arXiv subjects

Heeyuen Koh

Publications and source records attributed to Heeyuen Koh.

5 recordsLinked to original sources

arXiv2026

Bi-Hamiltonian in Semiflexible Polymer as Strongly Coupled System

Quantifying the interaction between a system of interest and its ambient conditions, the memory effect links the states of two distinct Hamiltonians: one for the target system and one for the environment. In this paper, we propose the diffusion process derived from the Smoluchowski equation that can derive the evolution process described by the memory effect integration in a non Markovian regime. The Smoluchowski picture, within the framework of stochastic thermodynamics, justifies a diffusion process incorporated into the equations of motion, and the result of the derivation enables a coarse-grained molecular dynamics simulation with the modified equation of motion to reproduce attenuation from collisions between single walled carbon nanotubes (SWCNTs) under far from equilibrium conditions. The results of the numerical experiments on the collision confirm that heat diffusion compensates for the correlated momentum arising from the memory effect between the two Hamiltonians in both equilibrium and far from equilibrium states.

physics.comp-ph↗

arXiv2026

Geometrically Given Constraints in Double Helical Strand

The versatility of helical structures in nature, such as DNA strands, tendrils, actin filaments, and more, in similar shapes across various life forms and molecular systems, indicates their readiness to manifest useful functionality that can conserve, spread, and assemble. However, it has not been fully explained why being in such structural forms is beneficial for developing their functionalities, which is crucial for designing an artificial system with helicity or molecular shape. For instance, the energetics of the bend-twist coupling of DNA strands has been studied and evaluated in various simulations and theoretical works. Yet it has not fully elucidated the structural features of the DNA strand, such as the roles of the major and minor grooves, which are related to its proneness to bend-twist coupling and associated dynamics. In this paper, the geometrical constraints from helicity yield an ansatz for the bend-twist coupling in the Darboux frame and the Frenet-Serret formula, addressing the conditional characteristics of deformation in a curved strand during wrapping around a simplified core structure, which is the quintessential step in DNA packaging. The constraints derived from differential geometry for B-DNA strands specify the bend-twist ratio required to form a superhelix in an open-ended strand, thereby offering free energy affinity preferences along sequence-dependent elasticity. The result of the ansatz shows conditional kurtosis, which is the deformation perpendicular to the plane defined by the curvature of the strand, determining the height of the superhelix and the role of the major-minor groove in forming these structural characteristics of the curved strand. Coarse-grained molecular dynamics simulation validates the derivation and sequence-dependent preferences during the wrapping process.

nlin.AO↗

arXiv2026

Toda lattice formed in nonequilibrium steady states of SWCNT

Toda lattice or FPUT chain-like dynamics have been regarded as the prerequisite condition to explain the length dependency of high thermal conductivity of low-dimensional systems at the nanoscale. In this paper, a hypothetical condition is introduced that establishes a theoretical connection between the thermal conductivity of a nanoscale low-dimensional system in nonequilibrium steady states(NESS) and the canonical motion of the equation in the Toda lattice in equilibrium. The hypothesis relies on a numerically driven coarse grained molecular dynamics(CGMD) system acquired from the trajectory data of nonequilibrium molecular dynamics(NEMD) simulation. It models the macroscopic motion from longitudinal and flexural modulation observed in NEMD as a separate Hamiltonian in CGMD with a perturbation term governed by an overdamping process, which is assumed to be dominant during heat transfer. The Smoluchowski equation for the perturbation, which is derived from the cross correlated states between two degrees of freedom, suggests that the potential energy function induced from NESS is identical to that of the Toda Lattice under the specific condition in the partition function for coarse grained particles. The restrictions derived from the model are well confirmed by the data from the numerically driven coarse grained model.

nlin.CD↗

arXiv2023

Continuous Function Structured in Multilayer Perceptron for Global Optimization

The gradient information of multilayer perceptron with a linear neuron is modified with functional derivative for the global minimum search benchmarking problems. From this approach, we show that the landscape of the gradient derived from given continuous function using functional derivative can be the MLP-like form with ax+b neurons. In this extent, the suggested algorithm improves the availability of the optimization process to deal all the parameters in the problem set simultaneously. The functionality of this method could be improved through intentionally designed convex function with Kullack-Liebler divergence applied to cost value as well.

cs.LG↗

arXiv2020

Heat diffusion related damping process in highly precise coarse-grained model for SWCNT's nonlinearity

Second sound and heat diffusion in single-walled carbon nanotubes (SWCNT) is well-known phenomena which is related to the high thermal conductivity of this material. In this paper, we have shown that the heat diffusion along the tube axis affects the macroscopic motion of SWCNT and adapting this phenomena to coarse-grained model can improve the precision of the coarse-grained molecular dynamics (CGMD) exceptionally. The nonlinear macroscopic motion of SWCNT in the free thermal vibration condition in adiabatic environment is demonstrated in the most simplified version of CG modeling as maintaining finite temperature and total energy with suggested dissipation process derived from internal heat diffusion. The internal heat diffusion related to the cross correlated momentum from different potential energy functions is considered, and it can reproduce the nonlinear dynamic nature of SWCNTs without external thermostatting in CG model. Memory effect and thermostat with random noise distribution are not included, and the effect of heat diffusion on memory effect is reviewed through Mori-Zwanzig formalism. This diffusion shows perfect syncronization of the motion between that of CGMD and MD simulation, which is started with initial conditions from the molecular dynamics (MD) simulation. The heat diffusion related to this process has shown the same dispersive characteristics to second wave in SWCNT. This replication with good precision indicates that the internal heat diffusion process is the essential cause of the nonlinearity of the tube. The nonlinear dynamic characteristics from the various scale of simple beads systems are examined with expanding its time step and node length simultaneously.

cond-mat.soft↗