Local changes in protein filament properties drive large-scale membrane transformations involved in endosome tethering and fusion.

Large-scale cellular transformations are triggered by subtle physical and structural changes to individual biomacromolecular and membrane components. A prototypical example of such an event is the orchestrated fusion of membranes within an endosome that enables transport of cargo and processing of biochemical moieties. In this work, we demonstrate how protein filaments on the endosomal membrane surface can leverage a rigid-to-flexible transformation to elicit a large-scale change in membrane flexibility to enable membrane fusion. We develop a polymer field-theoretic model that captures molecular alignment arising from nematic interactions with varying surface density and fraction of flexible filaments, which are biologically controlled within the endosomal membrane. We then predict the collective elasticity of the filament brush in response to changes in the filament alignment, predicting a greater than 20-fold increase of the effective membrane elasticity over the bare membrane elasticity that is triggered by filament alignment. These results show that the endosome can modulate the filament properties to orchestrate membrane fluidization that facilitates vesicle fusion, providing an example of how active processes that modulate local molecular properties can result in large-scale transformations that are essential to cellular survival.

Effect of local active fluctuations on structure and dynamics of flexible biopolymers.

Active fluctuations play a significant role in the structure and dynamics of biopolymers (e.g. chromatin and cytoskeletal proteins) that are instrumental in the functioning of living cells. For a large range of experimentally accessible length and time scales, these polymers can be represented as flexible chains that are subjected to spatially and temporally varying fluctuating forces. In this work, we introduce a mathematical framework that correlates the spatial and temporal patterns of the fluctuations to different observables that describe the dynamics and conformations of the polymer. We demonstrate the power of this approach by analyzing the case of a point fluctuation on the polymer with an exponential decay of correlation in time with a finite time constant. Specifically, we identify the length and time scale over which the behavior of the polymer exhibits a significant departure from the behavior of a Rouse chain and the range of impact of the fluctuation along the chain. Furthermore, we show that the conformation of the polymer retains the memory of the active fluctuation from earlier times. Altogether, this work sets the basis for understanding and interpreting the role of spatio-temporal patterns of fluctuations in the dynamics, conformation, and functionality of biopolymers in living cells.

Leveraging polymer modeling to reconstruct chromatin connectivity from live images.

Chromosomal dynamics plays a central role in a number of critical biological processes, such as transcriptional regulation, genetic recombination, and DNA replication. However, visualization of chromatin is generally limited to live imaging of a few fluorescently labeled chromosomal loci or high-resolution reconstruction of multiple loci from a single time frame. To aid in mapping the underlying chromosomal structure based on parsimonious experimental measurements, we present an exact analytical expression for the evolution of the polymer configuration based on a flexible-polymer model, and we propose an algorithm that tracks the polymer configuration from live images of chromatin marked with several fluorescent marks. Our theory identifies the resolution of microscopy needed to achieve high-accuracy tracking for a given spacing of markers, establishing the statistical confidence in the assignment of genome identity to the visualized marks. We then leverage experimental data of locus-tracking measurements to demonstrate the validity of our modeling approach and to establish a basis for the design of experiments with a desired resolution. Altogether, this work provides a computational approach founded on polymer physics that vastly improves the interpretation of in vivo measurements of biopolymer dynamics.

Active and thermal fluctuations in multi-scale polymer structure and dynamics.

The presence of athermal noise or biological fluctuations control and maintain crucial life-processes. In this work, we present an exact analytical treatment of the dynamic behavior of a flexible polymer chain that is subjected to both thermal and active forces. Our model for active forces incorporates temporal correlation associated with the characteristic time scale and processivity of enzymatic function (driven by ATP hydrolysis), leading to an active-force time scale that competes with relaxation processes within the polymer chain. We analyze the structure and dynamics of an active-Brownian polymer using our exact results for the dynamic structure factor and the looping time for the chain ends. The spectrum of relaxation times within a polymer chain implies two different behaviors at small and large length scales. Small length-scale relaxation is faster than the active-force time scale, and the dynamic and structural behavior at these scales are oblivious to active forces and, are thus governed by the true thermal temperature. Large length-scale behavior is governed by relaxation times that are much longer than the active-force time scale, resulting in an effective active-Brownian temperature that dramatically alters structural and dynamic behavior. These complex multi-scale effects imply a time-dependent temperature that governs living and non-equilibrium systems, serving as a unifying concept for interpreting and predicting their physical behavior.

Semiflexible polymer solutions. II. Fluctuations and Frank elastic constants.

We study the collective elastic behavior of semiflexible polymer solutions in a nematic liquid-crystalline state using polymer field theory. Our polymer field-theoretic model of semiflexible polymer solutions is extended to include second-order fluctuation corrections to the free energy, permitting the evaluation of the Frank elastic constants based on orientational order fluctuations in the nematic state. Our exact treatment of wormlike chain statistics permits the evaluation of behavior from the nematic state, thus accurately capturing the impact of single-chain behavior on collective elastic response. Results for the Frank elastic constants are presented as a function of aligning field strength and chain length, and we explore the impact of conformation fluctuations and hairpin defects on the twist, splay, and bend moduli. Our results indicate that the twist elastic constant Ktwist is smaller than both bend and splay constants (Kbend and Ksplay, respectively) for the entire range of polymer rigidity. Splay and bend elastic constants exhibit regimes of dominance over the range of chain stiffness, where Ksplay > Kbend for flexible polymers (large-N limit) while the opposite is true for rigid polymers. Theoretical analysis also suggests the splay modulus tracks exactly to that of the end-to-end distance in the transverse direction for semiflexible polymers at intermediate to large-N. These results provide insight into the role of conformation fluctuations and hairpin defects on the collective response of polymer solutions.

The role of collective elasticity on activated structural relaxation, yielding, and steady state flow in hard sphere fluids and colloidal suspensions under strong deformation.

We theoretically study the effect of external deformation on activated structural relaxation and aspects of the nonlinear mechanical response of glassy hard sphere fluids in the context of elastically collective nonlinear Langevin equation theory. This microscopic force-based approach describes activated relaxation as a coupled local-nonlocal event involving caging and longer range collective elasticity, with the latter becoming more important and ultimately dominant with increasing packing fraction under equilibrium conditions. The central new question we address is how this physical picture of activated relaxation, and the relative importance of local caging vs collective elasticity physics, depends on external deformation. Theoretical predictions are presented for deformation-induced enhancement of mobility, the onset of relaxation speed up at remarkably low values of stress, strain, or shear rate, apparent power law thinning of the steady state structural relaxation time and viscosity, a non-vanishing activation barrier in the shear thinning regime, an apparent Herschel-Bulkley form of the rate dependence of the steady state shear stress, exponential growth of different measures of a dynamic yield or flow stress with the packing fraction, and reduced fragility and dynamic heterogeneity under deformation. The results are contrasted with experiments and simulations, and qualitative or better agreement is found. An overarching conclusion is that deformation strongly reduces the importance of longer range collective elastic effects relative to the local caging aspect for most, but not all, physical questions, with deformation-dependent fragility and dynamic heterogeneity phenomena being qualitatively sensitive to collective elasticity. Overall, nonlinear rheology is predicted to be a more local problem than quiescent structural relaxation, albeit with deformation-modified activated processes still important.

Linear and nonlinear rheology and structural relaxation in dense glassy and jammed soft repulsive pNIPAM microgel suspensions.

We present an integrated experimental and quantitative theoretical study of the mechanics of self-crosslinked, slightly charged, repulsive pNIPAM microgel suspensions over a very wide range of concentrations (c) that span the fluid, glassy and putative "soft jammed" regimes. In the glassy regime we measure a linear elastic dynamic shear modulus over 3 decades which follows an apparent power law concentration dependence G' ∼ c5.64, a variation that appears distinct from prior studies of crosslinked ionic microgel suspensions. At very high concentrations there is a sharp crossover to a nearly linear growth of the modulus. To theoretically understand these observations, we formulate an approach to address all three regimes within a single conceptual Brownian dynamics framework. A minimalist single particle description is constructed that allows microgel size to vary with concentration due to steric de-swelling effects. Using a Hertzian repulsion interparticle potential and a suite of statistical mechanical theories, quantitative predictions under quiescent conditions of microgel collective structure, dynamic localization length, elastic modulus, and the structural relaxation time are made. Based on a constant inter-particle repulsion strength parameter which is determined by requiring the theory to reproduce the linear elastic shear modulus over the entire concentration regime, we demonstrate good agreement between theory and experiment. Testable predictions are then made. We also measured nonlinear rheological properties with a focus on the yield stress and strain. A theoretical analysis with no adjustable parameters predicts how the quiescent structural relaxation time changes under deformation, and how the yield stress and strain change as a function of concentration. Reasonable agreement with our observations is obtained. To the best of our knowledge, this is the first attempt to quantitatively understand structure, quiescent relaxation and shear elasticity, and nonlinear yielding of dense microgel suspensions using microscopic force based theoretical methods that include activated hopping processes. We expect our approach will be useful for other soft polymeric particle suspensions in the core-shell family.

Microscopic theory of the influence of strong attractive forces on the activated dynamics of dense glass and gel forming fluids.

We theoretically study the nonmonotonic (re-entrant) activated dynamics associated with a finite time scale kinetically defined repulsive glass to fluid to attractive glass transition in high volume fraction particle suspensions interacting via strong short range attractive forces. The classic theoretical "projection" approximation that replaces all microscopic forces by a single effective force determined solely by equilibrium pair correlations is revisited based on the "projectionless dynamic theory" (PDT). A hybrid-PDT approximation is formulated that explicitly quantifies how attractive forces induce dynamical constraints, while singular hard core interactions are treated based on the projection approach. Both the effects of interference between repulsive and attractive forces, and structural changes due to attraction-induced bond formation that competes with caging, are included. Combined with the microscopic Elastically Collective Nonlinear Langevin Equation (ECNLE) theory of activated relaxation, the resultant approach appears to properly capture both the re-entrant dynamic crossover behavior and the strong nonmonotonic variation of the activated structural relaxation time with attraction strength and range at very high volume fractions as observed experimentally and in simulations. Testable predictions are made. Major differences compared to both ideal mode coupling theory and ECNLE theory based on the full force projection approximation are identified. Calculations are also performed for smaller time and length scale intracage dynamics relevant to the non-Gaussian parameter based on analyzing the dynamic free energy that controls particle trajectories. Implications of the new theory for thermal glass forming liquids with relatively long range attractive forces are briefly analyzed.

Importance of Many Particle Correlations to the Collective Debye-Waller Factor in a Single-Particle Activated Dynamic Theory of the Glass Transition.

We theoretically study the importance of many body correlations on the collective Debye-Waller (DW) factor in the context of the Nonlinear Langevin Equation (NLE) single-particle activated dynamics theory of glass transition and its extension to include collective elasticity (ECNLE theory). This microscopic force-based approach envisions structural alpha relaxation as a coupled local-nonlocal process involving correlated local cage and longer range collective barriers. The crucial question addressed here is the importance of the deGennes narrowing contribution versus a literal Vineyard approximation for the collective DW factor that enters the construction of the dynamic free energy in NLE theory. While the Vineyard-deGennes approach-based NLE theory and its ECNLE theory extension yields predictions that agree well with experimental and simulation results, use of a literal Vineyard approximation for the collective DW factor massively overpredicts the activated relaxation time. The current study suggests many particle correlations are crucial for a reliable description of activated dynamics theory of model hard sphere fluids.

Statistical behavior of nonequilibrium and living biological systems subjected to active and thermal fluctuations.

We present a path-integral formulation of the motion of a particle subjected to fluctuating active and thermal forces. This general framework predicts the statistical behavior associated with the stochastic trajectories of the particle, accounting for all possible realizations of Brownian and active forces, over an arbitrary potential landscape. Temporal correlations in the active forces result in non-Markovian statistics, necessitating the inclusion of a fixed active-force value at specified times within the statistical treatment. We specialize our theory to that of exponentially correlated active forces for a particle in a harmonic potential. We find the exact results for the statistical distributions for the initial position of the particle, accounting for the impact of the correlated active forces at all times prior to the initial time. Our theory is then used to find the two-point distribution for the active Brownian particle, which governs the joint probability that a particle begins and ends at specified locations. Analyses of the active Brownian statistics demonstrate that the impact of active forces can be interpreted through a time-dependent temperature whose influence depends on the competition of timescales of the active-force correlation and the relaxation time of the particle in the harmonic potential. The general results presented in this work are transferable to a broad range of nonequilibrium systems with active and Brownian motion, and the time-dependent temperature serves as a governing principle to describe the competition of timescales associated with active forces and internal relaxation processes.

Physical Bond Breaking in Associating Copolymer Liquids.

We combine ideas from polymer and glassy liquid physics to construct a new model for the bond-breaking time scale of attractive sticker groups in associating copolymer liquids that form transient networks. The activated event is argued to be a two-step process, involving first the release of the nonsticker dynamic caging constraints that defines the primary alpha relaxation, followed by attractive stickers surmounting an association free-energy barrier subject to a local frictional resistance which can be strongly affected by relaxation-diffusion decoupling. The ideas embedded in the model produce a consistent and good description of the bond-breaking time scale for diverse polymer chemistries and architectures as a function of temperature and fraction of sticky groups. Chemically sensible values for association free energies are deduced. In strong contrast, the existing phenomenological models are shown to incur qualitative failures.

Linear and nonlinear viscoelasticity of concentrated thermoresponsive microgel suspensions.

We present an integrated experimental and theoretical study of the dynamics and rheology of self-crosslinked, slightly charged, temperature responsive soft poly(N-isopropylacrylamide) (pNIPAM) microgels over a wide range of concentration and temperature spanning the sharp change in particle size and intermolecular interactions across the lower critical solution temperature (LCST). Dramatic, non-monotonic changes in viscoelasticity are observed as a function of temperature, with distinct concentration dependence in the dense fluid, glassy, and soft-jammed regimes. Motivated by our experimental observations, we formulate a minimalistic model for the size dependence of a single microgel particle and the change of the interparticle interaction from purely repulsive to attractive upon heating. Using microscopic equilibrium and time-dependent statistical mechanical theories, theoretical predictions are quantitatively compared with experimental measurements of the shear modulus. Good agreement is found for the nonmonotonic temperature behavior that originates as a consequence of the competition between reduced microgel packing fraction and increasing interparticle attractions. Testable predictions are made for nonlinear rheological properties such as the yield stress and strain. To our knowledge, this is the first attempt to quantitatively understand in a unified manner the viscoelasticity of dense, temperature-responsive microgel suspensions spanning a wide range of temperatures and concentrations.

Microscopic theory of onset of decaging and bond-breaking activated dynamics in ultradense fluids with strong short-range attractions.

We theoretically study thermally activated "in cage" elementary dynamical processes that precede full structural relaxation in ultradense particle liquids interacting via strong short-range attractive forces. The analysis is based on a microscopic theory formulated at the particle trajectory level built on the dynamic free energy concept and an explicit treatment of how attractive forces control the formation and lifetime of physical bonds. Mean time scales for bond breaking, the early stage of cage escape, and non-Fickian displacement by a fixed amount are analyzed in the repulsive glass, bonded repulsive (attractive) glass, fluid, and dense gel regimes. The theory predicts a strong length-scale-dependent growth of these time scales with attractive force strength at fixed packing fraction, a much weaker slowing down with density at fixed attraction strength, and a strong decoupling of the shorter bond-breaking time with the other two time scales that are controlled mainly by perturbed steric caging. All results are in good accord with simulations, and additional testable predictions are made. The classic statistical mechanical projection approximation of replacing all bare attractive and repulsive forces with a single effective force determined by pair structure incurs major errors for describing processes associated with thermally activated escape from transiently localized states.