📰 "Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds"
https://arxiv.org/abs/2605.04482 #Physics.Bio-Ph
#Cond-Mat.Soft
#Q-Bio.Bm
#Mitosis #Cell
Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds
Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that condensin, a member of the SMC family involved in mitosis, takes occasional backward steps, thus coughing up the gains in the length of the extruded loop. To reveal the mechanism of the forward and backward steps simultaneously, we developed a theory using the stochastic kinetic model and the scrunching mechanism for LE. The calculations quantitatively account for the measured force-dependent step size and dwell time distributions in both the directions. By postulating the existence of an intermediate state in the ATP-driven cycle that is poised to take a forward or a backward step, we predict that its lifetime increases as the external mechanical force increases till a critical value and subsequently decreases at higher forces. The surprising finding of lifetime increase in an active motor, at sub-piconewton forces, is the characteristic of catch bonds, known in force-induced rupture of several passive protein complexes. The identification of catch bond-like states in condensin not only expands our understanding of LE but also highlights the significance of mechanical forces in regulating genome organization.
📰 "Nonreciprocity-enriched steady phases in open quantum systems"
https://arxiv.org/abs/2605.00101 #Cond-Mat.Quant-Gas
#Cond-Mat.Str-El
#Physics.Optics
#Quant-Ph
#Dynamics #Matrix
Nonreciprocity-enriched steady phases in open quantum systems
Nonreciprocity can profoundly alter the spectra and dynamics of open quantum systems, yet its impact on the long-time steady-state phases of matter has remained largely unexplored. Here we show that the interplay of nonreciprocity, symmetry defects, and spatial boundaries can generate phases beyond the standard spontaneous-symmetry-breaking paradigm. We demonstrate this mechanism by showing that sufficiently strong nonreciprocity turns boundaries into sources and drains of symmetry defects, while simultaneously endowing these defects with chiral dynamics in the bulk. As a result, the conventional uniform symmetry-broken state gives way to a domain-wall traveling-wave phase, in which symmetry defects form a persistent chiral wave. We showcase this mechanism in a bosonic model with \(Z_{2}\) symmetry, where periodic boundary conditions support only the conventional symmetric and symmetry-broken phases, whereas open boundary conditions allow the traveling-wave phase. We further show that even in the absence of symmetry breaking, the steady state can exhibit anomalous chiral relaxation: owing to the non-Hermitian skin effect in the stability matrix, local fluctuations are chirally amplified as they approach a boundary, where they eventually decay. Combining mean-field theory with truncated Wigner simulations, we characterize these phases, analyze the order parameter and Goldstone-mode fluctuations of the traveling-wave phase, and confirm its existence in three spatial dimensions.
📰 "Implementation of the hybrid exchange-correlation functionals in the SIESTA code"
https://arxiv.org/abs/2604.26108 #Cond-Mat.Mtrl-Sci
#Physics.Comp-Ph
#Matrix #Forces
Implementation of the hybrid exchange-correlation functionals in the SIESTA code
We present an efficient and accurate implementation of hybrid exchange-correlation (XC) functionals in the SIESTA code, enabling large-scale simulations based on Hartree-Fock-type exact exchange combined with strictly localized numerical atomic orbitals (NAOs). Our approach exploits a fitted representation of the NAOs in terms of Gaussian-type orbitals (GTOs), which allows for the analytical evaluation of four-center electron repulsion integrals (ERIs) via the LIBINT library. This framework is seamlessly integrated with SIESTA's real-space grid and sparse-matrix infrastructure, and is combined with multiple screening techniques to control the computational complexity. We also introduce a fully analytical formulation of hybrid-functional forces and a dynamic parallel distribution scheme that ensures excellent scalability. We validate our implementation through benchmark calculations on a broad set of systems (including semiconductors, insulators, and two-dimensional materials) and demonstrate that the HSE06 functional significantly improves the prediction of band gaps compared to PBE, in close agreement with G0W0 and experimental data. We analyze in detail the trade-offs between accuracy and computational efficiency as a function of the number of Gaussians, basis set range, and integral screening thresholds. Our results confirm that hybrid functional calculations in SIESTA are now feasible for large extended systems, making accurate first-principles predictions of electronic and structural properties accessible at scale.
📰 "Randomised measurements of a disorder-induced entanglement transition in a neutral atom quantum processor"
https://arxiv.org/abs/2604.24854 #Cond-Mat.Stat-Mech
#Physics.Atom-Ph
#Quant-Ph
#Dynamics #Matrix
Randomised measurements of a disorder-induced entanglement transition in a neutral atom quantum processor
The development and spread of entanglement in complex quantum systems is central to exploring many-body phenomena out of equilibrium. Measuring entanglement dynamics can shed light on information scrambling and thermalisation, namely on transitions from many-body quantum chaos to localisation in disordered, interacting systems. In quantum computing systems, entanglement entropy and other nonlinear functions of the density matrix have been recently measured, in particular by using the randomised measurement toolbox. However, it is difficult to implement the required arbitrary unitary rotations on specific subsystems without universal local control. Here we devise and demonstrate the measurement of entanglement entropy in a programmable analogue quantum simulator using a randomised measurement protocol that leverages local energy tuning together with a global field to bypass the need for local gate control. We implement this on a commercially available neutral-atom quantum simulator, QuEra's Aquila, and use it to show how programmable disorder in the local Hamiltonian parameters leads to a transition from chaotic to localised entanglement dynamics. Given current decoherence times, we clearly resolve disorder-specific, time-dependent entanglement spreading in small systems. Our work extends the utility of programmable analogue quantum simulators, and opens further opportunities for wider randomised measurement toolboxes in a range of other analogue systems.
📰 "Statistical mechanics in continuous space with tensor network methods"
https://arxiv.org/abs/2604.25060 #Cond-Mat.Stat-Mech
#Physics.Chem-Ph
#Mechanics #Cell
Statistical mechanics in continuous space with tensor network methods
Tensor network (TN) methods are well established for computing partition functions in statistical mechanics, though this use has traditionally been limited to lattice models. We extend the scope of TN methodology to interacting particle systems in continuous space. Through a real-space discretization combined with a cell-based coarse-graining scheme, we formulate an effective lattice model that explicitly preserves spatial locality. The partition function of this model is represented as a TN, and the thermodynamic quantities are computed via boundary contraction. We apply this framework to the two-dimensional hard-disk problem and demonstrate the strengths of the TN formulation compared to existing Monte Carlo simulations.
📰 "Maximum-Entropy Model of Colored Noise in Superdiffusive Axonal Growth"
https://arxiv.org/abs/2506.11272 #Physics.Bio-Ph
#Cond-Mat.Soft
#Q-Bio.Qm
#Adhesion #Q-Bio.Cb
#Nlin.Ao
#Force
Maximum-Entropy Model of Colored Noise in Superdiffusive Axonal Growth
We develop a coarse-grained stochastic theory for axonal growth on micropatterned substrates using the Shannon--Jaynes maximum entropy principle. Starting from a Langevin description of growth cone motion, we infer the effective distribution of traction force relaxation rates from experimentally motivated constraints rather than postulating the colored noise directly. The resulting relaxation rate distribution generates a stationary colored acceleration process with power-law temporal correlations and yields analytical predictions for the axonal mean squared displacement and velocity autocorrelation. The long-time behavior is controlled by the slow-relaxation part of the inferred distribution, corresponding physically to broadly distributed clutch or adhesion engagement times. For biologically relevant parameters, the model predicts a negative correlation exponent $α=-1/2$. This prediction is in close quantitative agreement with measurements on cortical neurons cultured on micropatterned poly-D-lysine-coated PDMS substrates, which are well described by $α\simeq -0.6$ and exhibit superdiffusive mean squared displacement scaling with exponent $1.4$. The same framework accounts for the crossover from early diffusive behavior to long-time anomalous growth and for the corresponding power law decay of the velocity autocorrelation. These results show how entropy-constrained active fluctuations can connect microscopic force generation processes to emergent growth laws in neuronal systems and, more broadly, in active matter.
📰 "Synchronized molecular dynamics method for thin-layer flows of complex fluids"
https://arxiv.org/abs/2604.24138 #Physics.Flu-Dyn
#Physics.Comp-Ph
#Cond-Mat.Soft
#Dynamics #Cell
Synchronized molecular dynamics method for thin-layer flows of complex fluids
We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication description. In thin layers, the flow can be decomposed into cross-sectional dynamics that are strongly influenced by interfacial effects, and streamwise transport along the channel. The SMD method exploits this separation of scales by sparsely distributing local MD cells along the channel and synchronizing them through macroscopic conservation laws.
In this framework, the macroscopic continuity equation is enforced by iteratively updating the external forces applied to each MD cell, thereby allowing the cross-sectional velocity profiles and the streamwise pressure distribution to be obtained without prescribing constitutive relations or boundary conditions. The method is validated for pressure-driven and wall-driven flows of Lennard--Jones fluids in a wedge-shaped channel, demonstrating excellent agreement with a modified Reynolds equation that accounts for boundary slip.
The SMD method is further applied to polymeric lubrication flows modeled by the Kremer--Grest chain model. At large pressure differences, the present approach naturally captures pronounced shear-thinning behavior coupled with microscopic polymer conformation dynamics. The results demonstrate that the SMD method provides an efficient and physically consistent framework for the multiscale simulation of complex fluid thin-layer flows.
📰 "A dialog between cell adhesion and topology at the core of morphogenesis"
https://arxiv.org/abs/2602.09867 #Cond-Mat.Stat-Mech
#Cond-Mat.Soft
#Morphogenesis #Q-Bio.To
#Cell
A dialog between cell adhesion and topology at the core of morphogenesis
During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is supported by multiple processes that induce the precise physical deformations required for tissues to ultimately form organs with complex geometries. Among the most active players shaping the morphogenetic path are fine-tuned changes in cell adhesion. We review here recent advances showing that changes on cell adhesion, a local, pair-wise property defined at the cell-cell contact level has important global consequences for embryonic tissue topology, being determinant in defining both the geometric and material properties of early embryo tissues.
📰 "A theory for coexistence and selection of branched actin networks in a shared and finite pool of monomers"
https://arxiv.org/abs/2511.23344 #Physics.Bio-Ph
#Cond-Mat.Soft
#Q-Bio.Sc
#Actin
A theory for coexistence and selection of branched actin networks in a shared and finite pool of monomers
Cellular actin structures are continuously turned over while keeping similar sizes. Since they all compete for a shared pool of actin monomers, the question arises how they can coexist in these dynamic steady states. Recently, the coexistence of branched actin networks with different densities growing in a shared and finite pool of purified proteins has been demonstrated in a biomimetic bead assay. However, theoretical work in the context of organelle size regulation has mainly been focused on linear architectures, such as single filaments and bundles, and thus is not able to explain this observation. Here we show theoretically that the local depletion of actin monomers caused by the growth of a branched network naturally gives rise to a negative feedback loop between network density and growth rate, and that this competition is captured by one central ordinary differential equation. A comprehensive bifurcation analysis shows that the theory leads to well-defined steady states even in the case of multiple networks sharing the same pool of monomers, without any need for specific molecular processes. Under increasing competition strength, coexistence is replaced by selection. We also show that our theory is in excellent agreement with spatiotemporal simulations, implemented in a finite element framework, and that local depletion even occurs in the presence of a large pool of non-polymerizable actin. In summary, our work suggests that local monomer depletion is the decisive and universal factor controlling growth of branched actin networks.
📰 "Dynamic Moir\'e Potentials and Robust Wigner Crystallization in Large-Scale Twisted Transition Metal Dichalcogenides"
https://arxiv.org/abs/2604.22343 #Cond-Mat.Mtrl-Sci
#Physics.Chem-Ph
#Physics.Comp-Ph
#Cond-Mat.Str-El
#Dynamics #Matrix
Dynamic Moiré Potentials and Robust Wigner Crystallization in Large-Scale Twisted Transition Metal Dichalcogenides
Understanding the dynamical evolution of large-scale moiré systems is crucial for connecting theoretical predictions with experimental observations. Here we develop a machine-learning-based workflow, integrating DeePMD and DeepH frameworks with first-principles calculations, to efficiently investigate time-dependent structural and electronic responses in twisted bilayer transition metal dichalcogenides (TMDs) with experimentally relevant moiré supercells containing over 3000 atoms. Using $\mathrm{WS_2}$ as a representative system, we show that low-temperature lattice vibrations and relaxation deepen the moiré potential wells, narrow the lowest conduction band, and facilitate the formation of strongly localized electronic states. Based on DFT-derived moiré potentials that incorporate these dynamical effects, density-matrix-renormalization-group (DMRG) simulations reveal robust Wigner crystallization and a kagomé-patterned three-electron state, consistent with recent experimental observations. Our workflow provides a practical route for exploring large moiré supercells beyond static configurations and offers new insight into the interplay between lattice dynamics, electronic localization, and emergent correlated states in twisted two-dimensional materials.
Rxiv mechanobio
Rxiv cytoskeleton