arXiv subjects

Ryota Takaki

Publications and source records attributed to Ryota Takaki.

8 recordsLinked to original sources

arXiv2026

Fluctuation-Response Theory of Non-Equilibrium Complex Fluids

A fundamental challenge in soft matter physics is to describe materials, such as the living cytoplasm and tissues, that are simultaneously active, chemically driven, and exhibit long-lasting memory of mechanical stresses. Here, we construct a generalized hydrodynamic framework at finite wavevectors and frequencies that is applicable to non-equilibrium fluids with memory. By leveraging stationary correlation identities, we derive a generalized linear response theory for non-equilibrium steady states. This framework serves as a formal extension of Onsager's regression hypothesis beyond thermal equilibrium. Our approach provides a direct pathway to derive transport coefficients from steady-state fluctuations without the traditional Mori-Zwanzig projection-operator formalism, generalizing the Green-Kubo relations to non-equilibrium systems. As a corollary, we derive two model-free variants of the non-equilibrium fluctuation-response relation for non-Markovian dynamics. These generalized relations explicitly capture the non-equilibrium circulating currents--an out-of-equilibrium signature that is invisible to conventional scalar formulations or frameworks that treat degrees of freedom independently. Applying our theory to chemically driven active fluids reveals the emergence of active viscoelastic memory, wherein chemical reaction cycles dynamically renormalize the macroscopic viscous response. Strikingly, this active memory can induce negative storage and loss moduli at finite frequencies, a behavior absent in ordinary viscoelastic fluids. Our first-principles framework rigorously extends linear rheology to non-equilibrium systems and provides a foundation for understanding non-Markovian dynamics across a broad range of biological and synthetic active matter.

cond-mat.soft↗

arXiv2026

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.

cond-mat.soft↗

arXiv2025

Active Loop Extrusion guides DNA-Protein Condensation

The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics simulation and theory we investigate this interplay. Our findings reveal that loop extrusion can enhance the dynamics of condensation and promotes coalescence and ripening of condensates. Further, the DNA loop enables condensate formation under DNA tension and position condensates. The concurrent presence of loop extrusion and condensate formation results in the formation of distinct domains similar to TADs, an outcome not achieved by either process alone.

physics.bio-ph↗

arXiv2024

Sequence Complexity and Monomer Rigidity Control the Morphologies and Aging Dynamics of Protein Aggregates

Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases. Simulations using a minimal model show that such structures are encoded in the sequence complexity and bending rigidity of the monomers. The low-complexity flexible sequences form liquid droplets, whose relaxation dynamics are ergodic. In contrast, rigid low and high-complexity sequences, which form ordered nematic fibril-like structures and amorphous aggregates, exhibit heterogenous, non-ergodic dynamics. The relaxation times under these conditions increase as the waiting time increases, which is a signature of aging. The implications of our findings for aging in intrinsically disordered proteins and repeat RNA sequences are outlined.

physics.bio-ph↗

arXiv2023

Theory of rheology and aging of protein condensates

Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that coexist in a surrounding fluid. Recently, quantitative studies on the material properties of biological condensates have become available, revealing complex material properties. In vitro experiments have shown that protein condensates exhibit time dependent material properties, similar to aging in glasses. To understand this phenomenon from a theoretical perspective, we develop a rheological model based on the physical picture of protein diffusion and stochastic binding inside condensates. The complex nature of protein interactions is captured by a distribution of binding energies, incorporated in a trap model originally developed to study glass transitions. Our model can describe diffusion of constituent particles, as well as the material response to time-dependent forces, and it recapitulates the age dependent relaxation time of Maxwell glass observed experimentally both in active and passive rheology. We derive a generalized fluctuation-response relations of our model in which the relaxation function does not obey time translation invariance. Our study sheds light on the complex material properties of biological condensates and provides a theoretical framework for understanding their aging behavior.

cond-mat.soft↗

arXiv2022

Information flow, Gating, and Energetics in dimeric molecular motors

Molecular motors belonging to the kinesin and myosin super family hydrolyze ATP by cycling through a sequence of chemical states. These cytoplasmic motors are dimers made up of two linked identical monomeric globular proteins. Fueled by the free energy generated by ATP hydrolysis, the motors walk on polar tracks (microtubule or filamentous actin) processively, which means that only one head detaches and executes a mechanical step while the other stays bound to the track. Thus, the one motor head must regulate chemical state of the other, referred to as "gating", a concept that is not fully understood. Inspired by experiments, showing that only a fraction of the energy from ATP hydrolysis is used to advance the kinesin motors against load, we demonstrate that additional energy is used for coordinating the chemical cycles of the two heads in the dimer - a feature that characterizes gating. To this end, we develop a general framework based on information theory and stochastic thermodynamics, and establish that gating could be quantified in terms of information flow between the motor heads. Applications of the theory to kinesin-1 and Myosin V show that information flow occurs, with positive cooperativity, at external resistive loads that are less than a critical value, $F_c$. When force exceeds $F_c$, effective information flow ceases. Interestingly, $F_c$, which is independent of the input energy generated through ATP hydrolysis, coincides with force at which the probability of backward steps starts to increase. Our findings suggest that transport efficiency is optimal only at forces less than $F_c$, which implies that these motors must operate at low loads under $\textit{in vivo}$ conditions.

physics.bio-ph↗

arXiv2021

Theory and Simulations of condensin mediated loop extrusion in DNA

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE) and measurements using magnetic tweezer experiments, we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open to closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over $\sim$ 50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.

cond-mat.soft↗

arXiv2019

How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics

Dimeric molecular motors walk on polar tracks by binding and hydrolyzing one ATP per step. Despite tremendous progress, the waiting state for ATP binding in the well-studied kinesin that walks on microtubule (MT), remains controversial. One experiment suggests that in the waiting state both heads are bound to the MT, while the other shows that ATP binds to the leading head after the partner head detaches. To discriminate between these two scenarios, we developed a theory to calculate accurately several experimentally measurable quantities as a function of ATP concentration and resistive force. In particular, we predict that measurement of the randomness parameter could discriminate between the two scenarios for the waiting state of kinesin, thereby resolving this standing controversy.

q-bio.SC↗