| 07/2024 Defect interactions in the non-reciprocal Cahn-Hilliard model Navdeep Rana et al. We present a computational study of the pairwise interactions between defects in the recently introduced non-reciprocal Cahn-Hilliard model. The evolution of a defect pair exhibits dependence upon their corresponding topological charges, initial separation, and the non-reciprocity coupling constant $\alpha$. We find that the stability of isolated topologically neutral targets significantly affects … |
| 07/2024 Binding and dimerization control phase separation in a compartment Riccardo Rossetto et al. Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the involved molecules, and their physical interactions. While physical interactions directly affect compartment binding and phase separation, they can also cause … |
| 07/2024 Chemically active droplets David Zwicker et al. These lecture notes describe a basic theory of chemically active droplets, which are droplets kept away from equilibrium by driven chemical reactions. The notes assume a basic familiarity with equilibrium thermodynamics of phase separation, and thus focus on three separate themes, which were discussed in three separate lectures: (i) The kinetics of phase separation, including the early-stage dynam … |
| 07/2024 Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription Michael Chiang et al. Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D chromatin structure in driving transcriptional noise. We study a simple polymer model where proteins – modeling complexes of transcription factors and polymerases – bin … |
| 07/2024 Enabling MPI communication within Numba/LLVM JIT-compiled Python code using numba-mpi v1.0 Kacper Derlatka et al. The numba-mpi package offers access to the Message Passing Interface (MPI) routines from Python code that uses the Numba just-in-time (JIT) compiler. As a result, high-performance and multi-threaded Python code may utilize MPI communication facilities without leaving the JIT-compiled code blocks, which is not possible with the mpi4py package, a higher-level Python interface to MPI. For debugging p … |
| 06/2024 Hydrodynamically consistent many-body Harada-Sasa relation Ramin Golestanian et al. The effect of hydrodynamic interactions on the non-equilibrium stochastic dynamics of particles — arising from the conservation of momentum in the fluid medium — is examined in the context of the relationship between fluctuations, response functions, and the entropy production rate. The multiplicative nature of the hydrodynamic interactions is shown to introduce subtleties that preclude a straig … |
| 05/2024 Nonlinear Response Theory of Molecular Machines Michalis Chatzittofi et al. Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling which arises naturally in these systems reveals a complex interplay between chemical and mechanical degrees of freedom with strong impact on their active mechanis … |
| 05/2024 Mobility-induced kinetic effects in multicomponent mixtures Filipe C. Thewes et al. We give an overview exploring the role of kinetics in multicomponent mixtures. Compared to the most commonly studied binary (single species plus solvent) case, multicomponent fluids show a rich interplay between kinetics and thermodynamics due to the possibility of fractionation, interdiffusion of mixture components and collective motion. This leads to a competition between multiple timescales tha … |
| 05/2024 Chirotactic response of microswimmers in fluids with odd viscosity Yuto Hosaka et al. Odd viscosity is a property of chiral active fluids with broken time-reversal and parity symmetries. We show that the flow of such a fluid around a rotating axisymmetric body is exactly solvable and use this solution to determine the orientational dynamics of surface-driven microswimmers. Swimmers with a force-dipole moment exhibit precession around the axis of the odd viscosity. In addition, push … |
| 05/2024 Scaling of phase count in multicomponent liquids Yicheng Qiang et al. Mixtures with many components can segregate into coexisting phases, e.g., in biological cells and synthetic materials such as metallic glass. The interactions between components dictate what phases form in equilibrium, but quantifying this relationship has proven difficult. We derive scaling relations for the number of coexisting phases in multicomponent liquids with random interactions and compos … |