arXiv subjects

Omar A. Saleh

Publications and source records attributed to Omar A. Saleh.

15 recordsLinked to original sources

arXiv2026

Cooperation and competition of basepairing and electrostatic interactions in mixtures of DNA nanostars and polylysine

Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have contrasting effects on phase behavior. Attractive electrostatic interactions between oppositely charged macromolecules are screened by added salt, reducing the driving force for coacervation. By contrast, base pairing interactions between nucleic acids are diminished by charge repulsion and thus enhanced by added salt, promoting associative phase separation. To explore this interplay, we combine experiment and theory to map the complex phase behavior of a model solution of poly-L-lysine (PLL) and self-complementary DNA nanostars (NS) as a function of temperature, ionic strength, and macromolecular composition. Despite having opposite salt dependences, we find that electrostatics and base pairing cooperate to stabilize NS-PLL coacervation at high ionic strengths and temperatures, leading to two- or three-phase coexistence under various conditions. We further observe a variety of kinetic pathways to phase separation at different salt concentrations, resulting in the formation of nonequilibrium aggregates or droplets whose compositions evolve on long timescales. Finally, we show that the cooperativity between electrostatics and base pairing can be used to create immiscible coacervates that partition various NS species at intermediate salt concentrations. Our results illustrate how the interplay between distinct interaction modes can greatly increase the complexity of the phase behavior relative to systems with a single type of interaction.

cond-mat.soft↗

arXiv2026

Bicontinuity in active phase separation

We study phase separation between coexisting active and passive fluids in three-dimensions, using numerical simulation and experiments. Chaotic flows of the active phase drive giant interfacial deformations, causing the co-existing phases to interpenetrate and generate a continuously reconfiguring bicontinuous morphology which persists over the lifetime of the active fluid. Active bicontinuous structures are dominated by sheet-like interfaces, in marked difference from passive liquid-liquid phase separation which is controlled by saddle-like surfaces. Activity and surface tension control the length scale of the bicontinuous structure. These results demonstrate how active stresses suppress the coarsening of conventional phase separation, generating steady-state reconfigurable morphologies not accessible with conventional surface-modifying agents or through quenching of transient phase separated structures.

cond-mat.soft↗

arXiv2026

Roadmap for Condensates in Cell Biology

Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants, clarifies key concepts for researchers, funding bodies, and journals. After unifying terminology that often separates disciplines, we outline the core physics of condensate formation, review their biological roles, and identify outstanding challenges in nonequilibrium theory, multiscale simulation, and quantitative in-cell measurements. We close with a forward-looking outlook to guide coordinated efforts toward predictive, experimentally anchored understanding and control of biomolecular condensates.

physics.bio-ph↗

arXiv2025

Diverse, Distinct, and Densely Packed DNA Droplets

The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of dense liquid (`condensate') phases. The relationship between sequence design and the diversity of the resultant phases is therefore of interest. Here, we explore this question using the DNA nanostar system which permits the creation of multi-phase condensate droplets through sequence engineering of the sticky end bonds that drive particle-particle attraction. We explore the theoretical limits of nanostar phase diversity, then experimentally demonstrate the ability to create 9 distinct, non-adhering nanostar phases that do not share components. We further study how thermal processing affects the morphology and dynamics of such a highly diverse condensate system. We particularly show that a rapid temperature quench leads to the formation of a densely packed 2-D layer of droplets that is transiently stabilized by caging effects enabled by the phase diversity, leading to glassy dynamics, such as slow coarsening and dynamic heterogeneity. Generally, our work provides experimental insight into the thermodynamics of phase separation of complex mixtures and demonstrates the rational engineering of complex, long-range, multi-phase droplet structures.

cond-mat.soft↗

arXiv2024

Condensation and activator/repressor control of a transcription-regulated biomolecular liquid

Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA) to compartmentalize biomolecules via liquid-liquid phase separation (LLPS). Here, we develop a model biomolecular system that permits quantitative investigation of such dynamics, particularly by coupling a phase-separating system of DNA nanostars to an in vitro transcription reaction. The DNA nanostars' sequence is designed such that they self-assemble into liquid droplets only in the presence of a transcribed single-stranded RNA linker. We find that nanostar droplets form with a substantial delay and non-linear response to the kinetics of RNA synthesis. In addition, we utilize the compartments generated by the phase-separation process to engineer an activator/repressor network, where the transcription reaction activates the formation of droplets, and then droplets suppress the transcription reaction by segregating transcription components inside them. Our work on transcription-driven liquid-liquid phase separation constitutes a robust and programmable platform to explore non-equilibrium reaction-phase transition dynamics and could also provide a foundation to understand the dynamics of transcriptional condensate assembly in cells.

cond-mat.soft↗

arXiv2024

From isolated polyelectrolytes to star-like assemblies: The role of sequence heterogeneity on the statistical structure of the intrinsically disordered Neurofilament-low tail domain

Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of Neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure, and, in turn, their implications on previously observed phenomena in NFL native and diseased states.

physics.bio-ph↗

arXiv2023

Controlling the size and adhesion of DNA droplets using surface-active DNA molecules

Liquid droplets of biomolecules serve as organizers of the cellular interior and are of interest in biosensing and biomaterials applications. Here, we investigate means to tune the interfacial properties of a model biomolecular liquid consisting of multi-armed DNA 'nanostar' particles. We find that long DNA molecules that have binding affinity for the nanostars are preferentially enriched on the interface of nanostar droplets, thus acting as surfactants. Fluorescent measurements indicate that, in certain conditions, the interfacial density of the surfactant is around 20 per square micron, indicative of a sparse brush-like structure of the long, polymeric DNA. Increasing surfactant concentration leads to decreased droplet size, down to the sub-micron scale, consistent with arrest of droplet coalescence by the disjoining pressure created by the brush-like surfactant layer. Added DNA surfactant also keeps droplets from adhering to both hydrophobic and hydrophilic solid surfaces, apparently due to this same disjoining effect of the surfactant layer. We thus demonstrate control of the size and adhesive properties of droplets of a biomolecular liquid, with implications for basic biophysical understanding of such droplets, as well as for their applied use.

cond-mat.soft↗

arXiv2023

Towards rational design of power-law rheology via DNA nanostar networks

We measure the rheology of transient hydrogels comprised of a single type of DNA nanostar that makes both strong and weak bonds. These gels exhibit power-law frequency-dependence of their storage and loss moduli, with scaling exponents that depend on the proportions of the two bonds. A diffusive stress-relaxation model, in which the strong-bond sub-network relieves stress by diffusing through an effective viscosity imposed by the weak bonds, explains the scaling of their moduli. The model has implications for the fractal dimensions of the strong-bond sub-network that are in good agreement with measurements and makes testable predictions for the viscoelasticity of other transient hydrogels. Overall, this work demonstrates the power of DNA nanotechnology to decipher, and potentially rationally design, power-law rheology.

cond-mat.soft↗

arXiv2023

Spatial Organization of Phase-separated DNA Droplets

Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model system consisting of DNA nanostars: finite-valence, self-assembled particles that form micron-scale liquid droplets via a binodal phase transition. We demonstrate that, upon phase separation, nanostar droplets spontaneously form hyperuniform structures, a type of disordered material with `hidden order' that combines the long-range order of crystals with the short-range isotropy of liquids. We find that the hyperuniformity of the DNA droplets reflects near-equilibrium dynamics, where phase separation drives the organization of droplets that then relax toward equilibrium via droplet Brownian motion. We engineer a two-species system of immiscible DNA droplets and find two distinctly hyperuniform structures in the same sample, but with random cross-species droplet correlations, which rules out explanations that rely on droplet-droplet hydrodynamic interactions. In addition, we perform experiments on the electrostatic coacervation of peptides and nucleotides which exhibit hyperuniform structures indistinguishable from DNA nanostars, indicating the phenomenon generally applies to phase-separating systems that experience Brownian motion. Our work on near-equilibrium droplet assembly and structure provides a foundation to investigate droplet organizational mechanisms in driven/biological environments. This approach also provides a clear path to implement phase-separated droplet patterns as exotic optical or mechanical metamaterials, or as efficient biochemical reactors.

cond-mat.soft↗

arXiv2023

Intramolecular Structural Heterogeneity altered by Long-range Contacts in an Intrinsically Disordered Protein

Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs' amino acid sequence. Here, using small-angle x-ray scattering (SAXS) and time-resolved Förster resonance energy transfer (trFRET), we study the intra-molecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt sub-segments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments' structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intra-molecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope it will allow us to model their biological function.

physics.bio-ph↗

arXiv2022

Controlling liquid-liquid phase behavior with an active fluid

Demixing of binary liquids is a ubiquitous transition, which is explained using a well-established thermodynamic formalism that requires equality of intensive thermodynamics parameters across the phase boundaries. Demixing transitions also occur when binary fluid mixtures are driven away from equilibrium, for example, by external shear flow. Predicting demixing transition under non-equilibrium non-potential conditions remains, however, a challenge. We drive liquid-liquid phase separation (LLPS) of attractive DNA nanostar molecules away from equilibrium using an internally driven microtubule-based active fluid. Activity lowers the critical temperature and narrows the coexistence concentrations, but only when there are mechanical bonds between the liquid droplets and the reconfiguring active fluid. Similar behaviors are observed in numerical simulations, suggesting that activity suppression of liquid-liquid phase separation is a generic feature of active LLPS. Our work describes a platform for building soft active materials with feedback control while also providing insight into cell biology, where phase separation emerged as a ubiquitous self-organizational principle.

cond-mat.soft↗

arXiv2021

Intrinsically Disordered Proteins at the Nano-scale

The human proteome is enriched in proteins that do not fold into a stable 3D structure. These intrinsically disordered proteins (IDPs) spontaneously fluctuate between a large number of configurations in their native form. Remarkably, the disorder does not lead to dysfunction as with denatured folded proteins. In fact, unlike denatured proteins, recent evidences strongly suggest that multiple biological functions stem from such structural plasticity. Here, focusing on the nanoscopic length-scale, we review the latest advances in IDP research and discuss some of the future directions in this highly promising field.

physics.bio-ph↗

arXiv2020

Single-molecule stretching shows glycosylation sets tension in the hyaluronan-aggrecan bottlebrush

Large bottlebrush complexes formed from the polysaccharide hyaluronan (HA) and the proteoglycan aggrecan contribute to cartilage compression resistance and are necessary for healthy joint function. A variety of mechanical forces act on these complexes in the cartilage extracellular matrix, motivating the need for a quantitative description which links their structure and mechanical response. Studies using electron microscopy have imaged the HA-aggrecan brush but require adsorption to a surface, dramatically altering the complex from its native conformation. We use magnetic tweezers force spectroscopy to measure changes in extension and mechanical response of an HA chain as aggrecan monomers bind and form a bottlebrush. This technique directly measures changes undergone by a single complex with time and under varying solution conditions. Upon addition of aggrecan, we find a large swelling effect manifests when the HA chain is under very low external tension (i.e. stretching forces less than ~1 pN). We use models of force-extension behavior to show that repulsion between the aggrecans induces an internal tension in the HA chain. Through reference to theories of bottlebrush polymer behavior, we demonstrate that the experimental values of internal tension are consistent with a polydisperse aggrecan population, likely caused by varying degrees of glycosylation. By enzymatically deglycosylating aggrecan, we show that aggrecan glycosylation is the structural feature which causes HA stiffening. We then construct a simple stochastic binding model to show that variable glycosylation leads to a wide distribution of internal tensions in HA, causing variations in the mechanics at much longer length-scales. Our results provide a mechanistic picture of how flexibility and size of HA and aggrecan lead to the brush architecture and mechanical properties of this important component of cartilage.

q-bio.BM↗

arXiv2020

Glassy dynamics and memory effects in an intrinsically disordered protein construct

Glassy, nonexponential relaxations in globular proteins are typically attributed to conformational behaviors that are missing from intrinsically disordered proteins. Yet, we show that single molecules of a disordered-protein construct display two signatures of glassy dynamics, logarithmic relaxations and a Kovacs memory effect, in response to changes in applied tension. We attribute this to the presence of multiple independent local structures in the chain, which we corroborate with a model that correctly predicts the force dependence of the relaxation. The mechanism established here likely applies to other disordered proteins.

cond-mat.soft↗

arXiv2019

Contraction of polymer gels created by the activity of molecular motors

We propose a theory based on non-equilibrium thermodynamics to describe the mechanical behavior of an active polymer gel created by the inclusion of molecular motors in its solvent. When activated, these motors attach to the chains of the polymer network and shorten them creating a global contraction of the gel, which mimics the active behavior of a cytoskeleton. The power generated by these motors is obtained by ATP hydrolysis reaction, which transduces chemical energy into mechanical work. The latter is described by an increment of strain energy in the gel due to an increased stiffness. This effect is described with an increment of the cross-link density in the polymer network, which reduces its entropy. The theory then considers polymer network swelling and species diffusion to describe the transient passive behavior of the gel. We finally formulate the problem of uniaxial contraction of a slab of gel and compare the results with experiments, showing good agreement.

cond-mat.soft↗