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1.
J Am Chem Soc ; 146(25): 17474-17486, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38860830

ABSTRACT

Soluble redox-active polymers (RAPs) enable size-exclusion nonaqueous redox flow batteries (NaRFBs) which promise high energy density. Pendants along the RAPs not only store charge but also engage in electron transfer to varying extents based on their designs. Here, we explore these phenomena in Metal-containing Redox Active Polymers (M-RAPs, M = Ru, Fe, Co). We assess by using cyclic voltammetry and chronoamperometry with ultramicroelectrodes the current response to electrolyte concentration spanning 3 orders of magnitude. Currents scaled as Ru-RAP > Fe-RAP ≫ Co-RAP, consistent with electron self-exchange trends in the small molecule analogues of the MII/III redox pair. Varying the ionic strength of the electrolyte also revealed nonmonotonic behavior, evidencing the impact of polyelectrolytic dynamics on M-RAP redox response. We developed a model to account for the behavior by combining kinetic Monte Carlo and Brownian dynamics near a boundary representing an electrode. While 1D pendant-to-pendant charge transfer along the chain is not a strong function of electrolyte concentration, the microstructure of the RAP at different electrolyte concentrations is decisively impacted, yielding qualitative trends to those observed experimentally. M-RAP size-exclusion NaRFBs using a poly viologen as negolyte varied in average potential with ∼1.54 V for Ru-RAP, ∼1.37 V for Fe-RAP, and ∼0.52 V for Co-RAP. Comparison of batteries at their optimal and suboptimal solution conditions as gauged from analytical experiments showed clear correlations in performance. This work provides a blueprint for understanding the factors underpinning charge transfer in solutions of RAPs for batteries and beyond.

2.
J Chem Phys ; 160(11)2024 Mar 21.
Article in English | MEDLINE | ID: mdl-38511661

ABSTRACT

The diffusion of dilute molecular penetrants within polymers plays a crucial role in the advancement of material engineering for applications such as coatings and membrane separations. The potential of highly cross-linked polymer networks in these applications stems from their capacity to adjust the size and shape selectivity through subtle changes in network structures. In this paper, we use molecular dynamics simulation to understand the role of penetrant shape (aspect ratios) and its interaction with polymer networks on its diffusivity. We characterize both local penetrant hopping and the long-time diffusive motion for penetrants and consider different aspect ratios and penetrant-network interaction strengths at a variety of cross-link densities and temperatures. The shape affects the coupling of penetrant motion to the cross-link density- and temperature-dependent structural relaxation of networks and also affects the way a penetrant experiences the confinement from the network meshes. The attractive interaction between the penetrant and network primarily affects the former since only the system of dilute limit is of present interest. These results offer fundamental insights into the intricate interplay between penetrant characteristics and polymer network properties and also suggest future directions for manipulating polymer design to enhance the separation efficiency.

3.
Proc Natl Acad Sci U S A ; 121(9): e2313617121, 2024 Feb 27.
Article in English | MEDLINE | ID: mdl-38377215

ABSTRACT

Additive manufacturing capable of controlling and dynamically modulating structures down to the nanoscopic scale remains challenging. By marrying additive manufacturing with self-assembly, we develop a UV (ultra-violet)-assisted direct ink write approach for on-the-fly modulation of structural color by programming the assembly kinetics through photo-cross-linking. We design a photo-cross-linkable bottlebrush block copolymer solution as a printing ink that exhibits vibrant structural color (i.e., photonic properties) due to the nanoscopic lamellar structures formed post extrusion. By dynamically modulating UV-light irradiance during printing, we can program the color of the printed material to access a broad spectrum of visible light with a single ink while also creating color gradients not previously possible. We unveil the mechanism of this approach using a combination of coarse-grained simulations, rheological measurements, and structural characterizations. Central to the assembly mechanism is the matching of the cross-linking timescale with the assembly timescale, which leads to kinetic trapping of the assembly process that evolves structural color from blue to red driven by solvent evaporation. This strategy of integrating cross-linking chemistry and out-of-equilibrium processing opens an avenue for spatiotemporal control of self-assembled nanostructures during additive manufacturing.

4.
J Phys Chem B ; 128(7): 1796-1811, 2024 Feb 22.
Article in English | MEDLINE | ID: mdl-38330099

ABSTRACT

Redox-active polymers (RAPs) are a subclass of polyelectrolytes that can store charge and undergo redox self-exchange reactions. RAPs are of great interest in the field of redox flow batteries (RFBs) due to their ability to quickly charge and discharge, their chemical modularity, and their molecular size. However, designing RAPs for efficient charge transport at the molecular level requires a fundamental understanding of the charge transport mechanisms that occur in RFBs. Previous work from our group has explored these mechanisms, and in this paper, we seek to improve upon the previous model by incorporating both hydrodynamic interactions (HIs) and out-of-equilibrium dynamics, which are both highly pertinent to flow battery systems. We use a hybrid Brownian dynamics and Monte Carlo simulation to model redox-active polymer chains in both dilute and semidilute solutions. This model is used to show that HI is an important feature when charge hopping is not the major mechanism for charge displacement and leads to more rapid segmental and translational motion of polymer chains that expedites charge transport at low polymer concentrations. We demonstrate that strong extensional flows may result in either enhanced or decreased transport depending on the fraction of charges present on the RAP chain. We show that flow not only can promote charge transport by extending polymer conformations but can also suppress nonadjacent charge hopping processes that are important for transport at high charge fractions. Shear flows can similarly enhance charge transport through chain extension, but tumbling dynamics lead to oscillatory displacements that become dominant features with high charge fractions and strong flows.

5.
J Chem Phys ; 160(4)2024 Jan 28.
Article in English | MEDLINE | ID: mdl-38258921

ABSTRACT

We study the dynamics of bottlebrush polymer molecules in dilute solutions subjected to shear and uniaxial extensional flows using Brownian dynamics simulations with hydrodynamic interaction (HI). Bottlebrush polymers are modeled using a coarse-grained representation, consisting of a set of beads interacting pairwise via a purely repulsive potential and connected by finitely extensible nonlinear springs. We present the results for molecular stretching, stress, and solution viscosity during the startup of flow as well as under steady state as a function of side chain length while keeping the backbone length fixed. In extensional flow, the backbone fractional extension and the first normal stress difference decrease with an increase in side chain length at a fixed Weissenberg number (Wi). Using simulation results both in the presence of and in the absence of HI, we show that this is primarily a consequence of steric interaction resulting from the dense grafting of side chains. In shear flow, we observe a shear-thinning behavior in all cases, although it becomes less pronounced with increasing side chain length. Furthermore, nonmonotonicity in the backbone fractional extension is observed under shear, particularly at high Wi. We contextualize our simulation results for bottlebrush polymers with respect to existing studies in the literature for linear polymers and show that the unique dynamical features characterizing bottlebrush polymers arise on account of their additional molecular thickness due to the presence of densely grafted side chains.

6.
Soft Matter ; 20(3): 681-692, 2024 Jan 17.
Article in English | MEDLINE | ID: mdl-38164983

ABSTRACT

The dynamics of phase separation for polymer blends is important in determining the final morphology and properties of polymer materials; in practical applications, this phase separation can be controlled by coupling to polymerization reaction kinetics via a process called 'polymerization-induced phase separation'. We develop a phase-field model for a polymer melt blend using a polymerizing Cahn-Hilliard (pCH) formalism to understand the fundamental processes underlying phase separation behavior of a mixture of two species independently undergoing linear step-growth polymerization. In our method, we explicitly model polydispersity in these systems to consider different molecular-weight components that will diffuse at different rates. We first show that this pCH model predicts results consistent with the Carothers predictions for step-growth polymerization kinetics, the Flory-Huggins theory of polymer mixing, and the classical predictions of spinodal decomposition in symmetric polymer blends. The model is then used to characterize (i) the competition between phase separation dynamics and polymerization kinetics, and (ii) the effect of unequal reaction rates between species. For large incompatibility between the species (i.e. high χ), our pCH model demonstrates that the strength for phase separation directly corresponds to the kinetics of phase separation. We find that increasing the reaction rate k̃, first induces faster phase separation but this trend reverses as we further increase k̃ due to the competition between molecular diffusion and polymerization. In this case, phase separation is delayed for faster polymerization rates due to the rapid accumulation of slow-moving, high molecular weight components.

7.
J Chem Phys ; 159(1)2023 Jul 07.
Article in English | MEDLINE | ID: mdl-37409769

ABSTRACT

The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these applications because dramatic differences in molecular diffusion can result from subtle changes in the network structure. In this paper, we use molecular simulation to understand the role that cross-linked network polymers have in governing the molecular motion of penetrants. By considering the local, activated alpha relaxation time of the penetrant and its long-time diffusive dynamics, we can determine the relative importance of activated glassy dynamics on penetrants at the segmental scale vs entropic mesh confinement on penetrant diffusion. We vary several parameters, such as the cross-linking density, temperature, and penetrant size, to show that cross-links primarily affect molecular diffusion through the modification of the matrix glass transition, with local penetrant hopping at least partially coupled to the segmental relaxation of the polymer network. This coupling is very sensitive to the local activated segmental dynamics of the surrounding matrix, and we also show that penetrant transport is affected by dynamic heterogeneity at low temperatures. To contrast, only at high temperatures and for large penetrants or when the dynamic heterogeneity effect is weak, does the effect of mesh confinement become significant, even though penetrant diffusion more broadly empirically follows similar trends as established models of mesh confinement-based transport.

8.
J Phys Chem B ; 127(26): 5978-5991, 2023 07 06.
Article in English | MEDLINE | ID: mdl-37350455

ABSTRACT

Complex coacervate droplets formed by the liquid-liquid phase separation of polyelectrolyte solutions capture several important features of membraneless organelles including their ability to accumulate guest molecules and to provide distinct microenvironments. Here, we examine how polyions in complex coacervates can influence localized guest molecules, leading to a shifted protonation state of the guest molecule in response to its electrostatic environment. A fluorescent ratiometric pH indicator dye was used as a model guest molecule able to report its protonation state in the coacervate phase. Experimentally observed differences in dye-reported local apparent pH inside versus outside of coacervate droplets were largest for polyion pairs having lower salt stabilities and/or larger polyion length mismatch, which we attribute to the relative concentration of open sites on polyions within the coacervates based on theoretical calculations. Using the transfer matrix method, we confirmed that theoretical phase diagrams and critical salt stabilities generated for each polyion pair were consistent with experimental turbidity measurements and estimated the amount of available binding sites on polyions for guest molecules. We conclude that dye molecules likely experience an effective pKa shift due to interactions with coacervate polyions rather than reporting directly on local proton concentrations. Such a local pKa shift can also be anticipated for other guest molecules having protonatable groups, including, for example, many metabolites, ligands, and/or drug molecules that partition into coacervates or membraneless organelles based on ion pairing interactions.


Subject(s)
Peptides , Sodium Chloride , Polyelectrolytes/chemistry , Peptides/chemistry , Hydrogen-Ion Concentration
9.
J Chem Phys ; 158(18)2023 May 14.
Article in English | MEDLINE | ID: mdl-37166070

ABSTRACT

We generalize a microscopic statistical mechanical theory of the activated dynamics of dilute spherical penetrants in glass-forming liquids to study the influence of crosslinking in polymer networks on the penetrant relaxation time and diffusivity over a wide range of temperature and crosslink fraction (fn). Our calculations are relevant to recent experimental studies of a nm-sized molecule diffusing in poly-(n-butyl methacrylate) networks. The theory predicts the penetrant relaxation time increases exponentially with the glass transition temperature, Tg(fn), which grows roughly linearly with the square root of fn due to the coupling of local hopping to longer-range collective elasticity. Moreover, Tg is also found to be proportional to a geometric confinement parameter defined as the ratio of the penetrant diameter to the mean network mesh size. The decoupling ratio of the penetrant and Kuhn segment alpha times displays a complex non-monotonic dependence on fn and temperature that is well collapsed based on the variable Tg(fn)/T. A model for the penetrant diffusion constant that combines activated relaxation and entropic mesh confinement is proposed, which results in a significantly stronger suppression of mass transport with degree of effective supercooling than predicted for the penetrant alpha time. This behavior corresponds to a new network-based type of "decoupling" of diffusion and relaxation. In contrast to the diffusion of larger nanoparticles in high temperature rubbery networks, our analysis in the supercooled regime suggests that for the penetrants studied the mesh confinement effects are of secondary importance relative to the consequences of crosslink-induced slowing down of activated hopping of glassy physics origin.

10.
ACS Cent Sci ; 9(3): 508-518, 2023 Mar 22.
Article in English | MEDLINE | ID: mdl-36968535

ABSTRACT

The diffusion of molecules ("penetrants") of variable size, shape, and chemistry through dense cross-linked polymer networks is a fundamental scientific problem broadly relevant in materials, polymer, physical, and biological chemistry. Relevant applications include separation membranes, barrier materials, drug delivery, and nanofiltration. A major open question is the relationship between transport, thermodynamic state, and penetrant and polymer chemical structure. Here we combine experiment, simulation, and theory to unravel these competing effects on penetrant transport in rubbery and supercooled polymer permanent networks over a wide range of cross-link densities, size ratios, and temperatures. The crucial importance of the coupling of local penetrant hopping to polymer structural relaxation and the secondary importance of mesh confinement effects are established. Network cross-links strongly slow down nm-scale polymer relaxation, which greatly retards the activated penetrant diffusion. The demonstrated good agreement between experiment, simulation, and theory provides strong support for the size ratio (penetrant diameter to the polymer Kuhn length) as a key variable and the usefulness of coarse-grained simulation and theoretical models that average over Angstrom scale structure. The developed theory provides an understanding of the physical processes underlying the behaviors observed in experiment and simulation and suggests new strategies for enhancing selective polymer membrane design.

11.
ACS Polym Au ; 2(4): 232-244, 2022 Aug 10.
Article in English | MEDLINE | ID: mdl-35971423

ABSTRACT

Bottlebrush polymers are a class of semiflexible, hierarchical macromolecules with unique potential for shape-, architecture-, and composition-based structure-property design. It is now well-established that in dilute to semidilute solution, bottlebrush homopolymers adopt a wormlike conformation, which decreases in extension (persistence length) as the concentration and molecular overlap increase. By comparison, the solution phase self-assembly of bottlebrush diblock copolymers (BBCP) in a good solvent remains poorly understood, despite critical relevance for solution processing of ordered phases and photonic crystals. In this work, we combine small-angle X-ray scattering, coarse-grained simulation, and polymer synthesis to map the equilibrium phase behavior and conformation of a set of large, nearly symmetric PS-b-PLA bottlebrush diblock copolymers in toluene. Three BBCP are synthesized, with side chains of number-averaged molecular weights of 4500 (PS) and 4200 g/mol (PLA) and total backbone degrees of polymerization of 100, 255, and 400 repeat units. The grafting density is one side chain per backbone repeat unit. With increasing concentration in solution, all three polymers progress through a similar structural transition: from dispersed, wormlike chains with concentration-dependent (decreasing) extension, through the onset of disordered PS/PLA compositional fluctuations, to the formation of a long-range ordered lamellar phase. With increasing concentration in the microphase-separated regimes, the domain spacing increases as individual chains partially re-extend due to block immiscibility. Increases in the backbone degree of polymerization lead to changes in the scattering profiles which are consistent with the increased segregation strength. Coarse-grained simulations using an implicit side-chain model are performed, and concentration-dependent self-assembly behavior is qualitatively matched to experiments. Finally, using the polymer with the largest backbone length, we demonstrate that lamellar phases develop a well-defined photonic band gap in solution, which can be tuned across the visible spectrum by varying polymer concentration.

12.
J Chem Phys ; 156(1): 014903, 2022 Jan 07.
Article in English | MEDLINE | ID: mdl-34998351

ABSTRACT

Bottlebrush polymers are a class of highly branched macromolecules that show promise for applications such as self-assembled photonic materials and tunable elastomers. However, computational studies of bottlebrush polymer solutions and melts remain challenging due to the high computational cost involved in explicitly accounting for the presence of side chains. Here, we consider a coarse-grained molecular model of bottlebrush polymers where the side chains are modeled implicitly, with the aim of expediting simulations by accessing longer length and time scales. The key ingredients of this model are the size of a coarse-grained segment and a suitably coarse-grained interaction potential between the non-bonded segments. Prior studies have not focused on developing explicit forms of such potentials, instead, relying on scaling arguments to model non-bonded interactions. Here, we show how to systematically calculate an interaction potential between the coarse-grained segments of bottlebrush from finer grained explicit side chain models using Monte Carlo and Brownian dynamics and then incorporate it into an implicit side chain model. We compare the predictions from our coarse-grained implicit side chain model with those obtained from models with explicit side chains in terms of the potential of mean force, the osmotic second virial coefficient, and the interpenetration function, highlighting the range of applicability and limitations of the coarse-grained representation. Although presented in the context of homopolymer bottlebrushes in athermal solvents, our proposed method can be extended to other solvent conditions as well as to different monomer chemistries. We expect that our implicit side chain model will prove useful for accelerating large-scale simulations of bottlebrush solutions and assembly.

13.
J Phys Chem B ; 125(31): 8965-8980, 2021 08 12.
Article in English | MEDLINE | ID: mdl-34328340

ABSTRACT

Oppositely charged polyelectrolytes can undergo an associative phase separation, in a process known as polymeric complex coacervation. This phenomenon is driven by the electrostatic attraction between polyanion and polycation species, leading to the formation of a polymer-dense coacervate phase and a coexisting polymer-dilute supernatant phase. There has been significant recent interest in the physical origin and features of coacervation; yet notably, experiments often use weak polyelectrolytes the charge state of which depends on solution pH, while theoretical or computational efforts typically assume strong polyelectrolytes that remain fully charged. There have been only a few efforts to address this limitation, and thus there has been little exploration of how pH can affect complex coacervation. In this paper, we modify a transfer matrix theory of coacervation to account for acid-base equilibria, taking advantage of its ability to directly account for some local ion correlations that will affect monomer charging. We show that coacervation can stabilize the charged state of a weak polyelectrolyte via the proximity of oppositely charged monomers, and can lead to asymmetric phase diagrams where the positively and negatively charged polyelectrolytes exhibit different behaviors near the pKa of either chain. Specifically, there is a partitioning of one of the salt species to a coacervate to maintain electroneutrality when one of the polyelectrolytes is only partially charged. This results in the depletion of the same salt species in the supernatant, and overall can suppress phase separation. We also demonstrate that, when one of the species is only partially charged, mixtures that are off-stoichiometric in volume fraction but stoichiometric in charge exhibit the greatest propensity to form coacervate phases.


Subject(s)
Polymers , Hydrogen-Ion Concentration , Macromolecular Substances
14.
Soft Matter ; 16(12): 2885-2914, 2020 Mar 28.
Article in English | MEDLINE | ID: mdl-32134099

ABSTRACT

Complex coacervation is an associative, liquid-liquid phase separation that can occur in solutions of oppositely-charged macromolecular species, such as proteins, polymers, and colloids. This process results in a coacervate phase, which is a dense mix of the oppositely-charged components, and a supernatant phase, which is primarily devoid of these same species. First observed almost a century ago, coacervates have since found relevance in a wide range of applications; they are used in personal care and food products, cutting edge biotechnology, and as a motif for materials design and self-assembly. There has recently been a renaissance in our understanding of this important class of material phenomena, bringing the science of coacervation to the forefront of polymer and colloid science, biophysics, and industrial materials design. In this review, we describe the emergence of a number of these new research directions, specifically in the context of polymer-polymer complex coacervates, which are inspired by a number of key physical and chemical insights and driven by a diverse range of experimental, theoretical, and computational approaches.

15.
J Chem Phys ; 152(2): 024902, 2020 Jan 14.
Article in English | MEDLINE | ID: mdl-31941285

ABSTRACT

Phase separation can be driven by the association of oppositely charged polyelectrolytes in solution, a process known as complex coacervation. This can manifest as macrophase separation, which arises when both polymer species are homopolyelectrolytes, or can lead to microphase separation when one or both of the charged species are block copolyelectrolytes. This is not a strict dichotomy; recently, macrophase separation was observed for a number of copolymers containing sequence-defined patterns of neutral vs charged monomers, including patterns with lengthy blocks. The specific pattern can affect the strength of this macrophase separation, yet at some block length, microphase separation is expected to emerge. In this article, we describe how to incorporate a theory of sequence-defined coacervation into self-consistent field theory, allowing the study of sequence-defined polyelectrolytes in inhomogeneous systems. We show that blocky sequences can affect electrostatically driven macrophase separation and can transition to microphase separation as the blockiness of sequences increases. This micro- to macrophase separation transition is a function of both the blockiness of the sequence, the number of blocks, and the concentration of salt.

16.
ACS Macro Lett ; 9(2): 216-225, 2020 Feb 18.
Article in English | MEDLINE | ID: mdl-35638672

ABSTRACT

Polymer science has been driven by ever-increasing molecular complexity, as polymer synthesis expands an already-vast palette of chemical and architectural parameter space. Copolymers represent a key example, where simple homopolymers have given rise to random, alternating, gradient, and block copolymers. Polymer physics has provided the insight needed to explore this monomer sequence parameter space. The future of polymer science, however, must contend with further increases in monomer precision, as this class of macromolecules moves ever closer to the sequence-monodisperse polymers that are the workhorses of biology. The advent of sequence-defined polymers gives rise to opportunities for material design, with increasing levels of chemical information being incorporated into long-chain molecules; however, this also raises questions that polymer physics must address. What properties uniquely emerge from sequence-definition? Is this circumstance-dependent? How do we define and think about sequence dispersity? How do we think about a hierarchy of sequence effects? Are more sophisticated characterization methods, as well as theoretical and computational tools, needed to understand this class of macromolecules? The answers to these questions touch on many difficult scientific challenges, setting the stage for a rich future for sequence-defined polymers in polymer physics.

17.
J Phys Chem B ; 123(48): 10152-10162, 2019 12 05.
Article in English | MEDLINE | ID: mdl-31710235

ABSTRACT

DNA supercoiling, where the DNA strand forms a writhe to relieve torsional stress, plays a vital role in packaging the genetic material in cells. Experiment, simulation, and theory have all demonstrated how supercoiling emerges due to the over- or underwinding of the DNA strand. Nucleoid-associated proteins (NAPs) help structure DNA in prokaryotes, yet the role that they play in the supercoiling process has not been as thoroughly investigated. We develop a coarse-grained simulation to model DNA supercoiling in the presence of proteins, providing a rigorous physical understanding of how NAPs affect supercoiling behavior. Specifically, we demonstrate how the force and torque necessary to form supercoils are affected by the presence of NAPs. NAPs that bend DNA stabilize the supercoil, thus shifting the transition between extended and supercoiled DNAs. We develop a theory to explain how NAP binding affects DNA supercoiling. This provides insight into how NAPs modulate DNA compaction via a combination of supercoiling and local protein-dependent deformations.


Subject(s)
DNA, Bacterial/chemistry , DNA, Superhelical/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/chemistry , Factor For Inversion Stimulation Protein/chemistry , Binding Sites , DNA, Bacterial/metabolism , DNA, Superhelical/metabolism , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Factor For Inversion Stimulation Protein/metabolism , Kinetics , Molecular Dynamics Simulation , Protein Binding , Thermodynamics , Torque
18.
Soft Matter ; 15(44): 9157-9158, 2019 11 28.
Article in English | MEDLINE | ID: mdl-31675045

ABSTRACT

Correction for 'Transfer matrix theory of polymer complex coacervation' by Tyler K. Lytle et al., Soft Matter, 2017, 13, 7001-7012.

19.
J Chem Phys ; 151(12): 124907, 2019 Sep 28.
Article in English | MEDLINE | ID: mdl-31575212

ABSTRACT

The dynamics and rheology of semidilute polymer solutions in strong flows are of great practical relevance. Processing applications can in principle be designed utilizing the relationship between nonequilibrium polymer conformations and the material properties of the solution. However, the interplay between concentration, flow, hydrodynamic interactions (HIs), and topological interactions which govern semidilute polymer dynamics is challenging to characterize. Brownian dynamics (BD) simulations are particularly valuable as a way to directly visualize how molecular interactions arise in these systems and are quantitatively comparable to single-molecule experiments. However, such simulations are often computationally intractable and are limited by the need to calculate the correlated Brownian noise via decomposition of the diffusion tensor. Previously, we have introduced an iterative conformational averaging (CA) method for BD simulations which bypasses these limitations by preaveraging the HI and Brownian noise in an iterative procedure. In this work, we generalize the CA method to flowing semidilute solutions by introducing a conformation dependent diffusion tensor and a strain dependent approximation to the conformationally averaged Brownian noise. We find that this approach nearly quantitatively reproduces both transient and steady state polymer dynamics and rheology while achieving an order of magnitude computational acceleration. We then utilize the CA method to investigate the concentration and flow rate dependence of polymer dynamics in planar extensional flows. Our results are consistent with previous experimental and simulation studies and provide a detailed view of broad conformational distributions in the semidilute regime. We observe interconversion between stretched and coiled states at steady state, which we conjecture occur due to the effect of concentration on the conformation dependent polymer drag. Additionally, we observe transient flow-induced intermolecular hooks in the startup of flow which lead to diverse and unique stretching pathways.

20.
Biophys J ; 117(6): 1085-1100, 2019 09 17.
Article in English | MEDLINE | ID: mdl-31427067

ABSTRACT

Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.


Subject(s)
DNA/metabolism , Proteins/metabolism , Biomechanical Phenomena , Computer Simulation , Kinetics , Models, Biological , Protein Binding
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