arXiv subjects

Akira Kakugo

Publications and source records attributed to Akira Kakugo.

4 recordsLinked to original sources

arXiv2026

Semantic analysis of behavior in a DNA-functionalized molecular swarm

In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm where the individuals are cytoskeletal filaments (called microtubules) propelled by surface-adhered kinesin motors, with the addition of DNA functionalization for further control. We extend a microtubule model with that additional interaction and show that the extracted semantic atoms from simulation results match the expected behaviors. Moreover, the decomposition of each frame in the simulations accurately describes the expected impact of the external control values. Those results provide relevant leads towards the explainability of simulated experiments, making them more reliable for designing and optimizing in-vitro systems.

cs.RO↗

arXiv2026

Self-Viscophoresis: Autonomous Motion by Biasing Thermal Fluctuations via Self-Generated Viscosity Asymmetry

Microscale transport often relies on ubiquitous yet intrinsically random thermal fluctuations. Understanding how such fluctuations can be biased into directed motion has long been a central theme of nonequilibrium physics. Here, we introduce self-viscophoresis, a mechanism of autonomous motion based on the rectification of thermal fluctuations in a self-generated nonequilibrium viscosity field. Asymmetric colloidal particles dispersed in a thermoresponsive polymer solution induce local heating under uniform illumination, producing a spatially asymmetric viscosity profile around the particle and resulting in persistent directed motion. To elucidate the physical origin of this behavior, we develop a minimal Langevin model coupling isotropic thermal fluctuations to a dynamically updating temperature-viscosity field. The model shows that viscosity asymmetry anisotropically damps stochastic dynamics, effectively biasing thermal fluctuations into a net drift. It thus reproduces the observed directed motion without invoking deterministic propulsion terms associated with effective potentials or environmental fluid flows. Our results distinguish self-viscophoresis from conventional self-propulsion mechanisms and establish it as a general framework enabling reversible control of both the direction and dimensionality of motion.

cond-mat.soft↗

arXiv2022

Collision-induced torque mediates transition of chiral dynamic patterns formed by active particles

It is still challenging to control dynamic self-organization patterns of self-propelled particles. Although varieties of patterns associated with chirality have been observed, essential control factors determining patterns remain unclear. Here, we explore numerically how torque upon particle collision affects dynamic self-organization. Based on the particle-based model with both collision-induced torque and torque in self-propulsion, we find that introducing collision-induced torque turns homogeneous bi-polar orientation templated by bi-directional alignment into rotating mono-polar flocks.

cond-mat.soft↗

arXiv2021

Tailoring collective motion of kinesin-driven microtubules via topographic landscapes

Biomolecular motor proteins that generate forces by consuming chemical energy obtained from ATP hydrolysis are pivotal for organizing broad cytoskeletal structures in living cells. The control of such cytoskeletal structures benefits programmable protein patterning; however, our current knowledge is limited owing to the underdevelopment of an engineering approach for controlling pattern formation. Here, we demonstrate the tailoring of assembled patterns of microtubules (MTs) driven by kinesin motors by designing the boundary shape in fabricated microwells. We found an MT bundle structure along the microwell wall and a bridging structure perpendicular to the wall. Corroborated by the theory of self-propelled rods, we further showed that the alignment of MTs defined by the boundary shape determined the transition of the assembled patterns, providing a blueprint to reconstruct bridge structures in microchannels. Our findings provide a geometric rule to tailor the self-organization of cytoskeletons and motor proteins for nanotechnological applications.

cond-mat.soft↗