Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

J Iwahara, AB Kolomeisky - Biophysical chemistry, 2021 - Elsevier
To perform their functions, transcription factors and DNA-repair/modifying enzymes
randomly search DNA in order to locate their specific targets on DNA. Discrete-state …

How pioneer transcription factors search for target sites on nucleosomal DNA

C Felipe, J Shin, AB Kolomeisky - The Journal of Physical …, 2022 - ACS Publications
All major biological processes start after protein molecules known as transcription factors
detect specific regulatory sequences on DNA and initiate genetic expression by associating …

Dynamical phase transition in the first-passage probability of a Brownian motion

B Besga, F Faisant, A Petrosyan, S Ciliberto… - Physical Review E, 2021 - APS
We study the first-passage time distribution (FPTD) F (tf| x 0, L) for a freely diffusing particle
starting at x 0 in one dimension, to a target located at L, averaged over the initial position x 0 …

Particle-environment interactions in arbitrary dimensions: A unifying analytic framework to model diffusion with inert spatial heterogeneities

S Sarvaharman, L Giuggioli - Physical Review Research, 2023 - APS
Inert interactions between randomly moving entities and spatial disorder play a crucial role
in quantifying the diffusive properties of a system, with examples ranging from molecules …

Self-assembly synthesis of diorganotin complexes based on arylformylhydrazone possessing ONO donor set: anticancer activity and mechanism

W Jiang, Z Zhang, P Ni, Y Tan - Metallomics, 2022 - academic.oup.com
Fourteen new organotin (IV) complexes were successfully synthesized and characterized by
elemental analyses, Fourier transform infrared spectroscopy (FT-IR), multinuclear (1H, 13C …

DNA looping and DNA conformational fluctuations can accelerate protein target search

C Felipe, J Shin, AB Kolomeisky - The Journal of Physical …, 2021 - ACS Publications
Protein searching and binding to specific sites on DNA is a fundamentally important process
that marks the beginning of all major cellular transformations. While the dynamics of protein …

Closed-form solutions to the dynamics of confined biased lattice random walks in arbitrary dimensions

S Sarvaharman, L Giuggioli - Physical Review E, 2020 - APS
Biased lattice random walks (BLRW) are used to model random motion with drift in a variety
of empirical situations in engineering and natural systems such as phototaxis, chemotaxis …

Synthesis, crystal structures, and biological activity of aroylhydrazone di-m-chlorobenzyltin complexes

W Jiang, P Zhou, L Chen, W Fu, Y Tan - JBIC Journal of Biological …, 2024 - Springer
Six aroylhydrazone di-m-chlorobenzyltin complexes {[X-C6H4 (O) C= N–N= C (Me)
COO](MeOH)(m-Cl-C6H4CH2) 2Sn} 2 (X= p-Me-(1), p-MeO-(2), p–t-Bu-(3), p-NO2-(4), p-OH …

Survival probability and position distribution of a run and tumble particle in potential with an absorbing boundary

SK Nath, S Sabhapandit - arXiv preprint arXiv:2405.18988, 2024 - arxiv.org
We study the late time exponential decay of the survival probability $ S_\pm (t, a| x_0)\sim
e^{-\theta (a) t} $, of a one-dimensional run and tumble particle starting from $ x_0< a $ with …

[PDF][PDF] Quantifying stochastic search: a unifying approach via lattice random walks

S Sarvaharman - 2023 - research-information.bris.ac.uk
Stochastic search plays a crucial role in many natural and artificial phenomena across
scales and disciplines. Examples range from the spread of misinformation in online social …