arXiv subjects

Sam Wilken

Publications and source records attributed to Sam Wilken.

9 recordsLinked to original sources

arXiv2025

Active diffusing crystals in a 2D non-equilibrium system

We investigate a 2D dynamical absorbing state model of monodisperse disks, in which rich phase behavior arises from interactions consisting solely of repulsive displacements between overlapping particles. The phase diagram reveals several unconventional features, including a disordered and static absorbing configuration, where no particles overlap, separated by a second-order phase transition to a continuously evolving active hexagonal crystal with collective ring diffusion, which in turn undergoes a first-order phase transition to an active isotropic liquid. The only driving parameter is $\epsilon$, the maximum size of the random repulsive kicks. Small $\epsilon$ facilitates self-organization into an ordered state, but large $\epsilon$ prevents this organization from occurring. This is very different from typical order-disorder transitions, where there are two competing influences, energy and entropy, that drive the transition.

cond-mat.soft↗

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↗

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↗

arXiv2022

Dynamical approach to the jamming problem

A simple dynamical model, Biased Random Organization, BRO, appears to produce configurations known as Random Close Packing (RCP) as BRO's densest critical point in dimension $d=3$. We conjecture that BRO likewise produces RCP in any dimension; if so, then RCP does not exist in $d=1-2$ (where BRO dynamics lead to crystalline order). In $d=3-5$, BRO produces isostatic configurations and previously estimated RCP volume fractions 0.64, 0.46, and 0.30, respectively. For all investigated dimensions ($d=2-5$), we find that BRO belongs to the Manna universality class of dynamical phase transitions by measuring critical exponents associated with the steady-state activity and the long-range density fluctuations. Additionally, BRO's distribution of near-contacts (gaps) displays behavior consistent with the infinite-dimensional theoretical treatment of RCP when $d \ge 4$. The association of BRO's densest critical configurations with Random Close Packing implies that RCP's upper-critical dimension is consistent with the Manna class $d_{uc} = 4$.

cond-mat.stat-mech↗

arXiv2022

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↗

arXiv2020

Sedimentation of a Colloidal Monolayer Down an Inclined Plane

We study the driven collective dynamics of a colloidal monolayer sedimentating down an inclined plane. The action of the gravity force parallel to the bottom wall creates a flow around each colloid, and the hydrodynamic interactions among the colloids accelerate the sedimentation as the local density increases. This leads to the creation of a universal "triangular" inhomogeneous density profile, with a traveling density shock at the leading front moving in the downhill direction. Unlike density shocks in a colloidal monolayer driven by applied torques rather than forces [Phys. Rev. Fluids, 2(9):092301, 2017], the density front during sedimentation remains stable over long periods of time even though it develops a roughness on the order of tens of particle diameters. Through experimental measurements and particle-based computer simulations, we find that the Burgers equation can model the density profile along the sedimentation direction as a function of time remarkably well, with a modest improvement if the nonlinear conservation law accounts for the sub-linear dependence of the collective sedimentation velocity on density.

cond-mat.soft↗

arXiv2020

Hyperuniform structures formed by shearing colloidal suspensions

In periodically sheared suspensions there is a dynamical phase transition characterized by a critical strain amplitude $\gamma_c$ between an absorbing state where particle trajectories are reversible and an active state where trajectories are chaotic and diffusive. Repulsive non-hydrodynamic interactions between "colliding" particles' surfaces have been proposed as a source of this broken time reversal symmetry. A simple toy model called Random Organization qualitatively reproduces the dynamical features of this transition. Random Organization and other absorbing state models exhibit hyperuniformity, a strong suppression of density fluctuations on long length-scales quantified by a structure factor $S(q \rightarrow 0) \sim q^\alpha$ with $\alpha > 0$, at criticality. Here we show experimentally that the particles in periodically sheared suspensions organize into structures with anisotropic short-range order but isotropic, long-range hyperuniform order when oscillatory shear amplitudes approach $\gamma_c$.

cond-mat.soft↗

arXiv2014

Dense Suspension Splat: Monolayer Spreading and Hole Formation After Impact

We use experiments and minimal numerical models to investigate the rapidly expanding monolayer formed by the impact of a dense suspension drop against a smooth solid surface. The expansion creates a lace-like pattern of particle clusters separated by particle-free regions. Both the expansion and the development of the spatial inhomogeneity are dominated by particle inertia, therefore robust and insensitive to details of the surface wetting, capillarity and viscous drag.

physics.flu-dyn↗