Entropic Trapping Research Articles

Electro-suppression of water nano-droplets' solidification in no man's land: Electromagnetic fields' entropic trapping of supercooled water.

Understanding water solidification, especially in "No Man's Land" (NML) (150 K < T < 235 K) is crucially important (e.g., upper-troposphere cloud processes) and challenging. A rather neglected aspect of tropospheric ice-crystallite formation is inevitably present electromagnetic fields' role. Here, we employ non-equilibrium molecular dynamics of aggressively quenched supercooled water nano-droplets in the gas phase under NML conditions, in externally applied electromagnetic (e/m) fields, elucidating significant differences between effects of static and oscillating fields: although static fields induce "electro-freezing," e/m fields exhibit the contrary - solidification inhibition. This anti-freeze action extends not only to crystal-ice formation but also restricts amorphisation, i.e., suppression of low-density amorphous ice which forms otherwise in zero-field NML environments. E/m-field applications maintain water in the deeply supercooled state in an "entropic trap," which is ripe for industrial impacts in cryo-freezing, etc.

Entropic trap purification of long DNA.

Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.

How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield of Dioxetane?

Chemiluminescence is the emission of light as a result of a nonadiabatic chemical reaction. The present work is concerned with understanding the yield of chemiluminescence, in particular how it dramatically increases upon methylation of 1,2-dioxetane. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction of various methyl-substituted dioxetanes have been simulated. Methyl-substitution leads to a significant increase in the dissociation time scale. The rotation around the O-C-C-O dihedral angle is slowed; thus, the molecular system stays longer in the "entropic trap" region. A simple kinetic model is proposed to explain how this leads to a higher chemiluminescence yield. These results have important implications for the design of efficient chemiluminescent systems in medical, environmental, and industrial applications.

Origin of proton affinity to membrane/water interfaces

Proton diffusion along biological membranes is vitally important for cellular energetics. Here we extended previous time-resolved fluorescence measurements to study the time and temperature dependence of surface proton transport. We determined the Gibbs activation energy barrier ΔG‡r that opposes proton surface-to-bulk release from Arrhenius plots of (i) protons’ surface diffusion constant and (ii) the rate coefficient for proton surface-to-bulk release. The large size of ΔG‡r disproves that quasi-equilibrium exists in our experiments between protons in the near-membrane layers and in the aqueous bulk. Instead, non-equilibrium kinetics describes the proton travel between the site of its photo-release and its arrival at a distant membrane patch at different temperatures. ΔG‡r contains only a minor enthalpic contribution that roughly corresponds to the breakage of a single hydrogen bond. Thus, our experiments reveal an entropic trap that ensures channeling of highly mobile protons along the membrane interface in the absence of potent acceptors.

Dynamical Insights into the Decomposition of 1,2-Dioxetane.

Chemiluminescence in 1,2-dioxetane occurs through a thermally activated decomposition reaction into two formaldehyde molecules. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction have been simulated, starting from the first O-O bond-breaking transition structure. The ground-state dissociation occurs between t = 30 fs and t = 140 fs. The so-called entropic trap leads to frustrated dissociations, postponing the decomposition reaction. Specific geometrical conditions are necessary for the trajectories to escape from the entropic trap and for dissociation to be possible. The singlet excited states participate as well in the trapping of the molecule: dissociation including the nonadiabatic transitions to singlet excited states now occurs from t = 30 fs to t = 250 fs and later. Specific regions of the seam of the S0/S1 conical intersections that would "retain" the molecule for longer on the excited state have been identified.

Path counting on simple graphs: from escape to localization

We study the asymptotic behavior of the number of paths of length N on several classes of infinite graphs with a single special vertex. This vertex can work as an ‘entropic trap’ for the path, i.e. under certain conditions the dominant part of long paths becomes localized in the vicinity of the special point instead of spreading to infinity. We study the conditions for such localization on decorated star graphs, regular trees and regular hyperbolic graphs as a function of the functionality of the special vertex. In all cases the localization occurs for large enough functionality. The particular value of the transition point depends on the large-scale topology of the graph. The emergence of localization is supported by analysis of the spectra of the adjacency matrices of corresponding finite graphs.

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.

Unimolecular Decomposition Mechanism of 1,2-Dioxetanedione: Concerted or Biradical? That is the Question!

Determination of the ground- and excited-state unimolecular decomposition mechanisms of 1,2-dioxetanedione gives a level of insight into bimolecular decomposition reactions of this kind for which some experimental results are reported. Although a few studies have put some effort to describe a biradical mechanism of this decomposition, there is still no systematic study that proves an existence of a biradical character. In the present study, state-of-the-art high-level multistate multiconfigurational reference second-order perturbation theory calculations are performed to describe the reaction mechanism of 1,2-dioxetanedione in detail. The calculations indicate that the decomposition of this four-membered ring peroxide containing two carbonyl carbon atoms occurs in concerted but not simultaneous fashion, so-called "merged", contrary to the case of unimolecular 1,2-dioxetane and 1,2-dioxetanone decompositions where biradical reaction pathways have been calculated. At the TS of the ground-state surface, the system enters an entropic trapping region, where four singlet and four triplet manifolds are degenerated, which can lead to the formation of triplet and singlet excited biradical species. However, these excited species have to overcome a second activation barrier for C-C bond cleavage for excited product formation, whereas the ground-state energy surface possesses only one TS. Thus our calculations indicate that the unimolecular decomposition of 1,2-dioxetanedione should not lead to efficient excited-state formation, in agreement with the lack of direct emission from the peroxyoxalate reaction.

Translocation Time through a Nanopore with an Internal Cavity Is Minimal for Polymers of Intermediate Length.

The translocation of polymers through nanopores with large internal cavities bounded by two narrow pores is studied via Langevin dynamics simulations. The total translocation time is found to be a nonmonotonic function of polymer length, reaching a minimum at intermediate length, with both shorter and longer polymers taking longer to translocate. The location of the minimum is shown to shift with the magnitude of the applied force, indicating that the pore can be dynamically tuned to favor different polymer lengths. A simple model balancing the effects of entropic trapping within the cavity against the driving force is shown to agree well with simulations. Beyond the nonmonotonicity, detailed analysis of translocation uncovers rich dynamics in which factors such as going to a high force regime and the emergence of a tail for long polymers dramatically change the behavior of the system. These results suggest that nanopores with internal cavities can be used for applications such as selective extraction of polymers by length and filtering of polymer solutions, extending the uses of nanopores within emerging nanofluidic technologies.

Bicontinuous Nanoporous Frameworks: Caged Longevity for Enzymes.

The preparation of bicontinuous nanoporous covalent frameworks, which are promising for caging active enzymes, is demonstrated. The frameworks have three- dimensionally continuous, hydrophilic pores with widths varying between 5 and 30 nm. Enzymes were infiltrated into the bicontinuous pore by applying a pressured enzyme solution. The new materials and methods allowed the amount of caged proteins to be controlled precisely. The resulting enzyme-loaded framework films could be recycled many times with nearly no loss of catalytic activity. Entropic trapping of proteins by a bicontinuous pore with the right size distribution is an unprecedented strategy toward facile in vitro utilization of biocatalysts.

Bicontinuous Nanoporous Frameworks: Caged Longevity for Enzymes

AbstractThe preparation of bicontinuous nanoporous covalent frameworks, which are promising for caging active enzymes, is demonstrated. The frameworks have three‐ dimensionally continuous, hydrophilic pores with widths varying between 5 and 30 nm. Enzymes were infiltrated into the bicontinuous pore by applying a pressured enzyme solution. The new materials and methods allowed the amount of caged proteins to be controlled precisely. The resulting enzyme‐loaded framework films could be recycled many times with nearly no loss of catalytic activity. Entropic trapping of proteins by a bicontinuous pore with the right size distribution is an unprecedented strategy toward facile in vitro utilization of biocatalysts.

Interstate Crossing-Induced Chemiexcitation Mechanism as the Basis for Imidazopyrazinone Bioluminescence

Imidazopyrazinone dioxetanone is a central molecule in bioluminescence, as it is the scaffold responsible for light emission in many marine species. Herein, we have theoretically studied the thermolysis of its neutral and anionic forms. Our results allowed us to explain imidazopyrazinone bioluminescence with the Interstate Crossing-Induced Chemiexcitation (ICIC) mechanism, and explain why neutral forms emit light efficiently to the contrary of anionic ones. Both forms decompose via a stepwise-biradical pathway, but the biradical is formed either via an electron transfer (anion) or due to homolytic bond cleavage (neutral species). Absence of electron transfer leads to an entropic trap, a flat region where infinite possibilities for chemiexcitation exist. However, the resulting products can be in either triplet or singlet excited states. The triplet to singlet ratio is determined by the electron spin density distribution, which controls the rates of intersystem crossing.

Fractional separation of polymers in nanochannels: Combined influence of wettability and structure

Trapping macromolecules in nanopits finds diverse applications in polymer separation, filtering biomolecules etc. However, tuning the locomotion of polymers in channels of nanoscopic dimensions is greatly restricted by the comparative advective and diffusive components of velocities. Using the polymer affinity toward the solvent and the wall, and the polymer structure, a mechanism is proposed to induce selective trapping of polymers. Similar to fractional distillation of hydrocarbons based on molecular weight, a technique of fractional segregation, depending on the channel wettability of polymeric chains at different depths in a pit that is located perpendicular to the flow is suggested. Depending on the properties of the polymeric chains and the surface chemistry, the segregation of the polymer at a particular level in the pit can be predicted. This behavior stems from the difference in polymer structure leading to a competition between wettability based enthalpic trapping and structure based entropic trapping. The results of this study suggest a novel way of separating biopolymers based on their structure without relying on the channel geometry. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 2118–2125

Correlated Fluctuations of DNA between Nanofluidic Entropic Traps

Here we explore thermally driven contour fluctuations within a single DNA chain partitioned between two embedded cavity reservoirs in a nanofluidic slit. Analysis of integrated cavity intensity suggests that contour is exchanged dynamically between the reservoirs via modes that resemble the symmetric and antisymmetric modes of a coupled harmonic oscillator. The relaxation time of the modes is measured as a function of cavity width and spacing. Langevin dynamics simulations reproduce our observations and motivate a free energy model with a blob-type hydrodynamic friction, developed and used to deduce how the measured relaxation times for the modes depend on device parameters. The relaxation time of the antisymmetric mode was found to be consistent with an excluded volume-based stiffness while the faster symmetric mode depends on additional entropic and elastic parameters.

Thermodynamically induced particle transport: Order-by-induction and entropic trapping at the nano-scale

A theory for thermodynamic induction (TI) under isothermal conditions is presented. This includes a treatment of the Helmholtz free energy budget available for a gate variable to utilize towards aiding another variable’s approach towards thermodynamic equilibrium. This energy budget could be used to help create interesting physical structures and examples of order-by-induction. I also show how to treat TI in the continuum limit which can be obtained from a variational principle.Several important examples of isothermal TI have been discussed, including a type of electromigration that may be detectable in electrolytes, superfluids and semiconductors. As an example of a bottlenecked system exhibiting enhanced TI, manipulation of atoms and molecules by STM has been discussed in detail. My considerations provide strong support for microscopic bond-breaking mechanisms being governed by a general thermodynamic principle. In particular, I show that induced entropy trapping can explain the level of control that sliding-type manipulations demonstrate. The most reasonable choices for the parameters input into the simple formula give a threshold condition for STM manipulations that is strikingly close to what is required to match results reported in the literature. My continuum model predicts the shape of the adsorbate potential well for the STM case and from this I predict a level of force detectable by AFM. A final proposal, and example of order-by-induction, predict a long tether may be constructed between sample and tip that is just one atom thick.

Mechanistic insight into marine bioluminescence: photochemistry of the chemiexcited Cypridina (sea firefly) lumophore.

Cypridina hilgendorfii (sea firefly) is a bioluminescent crustacean whose bioluminescence (BL) reaction is archetypal for a number of marine organisms, notably other bioluminescent crustaceans and coelenterates. Unraveling the mechanism of its BL is paramount for future applications of its strongly emissive lumophore. Cypridina produces light in a three-step reaction: First, the cypridinid luciferin is activated by an enzyme to produce a peroxide intermediate, cypridinid dioxetanone (CDO), which then decomposes to generate excited oxyluciferin (OxyCLnH*). Finally, OxyCLnH* deexcites to its ground state along with emission of bright blue light. Unfortunately, the detailed mechanism of the critical step, the thermolysis of CDO, remains unknown, and it is unclear whether the light emitter is generated from a neutral form (CDOH) or anionic form (CDO(-)) of the CDO precursor. In this work, we investigated the key step in the process by modeling the thermal decompositions of both CDOH and CDO(-). The calculated results indicate that the decomposition of CDO(-) occurs via the gradually reversible charge transfer (CT)-initiated luminescence (GRCTIL) mechanism, whereas CDOH decomposes through an entropic trapping mechanism without an obvious CT process. The thermolysis of CDO(-) is sensitive to solvent effects and is energetically favorable in polar environments compared with the thermolysis of CDOH. The thermolysis of CDO(-) produces the excited oxyluciferin anion (OxyCLn(-)*), which combines with a proton from the environment to form OxyCLnH*, the actual light emitter for the natural system.

Giant enhancement of hydrodynamically enforced entropic trapping in thin channels

Using our generalized Fick-Jacobs approach [Martens et al., PRL 110, 010601 (2013); Martens et al., Eur. Phys. J. Spec. Topics 222, 2453-2463 (2013)] and extensive Brownian dynamics simulations, we study particle transport through three-dimensional periodic channels of different height. Directed motion is caused by the interplay of constant bias acting along the channel axis and a pressure-driven flow. The tremendous change of the flow profile shape in channel direction with the channel height is reflected in a crucial dependence of the mean particle velocity and the effective diffusion coefficient on the channel height. In particular, we observe a giant suppression of the effective diffusivity in thin channels; four orders of magnitude compared to the bulk value.

Biomolecule transport across biomembranes in the presence of crowding: polymer translocation driven by concentration and disorder gradients.

The transport of biomolecules across biomembranes occurs in a complex environment where the fluid on both sides of the membrane contains many inclusions. We investigate the translocation of a polymer through a nanopore in such crowded environments via computer simulations. Modeling intracellular and extracellular inclusions as spherical obstacles, the emergence of an entropic driving force is demonstrated for (i) a gradient in the number of obstacles on either side of the pore and (ii) having the obstacles in an ordered arrangement on one side and disordered on the other. With a directional preference of ≈90% of events occurring towards the disordered side and a reduction in the translocation time of ≈30%, the latter case represents a manifestation of entropic trapping. Simple estimates for the magnitude of the driving force are developed for both cases. The effect of allowing the obstacles to move as well as systems containing opposing concentration and disorder gradients are also explored. Demonstrating a robust conclusion that translocation to lower obstacle densities and higher degrees of disorder will be accelerated, these results suggest that accounting for such effects will be critical in developing a realistic model of in vivo translocation.

Electrophoretic Mobility of Double-Stranded DNA in Polymer Solutions and Gels with Tuned Structures

We report a systematic experimental study on the migration behavior of double-stranded DNA (dsDNA) in polymer networks with precisely controlled network structures. The electrophoretic mobility (μ) appeared to be a power law function of the number of base pairs (n), μ ∼ n–γ, with 0.36 < γ < 1.46. The variance in γ has been commonly explained using the reptation model with constraint release or using the entropic trapping (ET) model. However, our results indicated that the μ values were expressed as products of a power law function and an exponential function of n, which differs from any of the existing models. The power law function terms corresponded to the existing models, the Rouse model or the reptation model. In polymer gels, we observed a crossover from the Rouse to the reptation model with an increase in n, while the migration behavior in polymer solutions always obeyed the Rouse model. These results revealed that the continuous change in γ was accommodated by the exponential function terms.

Biopolymer Filtration in Corrugated Nanochannels

We examine pressure-driven nonequilibrium transport of linear, circular, and star polymers through a nanochannel containing a rectangular pit with full hydrodynamic interactions and thermal fluctuations. We demonstrate that with sufficiently small pressure differences, there is contour length-dependent entropic trapping of the polymer in the pit when the pit and the polymer sizes are compatible. This is due to competition between flow and chain relaxation in the pit, which leads to a nonmonotonic dependence of the polymer mobility on its size and should aid in the design of nanofiltration devices based on the polymer size and shape.