Modeling homologous chromosome recognition via nonspecific interactions.

In many organisms, most notably Drosophila, homologous chromosomes associate in somatic cells, a phenomenon known as somatic pairing, which takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, mediated by different proteins that bind to these different regions. Here, we use computational modeling to evaluate an alternative "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. In this model, buttons are nonuniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a nonhomolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. By simulating randomly generated nonuniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.

Entropic barrier of topologically immobilized DNA in hydrogels.

The single most intrinsic property of nonrigid polymer chains is their ability to adopt enormous numbers of chain conformations, resulting in huge conformational entropy. When such macromolecules move in media with restrictive spatial constraints, their trajectories are subjected to reductions in their conformational entropy. The corresponding free energy landscapes are interrupted by entropic barriers separating consecutive spatial domains which function as entropic traps where macromolecules can adopt their conformations more favorably. Movement of macromolecules by negotiating a sequence of entropic barriers is a common paradigm for polymer dynamics in restrictive media. However, if a single chain is simultaneously trapped by many entropic traps, it has recently been suggested that the macromolecule does not undergo diffusion and is localized into a topologically frustrated dynamical state, in apparent violation of Einstein's theorem. Using fluorescently labeled λ-DNA as the guest macromolecule embedded inside a similarly charged hydrogel with more than 95% water content, we present direct evidence for this new state of polymer dynamics at intermediate confinements. Furthermore, using a combination of theory and experiments, we measure the entropic barrier for a single macromolecule as several tens of thermal energy, which is responsible for the extraordinarily long extreme metastability. The combined theory-experiment protocol presented here is a determination of single-molecule entropic barriers in polymer dynamics. Furthermore, this method offers a convenient general procedure to quantify the underlying free energy landscapes behind the ubiquitous phenomenon of movement of single charged macromolecules in crowded environments.

Microscopic observation of the effects of elongation on the polymer chain dynamics of crosslinked polybutadiene using quasi-elastic γ-ray scattering.

A synchrotron-radiation-based quasi-elastic γ-ray scattering system has been developed that uses time-domain interferometry to observe microscopic polymer dynamics under uniaxial deformation. The stress-producing mechanism of crosslinked polybutadiene has been studied from a microscopic viewpoint. It was found that the mean relaxation time ⟨τ⟩ of the microscopic polymer motion observed over a relatively high temperature (T) range (i.e. T-1 < 0.0045 K-1) increased with elongation on both the intra- and intermolecular scales. Following an extensive strain dependence study, it was found that the strain dependences of both the intra- and intermolecular ⟨τ⟩ changed with the stress dependence. It was therefore suggested that ⟨τ⟩ increased due to the constraint of the local polymer chain motion caused by elongation. The local molecular dynamics of polymer chains under uniaxial deformation could be evaluated at intra- and intermolecular scales separately for the first time using our method.

Modulating Polymer Dynamics via Supramolecular Interaction with Ultrasmall Nanocages for Recyclable Gas Separation Membranes with Intrinsic Microporosity.

The engineering of mixed-matrix membranes is severely hindered by the trade-off between mechanical performance and effective utilization of inorganic fillers' microporosity. Herein, we report a feasible approach for optimal gas separation membranes through the fabrication of coordination nanocages with poly(4-vinylpyridine) (P4VP) via strong supramolecular interactions, enabling the homogeneous dispersion of nanocages in polymer matrixes with long-term structural stability. Meanwhile, suggested from dynamics studies, the strong attraction between P4VP and nanocages slows down polymer dynamics and rigidifies the polymer chains, leading to frustrated packing and lowered densities of the polymer matrix. This effect allows the micropores of nanocages to be accessible to external gas molecules, contributing to the intrinsic microporosity of the nanocomposites and the simultaneous enhancement of permselectivities. The facile strategy for supramolecular synthesis and polymer dynamics attenuation paves avenues to rational design of functional hybrid membranes for gas separation applications.

Extensile motor activity drives coherent motions in a model of interphase chromatin.

The 3D spatiotemporal organization of the human genome inside the cell nucleus remains a major open question in cellular biology. In the time between two cell divisions, chromatin-the functional form of DNA in cells-fills the nucleus in its uncondensed polymeric form. Recent in vivo imaging experiments reveal that the chromatin moves coherently, having displacements with long-ranged correlations on the scale of micrometers and lasting for seconds. To elucidate the mechanism(s) behind these motions, we develop a coarse-grained active polymer model where chromatin is represented as a confined flexible chain acted upon by molecular motors that drive fluid flows by exerting dipolar forces on the system. Numerical simulations of this model account for steric and hydrodynamic interactions as well as internal chain mechanics. These demonstrate that coherent motions emerge in systems involving extensile dipoles and are accompanied by large-scale chain reconfigurations and nematic ordering. Comparisons with experiments show good qualitative agreement and support the hypothesis that self-organizing long-ranged hydrodynamic couplings between chromatin-associated active motor proteins are responsible for the observed coherent dynamics.

Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis.

Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.

FRET-Integrated Polymer Brushes for Spatially Resolved Sensing of Changes in Polymer Conformation.

Polymer brush surfaces that alter their physical properties in response to chemical stimuli have the capacity to be used as new surface-based sensing materials. For such surfaces, detecting the polymer conformation is key to their sensing capabilities. Herein, we report on FRET-integrated ultrathin (<70 nm) polymer brush surfaces that exhibit stimuli-dependent FRET with changing brush conformation. Poly(N-isopropylacrylamide) polymers were chosen due their exceptional sensitivity to liquid mixture compositions and their ability to be assembled into well-defined polymer brushes. The brush transitions were used to optically sense changes in liquid mixture compositions with high spatial resolution (tens of micrometers), where the FRET coupling allowed for noninvasive observation of brush transitions around complex interfaces with real-time sensing of the liquid environment. Our methods have the potential to be leveraged towards greater surface-based sensing capabilities at intricate interfaces.

Statistical physics and mesoscopic modeling to interpret tethered particle motion experiments.

Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques provide raw data such as the tracked particle amplitude of movement, from which relevant information about DNA conformations or states must be recovered. Solving this inverse problem appeals to specific theoretical tools that have been designed in the two last decades, together with the data pre-processing procedures that ought to be implemented to avoid biases inherent to these experimental techniques. These statistical tools and models are reviewed in this paper.

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics.

Quantifying the mechanical forces produced by fluid flows within the ocean is critical to understanding the ocean's environmental phenomena. Such forces may have been instrumental in the origin of life by driving a primitive form of self-replication through fragmentation. Among the intense sources of hydrodynamic shear encountered in the ocean are breaking waves and the bursting bubbles produced by such waves. On a microscopic scale, one expects the surface-tension-driven flows produced during bubble rupture to exhibit particularly high velocity gradients due to the small size scales and masses involved. However, little work has examined the strength of shear flow rates in commonly encountered ocean conditions. By using DNA nanotubes as a novel fluid flow sensor, we investigate the elongational rates generated in bursting films within aqueous bubble foams using both laboratory buffer and ocean water. To characterize the elongational rate distribution associated with a bursting bubble, we introduce the concept of a fragmentation volume and measure its form as a function of elongational flow rate. We find that substantial volumes experience surprisingly large flow rates: during the bursting of a bubble having an air volume of 10 mm(3), elongational rates at least as large as [Formula: see text] s(-1) are generated in a fragmentation volume of [Formula: see text] [Formula: see text]. The determination of the elongational strain rate distribution is essential for assessing how effectively fluid motion within bursting bubbles at the ocean surface can shear microscopic particles and microorganisms, and could have driven the self-replication of a protobiont.

Comparison of Compressive Stress-Relaxation Behavior in Osteoarthritic (ICRS Graded) Human Articular Cartilage.

Osteoarthritis (OA) is a common joint disorder found mostly in elderly people. The role of mechanical behavior in the progression of OA is complex and remains unclear. The stress-relaxation behavior of human articular cartilage in clinically defined osteoarthritic stages may have importance in diagnosis and prognosis of OA. In this study we investigated differences in the biomechanical responses among human cartilage of ICRS grades I, II and III using polymer dynamics theory. We collected 24 explants of human articular cartilage (eight each of ICRS grade I, II and III) and acquired stress-relaxation data applying a continuous load on the articular surface of each cartilage explant for 1180 s. We observed a significant decrease in Young's modulus, stress-relaxation time, and stretching exponent in advanced stages of OA (ICRS grade III). The stretch exponential model speculated that significant loss in hyaluronic acid polymer might be the reason for the loss of proteoglycan in advanced OA. This work encourages further biomechanical modelling of osteoarthritic cartilage utilizing these data as input parameters to enhance the fidelity of computational models aimed at revealing how mechanical behaviors play a role in pathogenesis of OA.

Physical characterization using diffusion NMR spectroscopy.

NMR diffusion measurements (or dNMR) provide a powerful tool for analysis of solution organization and microgeometry of the environment by probing random molecular motion. Being a very versatile method, dNMR can be applied to a large variety of samples and systems. Here, a brief introduction into dNMR and a summary of recent advances in the field are presented. The research topics include restricted diffusion, anisotropic diffusion, polymer dynamics, solution structuring and dNMR method development. The dNMR studied systems include plants, cells (cell models), liquid crystals, polymer solutions, ionic liquids, supercooled solutions, untreated water, amino acid solutions and more. It is demonstrated how a variety of dNMR methods can be applied to a system to extract the data on particular structures present among, formed by or surrounding the diffusing particles. It is also demonstrated how dNMR methods can be developed to allow probing larger geometries, low sample concentrations and faster processes. Copyright © 2016 John Wiley & Sons, Ltd.

Thematic Minireview Series: The State of the Cytoskeleton in 2015.

The study of cytoskeletal polymers has been an active area of research for more than 70 years. However, despite decades of pioneering work by some of the brightest scientists in biochemistry, cell biology, and physiology, many central questions regarding the polymers themselves are only now starting to be answered. For example, although it has long been appreciated that the actin cytoskeleton provides contractility and couples biochemical responses with mechanical stresses in cells, only recently have we begun to understand how the actin polymer itself responds to mechanical loads. Likewise, although it has long been appreciated that the microtubule cytoskeleton can be post-translationally modified, only recently have the enzymes responsible for these modifications been characterized, so that we can now begin to understand how these modifications alter the polymerization and regulation of microtubule structures. Even the septins in eukaryotes and the cytoskeletal polymers of prokaryotes have yielded new insights due to recent advances in microscopy techniques. In this thematic series of minireviews, these topics are covered by some of the very same scientists who generated these recent insights, thereby providing us with an overview of the State of the Cytoskeleton in 2015.

Basic principles of static proton low-resolution spin diffusion NMR in nanophase-separated materials with mobility contrast.

We review basic principles of low-resolution proton NMR spin diffusion experiments, relying on mobility differences in nm-sized phases of inhomogeneous organic materials such as block-co- or semicrystalline polymers. They are of use for estimates of domain sizes and insights into nanometric dynamic inhomogeneities. Experimental procedures and limitations of mobility-based signal decomposition/filtering prior to spin diffusion are addressed on the example of as yet unpublished data on semicrystalline poly(ϵ-caprolactone), PCL. Specifically, we discuss technical aspects of the quantitative, dead-time free detection of rigid-domain signals by aid of the magic-sandwich echo (MSE), and magic-and-polarization-echo (MAPE) and double-quantum (DQ) magnetization filters to select rigid and mobile components, respectively. Such filters are of general use in reliable fitting approaches for phase composition determinations. Spin diffusion studies at low field using benchtop instruments are challenged by rather short (1)H T1 relaxation times, which calls for simulation-based analyses. Applying these, in combination with domain sizes as determined by small-angle X-ray scattering, we have determined spin diffusion coefficients D for PCL (0.34, 0.19 and 0.032nm(2)/ms for crystalline, interphase and amorphous parts, respectively). We further address thermal-history effects related to secondary crystallization. Finally, the state of knowledge concerning the connection between D values determined locally at the atomic level, using (13)C detection and CP- or REDOR-based "(1)H hole burning" procedures, and those obtained by calibration experiments, is summarized. Specifically, the non-trivial dependence of D on the magic-angle spinning (MAS) frequency, with a minimum under static and a local maximum under moderate-MAS conditions, is highlighted.

Primitive Chain Network Simulations for Double Peaks in Shear Stress under Fast Flows of Bidisperse Entangled Polymers.

A few experiments have reported that the time development of shear stress under fast-startup shear deformations exhibits double peaks before reaching a steady state for bimodal blends of entangled linear polymers under specific conditions. To understand this phenomenon, multi-chain slip-link simulations, based on the primitive chain network model, were conducted on the literature data of a bimodal polystyrene solution. Owing to reasonable agreement between their data and our simulation results, the stress was decomposed into contributions from long- and short-chain components and decoupled into segment number, stretch, and orientation. The analysis revealed that the first and second peaks correspond to the short-chain orientation and the long-chain stretch, respectively. The results also implied that the peak positions are not affected by the mixing of short and long chains, although the intensity of the second peak depends on mixing conditions in a complicated manner.

Particle dispersion governs nano to bulk dynamics for tailored nanocomposite design.

Nanoparticle addition can expand bioplastic use, as the resultant nanocomposite features e.g., improved mechanical properties. HYPOTHESIS: It is generally hypothesised that the nanoparticle-polymer interaction strength is pivotal to reduce polymer dynamics within the interphasial region and beyond. EXPERIMENTS: Translating nanoscale phenomena to bulk properties is challenging, as traditional techniques that probe interphasial dynamics are limited to well-dispersed systems. Laser speckle imaging (LSI) enabled us to probe interphasial nanoscale dynamics of samples containing aggregated nanoparticles. We relate these LSI-derived relaxation times to bulk rheological properties at a micro scale. FINDINGS: Nanocomposites with well-dispersed PDMS-coated titanium dioxide nanoparticles of ∼100 nm showed higher viscosities than nanocomposites containing aggregated PVP- and PAA-coated nanoparticles of 200-2000 nm. Within the interphasial region, nanoparticle addition increased relaxation times by a factor 101-102, reaching ultraslow relaxations of ∼103 s. While the viscosity increased upon nanoparticle loading, interphasial relaxation times plateaued at 5 wt% for nanocomposites containing well-dispersed nanoparticles and 10 wt% for nanocomposites containing aggregated nanoparticles. Likely, interphasial regions between nanoparticles interact, which is more prominent in systems with well-dispersed nanoparticles and at higher loadings. Our results highlight that, contrary to general belief, nanoparticle dispersion seems of greater importance for mechanical reinforcement than the interaction between polymer and particle.

Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities.

The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.

Interpretation of 1H and 2H spin-lattice relaxation dispersions: insights from molecular dynamics simulations of polymer melts.

We demonstrate that molecular dynamics simulations are a versatile tool to ascertain the interpretation of spin-lattice relaxation data. For (1)H, our simulation approach allows us to separate and to compare intra- and inter-molecular contributions to spin-lattice relaxation dispersions. Dealing with the important example of polymer melts, we show that the intramolecular parts of (1)H spectral densities and correlation functions are governed by rotational motion, while their inter-molecular counterparts provide access to translational motion, in particular, to mean-squared displacements and self-diffusion coefficients. Exploiting that the full microscopic information is available from molecular dynamics simulations, we determine the range of validity of experimental approaches, which often assume Gaussian dynamics, and we provide guidelines for the determination of free parameters required in experimental analyses. For (2)H, we examine the traditional methodology to extract correlation times of complex dynamics from relaxation data. Furthermore, based on knowledge from our computational study, it is shown that measurement of (2)H spin-lattice relaxation dispersions allows one to disentangle the intra- and inter-molecular contributions to the corresponding (1)H data in experimental work. Altogether, our simulation results yield a solid basis for future (1)H and (2)H spin-lattice relaxation analysis.

Polymer segmental dynamics near the interface of silica particles in the particle/polymer composites.

We demonstrate an approach to examine the local segmental dynamics of a polymer near the interface of an inorganic filler by observing the rotational dynamics of the fluorescent probe at the chain ends of polymer brushes grafted onto the surface of the filler particles. Localization of the fluorescent probe was realized by designing and synthesizing fluorophore-tethered polystyrene (PS) brushes anchored on the surface of silica particles of controlled sizes. Fluorophore-functionalized telechelic PS with an azide functionality at the other chain end was achieved via a combination of atom transfer radical polymerization and post-polymerization modification. The azide-bearing PS chains were tethered to alkyne-functionalized particles via copper-catalyzed cycloaddition reaction. The molecular weight of the grafted polymer chains was controlled to be less than the critical entanglement molecular weight, and the chain density was controlled to be low enough so that the observed dynamics was not perturbed by the polymer brush conformation and brush-matrix polymer entanglement. The polymer dynamics near the surface of the particles at low concentrations was closely examined in the bulk film geometry by employing imaging rotational fluorescence correlation microscopy (irFCM). The observed polymer dynamics near the interface were not altered in the inorganic/polymer composite geometry when the surface did not have favorable interaction with the matrix polymer. The presented rational design of the chemical route and examination of local dynamics highlight a feasible approach to construct material systems with high complexities towards a deeper understanding of composite materials.

Kinetic analysis of synaptonemal complex dynamics during meiosis of yeast Saccharomyces cerevisiae reveals biphasic growth and abortive disassembly.

The synaptonemal complex (SC) is a dynamic structure formed between chromosomes during meiosis which stabilizes and supports many essential meiotic processes such as pairing and recombination. In budding yeast, Zip1 is a functionally conserved element of the SC that is important for synapsis. Here, we directly measure the kinetics of Zip1-GFP assembly and disassembly in live cells of the yeast S. cerevisiae. The imaging of SC assembly in yeast is challenging due to the large number of chromosomes packed into a small nucleus. We employ a zip3Δ mutant in which only a few chromosomes undergo synapsis at any given time, initiating from a single site on each chromosome, thus allowing the assembly and disassembly kinetics of single SCs to be accurately monitored in living cells. SC assembly occurs with both monophasic and biphasic kinetics, in contrast to the strictly monophasic assembly seen in C. elegans. In wild-type cells, once maximal synapsis is achieved, programmed final disassembly rapidly follows, as Zip1 protein is actively degraded. In zip3Δ, this period is extended and final disassembly is prolonged. Besides final disassembly, we found novel disassembly events involving mostly short SCs that disappeared in advance of programmed final disassembly, which we termed "abortive disassembly." Abortive disassembly is distinct from final disassembly in that it occurs when Zip1 protein levels are still high, and exhibits a much slower rate of disassembly, suggesting a different mechanism for removal in the two types of disassembly. We speculate that abortive disassembly events represent defective or stalled SCs, possibly representing SC formation between non-homologs, that is then targeted for dissolution. These results reveal novel aspects of SC assembly and disassembly, potentially providing evidence of additional regulatory pathways controlling not just the assembly, but also the disassembly, of this complex cellular structure.

Simulational Tests of the Rouse Model.

An extensive review of literature simulations of quiescent polymer melts is given, considering results that test aspects of the Rouse model in the melt. We focus on Rouse model predictions for the mean-square amplitudes ⟨(Xp(0))2⟩ and time correlation functions ⟨Xp(0)Xp(t)⟩ of the Rouse mode Xp(t). The simulations conclusively demonstrate that the Rouse model is invalid in polymer melts. In particular, and contrary to the Rouse model, (i) mean-square Rouse mode amplitudes ⟨(Xp(0))2⟩ do not scale as sin-2(pπ/2N), N being the number of beads in the polymer. For small p (say, p≤3) ⟨(Xp(0))2⟩ scales with p as p-2; for larger p, it scales as p-3. (ii) Rouse mode time correlation functions ⟨Xp(t)Xp(0)⟩ do not decay with time as exponentials; they instead decay as stretched exponentials exp(-αtß). ß depends on p, typically with a minimum near N/2 or N/4. (iii) Polymer bead displacements are not described by independent Gaussian random processes. (iv) For p≠q, ⟨Xp(t)Xq(0)⟩ is sometimes non-zero. (v) The response of a polymer coil to a shear flow is a rotation, not the affine deformation predicted by Rouse. We also briefly consider the Kirkwood-Riseman polymer model.