Project description:Para-nematic phases, induced by unwinding chiral helices, spontaneously relax to a chiral ground state through phase ordering dynamics that are of great interest and crucial for applications such as stimuli-responsive and biomimetic engineering. In this work, we characterize the cholesteric phase relaxation behaviors of β-lactoglobulin amyloid fibrils and cellulose nanocrystals confined into cylindrical capillaries, uncovering two different equilibration pathways. The integration of experimental measurements and theoretical predictions reveals the starkly distinct underlying mechanism behind the relaxation dynamics of β-lactoglobulin amyloid fibrils, characterized by slow equilibration achieved through consecutive sigmoidal-like steps, and of cellulose nanocrystals, characterized by fast equilibration obtained through smooth relaxation dynamics. Particularly, the specific relaxation behaviors are shown to emerge from the order parameter of the unwound cholesteric medium, which depends on chirality and elasticity. The experimental findings are supported by direct numerical simulations, allowing to establish hard-to-measure viscoelastic properties without applying magnetic or electric fields.
Project description:Topological superconductors host new states of quantum matter which show a pairing gap in the bulk and gapless surface states providing a platform to realize Majorana fermions. Recently, alkaline-earth metal Sr intercalated Bi2Se3 has been reported to show superconductivity with a Tc ~ 3 K and a large shielding fraction. Here we report systematic normal state electronic structure studies of Sr0.06Bi2Se3 (Tc ~ 2.5 K) by performing photoemission spectroscopy. Using angle-resolved photoemission spectroscopy (ARPES), we observe a quantum well confined two-dimensional (2D) state coexisting with a topological surface state in Sr0.06Bi2Se3. Furthermore, our time-resolved ARPES reveals the relaxation dynamics showing different decay mechanism between the excited topological surface states and the two-dimensional states. Our experimental observation is understood by considering the intra-band scattering for topological surface states and an additional electron phonon scattering for the 2D states, which is responsible for the superconductivity. Our first-principles calculations agree with the more effective scattering and a shorter lifetime of the 2D states. Our results will be helpful in understanding low temperature superconducting states of these topological materials.
Project description:Ring polymers have fascinated scientists for decades, but experimental progress has been challenging due to the presence of linear chain contaminants that fundamentally alter dynamics. In this work, we report the unexpected slow stress relaxation behavior of concentrated ring polymers that arises due to ring-ring interactions and ring packing structure. Topologically pure, high molecular weight ring polymers are prepared without linear chain contaminants using cyclic poly(phthalaldehyde) (cPPA), a metastable polymer chemistry that rapidly depolymerizes from free ends at ambient temperatures. Linear viscoelastic measurements of highly concentrated cPPA show slow, non-power-law stress relaxation dynamics despite the lack of linear chain contaminants. Experiments are complemented by molecular dynamics (MD) simulations of unprecedentedly high molecular weight rings, which clearly show non-power-law stress relaxation in good agreement with experiments. MD simulations reveal substantial ring-ring interpenetrations upon increasing ring molecular weight or local backbone stiffness, despite the global collapsed nature of single ring conformation. A recently proposed microscopic theory for unconcatenated rings provides a qualitative physical mechanism associated with the emergence of strong inter-ring caging which slows down center-of-mass diffusion and long wavelength intramolecular relaxation modes originating from ring-ring interpenetrations, governed by the onset variable N/ND, where the crossover degree of polymerization ND is qualitatively predicted by theory. Our work overcomes challenges in achieving ring polymer purity and by characterizing dynamics for high molecular weight ring polymers. Overall, these results provide a new understanding of ring polymer physics.
Project description:Bacteriophages initiate infection by releasing their double-stranded DNA into the cytosol of their bacterial host. However, what controls and sets the timescales of DNA ejection? Here we provide evidence from stochastic simulations which shows that the topology and organization of DNA packed inside the capsid plays a key role in determining these properties. Even with similar osmotic pressure pushing out the DNA, we find that spatially ordered DNA spools have a much lower effective friction than disordered entangled states. Such spools are only found when the tendency of nearby DNA strands to align locally is accounted for. This topological or conformational friction also depends on DNA knot type in the packing geometry and slows down or arrests the ejection of twist knots and very complex knots. We also find that the family of (2, 2k+1) torus knots unravel gradually by simplifying their topology in a stepwise fashion. Finally, an analysis of DNA trajectories inside the capsid shows that the knots formed throughout the ejection process mirror those found in gel electrophoresis experiments for viral DNA molecules extracted from the capsids.
Project description:Surface microstructures in nature enable diverse and intriguing properties, from the iridescence of butterfly wings to the hydrophobicity of lotus leaves to the controllable adhesion of gecko toes. Many artificial analogues exist; however, there is a key characteristic of the natural materials that is largely absent from the synthetic versions-spatial variation. Here we show that exploiting spatial variation in the design of one class of synthetic microstructure, gecko-inspired adhesives, enables one-way friction, an intriguing property of natural gecko adhesive. When loaded along a surface in the preferred direction, our adhesive material supports forces 100 times larger than when loaded in the reverse direction, representing an asymmetry significantly larger than demonstrated in spatially uniform adhesives. Our study suggests that spatial variation has the potential to advance artificial microstructures, helping to close the gap between synthetic and natural materials.
Project description:DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realized using engineered DNA in the presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems, there is a topological gelation transition, which can be triggered by increasing either the stiffness or the concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked, and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked, and mixed loops, many of which are knotted. We predict that the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilized container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids-e.g., DNA-based complex fluids or living polymer networks-with desired topologies.
Project description:In the last decade, the friction stir welding of polymers has been increasingly investigated by the means of more and more sophisticated approaches. Since the early studies, which were aimed at proving the feasibility of the process for polymers and identifying suitable processing windows, great improvements have been achieved. This owes to the increasing care of academic researchers and industrial demands. These improvements have their roots in the promising results from pioneer studies; however, they are also the fruits of the adoption of more comprehensive approaches and the multidisciplinary analyses of results. The introduction of instrumented machines has enabled the online measurement of processing loads and temperature, and critical understanding of the principal aspects affecting the material flow and welds quality. Such improvements are also clearly demonstrated by the increase of the strength of recent joints (up to 99% of joining efficiency) as compared to those reached in early researches (almost 47%). This article provides a comprehensive review of the recent progresses on the process fundamentals, quality assessment and the influence of process parameters on the mechanical behavior. In addition, emphasis is given to new developments and future perspectives.
Project description:We study active topological glass under spherical confinement, allowing us to exceed the chain lengths simulated previously and determine the critical exponents of the arrested conformations. We find a previously unresolved "tank-treading" dynamic mode of active segments along the ring contour. This mode can enhance active-passive phase separation in the state of active topological glass when both diffusional and conformational relaxation of the rings are significantly suppressed. Within the observational time, we see no systematic trends in the positioning of the separated active domains within the confining sphere. The arrested state exhibits coherent stochastic rotations. We discuss possible connections of the conformational and dynamic features of the system to chromosomes enclosed in the nucleus of a living cell.
Project description:Pancreatic ductal adenocarcinoma (PDAC) remains resistant to most treatments and demonstrates a complex pathobiology. Here, we deconvolute regional heterogeneity in the human PDAC tumor microenvironment (TME), a long-standing obstacle, to define precise stromal contributions to PDAC progression. Large scale integration of histology-guided multiOMICs profiling with clinical data sets and functional in vitro models uncovered two microenvironmental programs in PDAC that were anchored in fibroblast differentiation states. These sub-tumor microenvironments (subTMEs) co-occurred intratumorally and were spatially confined, producing patient-specific cellular and molecular heterogeneity associated with shortened patient survival. Each subTME was uniquely structured to support discrete aspects of tumor biology: reactive regions rich in activated fibroblast communities were immune-hot and promoted aggressive tumor progression while deserted regions enriched in extracellular matrix supported tumor differentiation yet were markedly chemoprotective. In conclusion, PDAC regional heterogeneity derives from biologically distinct reactive and protective TME elements with a defined, active role in PDAC progression.
Project description:Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In particularly, they ignore that each chromosome occupies a confined space, i.e., the chromosome territory. Here, we present a polymer model that is able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb. This random loop (RL) model assumes a self-avoiding random walk folding of the polymer backbone and defines a probability P for 2 monomers to interact, creating loops of a broad size range. Model predictions are compared with systematic measurements of chromatin folding of the q-arms of chromosomes 1 and 11. The RL model can explain our observed data and suggests that on the tens-of-megabases length scale P is small, i.e., 10-30 loops per 100 Mb. This is sufficient to enforce folding inside the confined space of a chromosome territory. On the 0.5- to 3-Mb length scale chromatin compaction differs in different subchromosomal domains. This aspect of chromatin structure is incorporated in the RL model by introducing heterogeneity along the fiber contour length due to different local looping probabilities. The RL model creates a quantitative and predictive framework for the identification of nuclear components that are responsible for chromatin-chromatin interactions and determine the 3-dimensional organization of the chromatin fiber.