arXiv subjects

Charley Schaefer

Publications and source records attributed to Charley Schaefer.

10 recordsLinked to original sources

arXiv2026

Biophysics of the Pyrenoid

Phase-separated liquid droplets organize molecules in cells, but the underlying physical principles differ from abiotic mixing and quantitative rules in living systems remain poorly understood. The pyrenoid -- a liquid-like organelle that enhances photosynthetic carbon fixation in algae and hornworts -- provides an unusually tractable model system. Here, we review recent advances in our understanding of pyrenoids from the perspective of biophysics. We highlight how reaction-diffusion models connect compartment architecture to catalytic performance, how soft matter theories link molecular interactions to condensate assembly, and how modern experimental methods enable these predictions to be tested quantitatively. Recent studies suggest that pyrenoid function may be described by a small number of effective transport and reaction processes, while condensate assembly can be understood through molecular design parameters and thermodynamic constraints. Together, these findings establish the pyrenoid as a powerful system for investigating catalytic compartmentalization, biomolecular self-organization and the emergence of effective physical descriptions in living systems.

physics.bio-ph↗

arXiv2026

Protein Dynamics Beyond Structure Prediction

The ability to predict protein three-dimensional structures from amino acid sequences is a landmark achievement in molecular biology, where recent deep learning approaches such as AlphaFold are the culmination of decades of work. Yet, the quantitative understanding of how protein sequences give rise to dynamic conformational changes and higher-order assemblies remains unsolved. Folding and conformational states are dynamic, stochastic processes, shaped by sequence, energy, co-translational constraints, chaperone machineries, and the physicochemical conditions of the cellular environment. Recent advances now position the field to move beyond static structural endpoints toward a mechanistic understanding of folding dynamics in living systems. Single-molecule techniques enable time-resolved observation of folding trajectories and intermediate states hitherto hidden by traditional structural biology approaches, while computational innovations and data-driven approaches offer new ways to integrate heterogeneous data across scales. In this Roadmap, we review the current conceptual landscape of protein folding, examine the experimental and theoretical gaps that remain, and discuss emerging strategies that integrate high-resolution measurements with multiscale modeling. We outline a roadmap toward a quantitative and predictive science of protein folding dynamics, conformational kinetics, and macromolecular self-assembly. Realizing this vision would transform our understanding of the dynamics of molecular self-organization, from the folding of individual polypeptides to the emergence of dynamic macromolecular complexes. This will enable rational control of folding and misfolding in health and disease, extend protein engineering principles beyond static structural design, and establish a mechanistic foundation for predictive and personalized interventions in proteostasis-related disorders.

q-bio.BM↗

arXiv2024

Bacterial stress granule protects mRNA through ribonucleases exclusion

Membraneless droplets formed through liquid-liquid phase separation (LLPS) play a crucial role in mRNA storage, enabling organisms to swiftly respond to environmental changes. However, the mechanisms underlying mRNA integration and protection within droplets remain unclear. Here, we unravel the role of bacterial aggresomes as stress granules (SGs) in safeguarding mRNA during stress. We discovered that upon stress onset, mobile mRNA molecules selectively incorporate into individual proteinaceous SGs based on length-dependent enthalpic gain over entropic loss. As stress prolongs, SGs undergo compaction facilitated by stronger non-specific RNA-protein interactions, thereby promoting recruitment of shorter RNA chains. Remarkably, mRNA ribonucleases are repelled from bacterial SGs, due to the influence of protein surface charge. This exclusion mechanism ensures the integrity and preservation of mRNA within SGs during stress conditions, explaining how mRNA can be stored and protected from degradation. Following stress removal, SGs facilitate mRNA translation, thereby enhancing cell fitness in changing environments. These droplets maintain mRNA physiological activity during storage, making them an intriguing new candidate for mRNA therapeutics manufacturing.

physics.bio-ph↗

arXiv2024

Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA

Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.

physics.bio-ph↗

arXiv2023

Predicting Rubisco:Linker Condensation from Titration in the Dilute Phase

The condensation of Rubisco holoenzymes and linker proteins into 'pyrenoids', a crucial super-charger of photosynthesis in algae, is qualitatively understood in terms of 'sticker-and-spacer' theory. We derive semi-analytical partition sums for small Rubisco:linker aggregates, which enable the calculation of both dilute-phase titration curves and dimerisation diagrams. By fitting the titration curves to Surface Plasmon Resonance and Single-Molecule Fluorescence Microscopy data, we extract the molecular properties needed to predict dimerisation diagrams. We use these to estimate typical concentrations for condensation, and successfully compare these to microscopy observations.

cond-mat.soft↗

arXiv2021

Theoretical rheo-physics of silk: Intermolecular associations reduce the critical specific work for flow-induced crystallisation

Silk is a semi-dilute solution of randomly coiled associating polypeptide chains that crystallise following the stretch-induced disruption, in the strong extensional flow of extrusion, of the solvation shell around their amino acids. We propose that natural silk spinning exploits both the exponentially-broad stretch-distribution generated by associating polymers in extensional flow and the criterion of a critical concentration of sufficiently-stretched chains to nucleate flow-induced crystallisation. To investigate the specific-energy input needed to reach this criterion in start-up flow, we have coupled a model for the coarse-grained Brownian dynamics of the chain to the stochastic, strain-dependent binding and unbinding of their associations. Our simulations indicate that the associations hamper chain alignment in the initial slow flow, but, on the other hand, facilitate chain stretching at low specific work at later, high rates. We identify a minimum in the critical specific work at a strain rate just above the stretch transition (i.e, where the mean stretch diverges), which we explain in terms of analytical solutions of a two-state master equation. We further discuss how the silkworm appears to exploit the chemical tunability of the associations to optimise chain alignment and stretching in different locations along the spinning duct: this delicate mechanism also highlights the potential biomimetic industrial benefits of chemically tunable processing of synthetic association polymers.

cond-mat.soft↗

arXiv2021

Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness

Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their function in bacteria, which in general lack membrane-bound compartments, remains less clear. Here, we used high-resolution optical microscopy to observe single bacterial aggresomes, nanostructured intracellular assemblies of proteins, to undercover their role in cell stress. We find that proteins inside aggresomes are mobile and undergo dynamic turnover, consistent with a liquid state. Our observations are in quantitative agreement with phase-separated liquid droplet formation driven by interacting proteins under thermal equilibrium that nucleate following diffusive collisions in the cytoplasm. We have discovered aggresomes in multiple species of bacteria, and show that these emergent, metastable liquid-structured protein assemblies increase bacterial fitness by enabling cells to tolerate environmental stresses.

q-bio.BM↗

arXiv2020

Power-Law Stretching of Associating Polymers in Steady-State Extensional Flow

We present a tube model for the Brownian dynamics of associating polymers in extensional flow. In linear response, the model confirms the analytical predictions for the sticky diffusivity by Leibler- Rubinstein-Colby theory. Although a single-mode DEMG approximation accurately describes the transient stretching of the polymers above a 'sticky' Weissenberg number (product of the strain rate with the sticky-Rouse time), the pre-averaged model fails to capture a remarkable development of a power-law distribution of stretch in steady-state extensional flow: while the mean stretch is finite, the fluctuations in stretch may diverge. We present an analytical model that shows how strong stochastic forcing drive the long tail of the distribution, gives rise to rare events of reaching a threshold stretch and constitutes a framework within which nucleation rates of flow-induced crystallization may understood in systems of associating polymers under flow. The model also exemplifies a wide class of driven systems possessing strong, and scaling, fluctuations.

cond-mat.soft↗

arXiv2019

Morphology Formation in Binary Mixtures upon Gradual Destabilisation

Spontaneous liquid-liquid phase separation is commonly understood in terms of phenomenological mean-field theories. These theories correctly predict the structural features of the fluid at sufficiently long time scales and wavelengths. However, these conditions are not met in various examples in biology and materials science where the mixture is slowly destabilised, and phase separation takes place close to the critical point. Using kinetic Monte Carlo and molecular dynamics simulations of a binary surface fluid under these conditions, we show that the characteristic length scale of the emerging structure decreases, in 2D, with the 4/15 dynamic critical exponent of the quench rate rather than the mean-field 1/6th power. Hence, the dynamics of cluster formation governed by thermodynamically undriven Brownian motion is much more sensitive on the rate of destabilisation than expected from mean-field theory. We discuss the expected implications of this finding to 3D systems with ordering liquid crystals, as well as phase-separating passive or active particles.

cond-mat.soft↗

arXiv2017

Structuring of fluid adlayers upon ongoing unimolecular adsorption

Fluids with spatial density variations of single or mixed molecules play a key role in biophysics, soft matter and materials science. The fluid structures usually form via spinodal decomposition or nucleation following an instantaneous destabilisation of the initially disordered fluid. However, in practice an instantaneous quench is often not viable, and the rate of destabilisation may be gradual rather than instantaneous. In this work we show that the commonly used phenomenological descriptions of fluid structuring are inadequate under these conditions. We come to that conclusion in the context of surface catalysis, where we employ kinetic Monte Carlo simulations to describe the unimolecular adsorption of gaseous molecules onto a metal surface. The adsorbates diffuse at the surface and, as a consequence of lateral interactions and due to an ongoing increase of the surface coverage, phase separate into coexisting low- and high-density regions. The typical size of these regions turns out to depend much more strongly on the rate of adsorption than predicted from recently reported phenomenological models. We discuss how this finding contributes to the fundamental understanding of the crossover from liquid-liquid to liquid-solid demixing of solution-cast polymer blends.

physics.chem-ph↗