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Combining experiments on active colloids, whose propulsion velocity can be controlled via a feedback loop, and theory of active Brownian motion, we explore the dynamics of an overdamped active particle with a motility that depends…
In online video platforms, accurate watch time prediction has become a fundamental and challenging problem in video recommendation. Previous research has revealed that the accuracy of watch time prediction highly depends on both the…
Particle-laden turbulence involves complex interactions between the dispersed and continuous phases. Given that particles can exhibit a wide range of properties, such as varying density, size, and shape, their interplay with the flow can…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
The rotational Brownian motion of colloidal spheres in dense suspensions reflects local hydrodynamics and friction, both key to non-linear rheological phenomena such as shear-thickening and jamming, and transport in crowded environments,…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
In nanoscale space and pico- to nanoseconds enormous physical, chemical and biological processes take place, while the motions of involved particles/molecules under thermal fluctuations are usually analyzed using the conventional theory of…
We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…
Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
We introduce and study a model in one dimension of $N$ run-and-tumble particles (RTP) which repel each other logarithmically in the presence of an external quadratic potential. This is an "active'' version of the well-known Dyson Brownian…
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ…
We study the dynamical phase transitions (DPTs) appearing for a single Brownian particle without drift. We first explore how first-order DPTs in large deviations can be found even for a single Brownian particle without any force upon…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
DNA translocation through nanopores is one of the most promising strategies for the next-generation sequencing technologies. Most part of experimental and numerical works has focused on polymer translocation biased by electrophoresis, where…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
Gene transcription by a RNA Polymerase (RNAP) enzyme requires that double-stranded DNA be locally and transiently opened, which results in an increase of DNA supercoiling downstream of the RNAP and a decrease of supercoiling upstream of it.…
In this article we present methods for measuring hindered Brownian motion in the confinement of complex 3D geometries using digital video microscopy. Here we discuss essential features of automated 3D particle tracking as well as diffusion…
The methods of Nuclear Magnetic Resonance belong to the best developed and often used tools for studying random motion of particles in different systems, including soft biological tissues. In the long-time limit the current mathematical…
We derive the quantum thermodynamics of quantum Brownian motion from the exact solution of its reduced density matrix. We start from the total equilibrium thermal state between the Brownian particle and its reservoir, and solve analytically…