller the silica sphere size of the templates, the more remarkable is the confinement, which could be explained by entropic confinement of the polymer chains within a fixed inorganic meso-framework (T. P. Russell, Science 2001, 293, 446).

Comparison of the van der Waals and Undulation Interactions between Uncharged Lipid Bilayers

A calculation of the long-range interaction energies between two undulating neutral lipid bilayers was performed. At bilayer spacings above several nanometers, the bilayer interaction can be considered to be composed solely of an attractive van der Waals component plus a repulsive undulation component arising from the entropic confinement of thermally excited out-of-plane motion of the bilayers by neighboring bilayers. The objective of this work was to determine if the long-range swelling behavior that has been observed in neutral multilamellar lecithin systems (e.g., bilayer spacings as large as 150 A), can in fact be explained by the undulation repulsion, which is the currently accepted explanation. It was found that the relative magnitudes of the long-range van der Waals and undulation energies are essentially determined by the magnitude of the dimensionless ratio AHKb/(kT)2, where AH is the Hamaker constant, Kb is the elastic bending modulus of the bilayer, and kT is the thermal energy. When this valu...

Entropic Confinement of Colloidal Spheres in Corners on Silicon Substrates

We have investigated depletion effects among dispersed, submicron, polystyrene spheres of two different sizes near a faceted silicon substrate. The larger spheres were confined to the corners where two silicon facets intersected (as where a wall meets a floor). The entropic confinement potential increased by 1.2kBT when the small-sphere volume fraction was increased by 14% to 0.37. Large-sphere crystallites nucleated along the corner and grew out along the flat surfaces before crystals nucleated on the flat surface or in the bulk. The results demonstrate a novel way to sort particles or to organize them along geometric features in a substrate for microfabrication.

Adsorption and Interaction Forces of Micellar and Microemulsion Solutions in Ultrathin Films

The interactions between surfaces across a nonionic surfactant (tetraoxyethylene dodecyl ether, C12E4) solution and its microemulsion in the dilute regime have been directly measured using the surface force apparatus. The results show that the structure of the adsorbed surfactant layer depends dramatically on the size and shape of the self-assembled structures in the bulk solution as well as the chemical nature of the substrate. On hydrophilic surfaces, the adsorption from surfactant solutions is relatively weak and the resulting long-range repulsive force is attributed to entropic confinement and elastic compression of adsorbed micelles. Microemulsion droplets adsorb much more strongly. On hydrophobic surfaces, a compact surfactant monolayer adsorbs leading, to a strong but shorter-ranged force. In contrast to the results with hydrophilic surfaces, the adsorbed surfactant layer is “destabilized” by the presence of oil from the microemulsion solution and is easily expelled upon compression. Quantitative assessments of the DLVO contribution and the entropic component of the measured force profiles are given. The entropic contribution can be explained and quantified when both the nature of the surface−surfactant interaction and the self-assembled structures in the bulk are known.