arXiv subjects

Deniz Mostarac

Publications and source records attributed to Deniz Mostarac.

4 recordsLinked to original sources

arXiv2024

Polymeric Properties of Higher-Order G-Quadruplex Telomeric Structures: Effects of Chemically Inert Crowders

G-quadruplexes are non-canonical DNA structures rather ubiquitous in human genome, which are thought to play a crucial role in the development of 85-90 % of cancers. Here, we present a novel coarse-grained approach in modeling G-quadruplexes which accounts for their structural flexibility. We apply it to study the polymeric properties of G-quadruplex multimers, with and without crowder particles, to mimic in-vivo conditions. We find that, contrary to some suggestions found in the literature, long G-quadruplex multimers are rather flexible polymeric macromolecules, with a local persistence length comparable to monomer size, exhibiting chain stiffness variation profile consistent with a real polymer in good solvent. Moreover, in a crowded environment (up to 10% volume fraction), we report that G-quadruplex multimers exhibit an increased propensity for coiling, with a corresponding decrease in the measured chain stiffness. Accurately accounting for the polymeric properties of G4 multimers is crucial for understanding their interactions with anticancer G4-targeting drugs, thereby significantly enhancing the design and effectiveness of these drugs.

physics.comp-ph↗

arXiv2024

Thermal Stoner-Wohlfarth Model for Magnetodynamics of Single Domain Nanoparticles: Implementation and Validation

We present the thermal Stoner-Wohlfarth (tSW) model and apply it in the context of Molecular Dynamics simulations. The model is validated against an ensemble of immobilized, randomly oriented uniaxial particles (solid superparamagnet) and a classical dilute ferrofluid for different combinations of anisotropy strength and magnetic field/moment coupling, at a fixed temperature. We compare analytical and simulation results to quantify the viability of the tSW model in reproducing the equilibrium (with and without dipole-dipole interactions) and dynamic (without dipole-dipole interactions) properties of magnetic soft matter systems. We show that if the anisotropy of a particle is more than five times higher than the thermal fluctuations, tSW is applicable and efficient. This approach allows one to consider the interplay between N\'eel and Brownian relaxation, often neglected in the fixed point-dipole representation-based magnetic soft matter theoretical investigations.

physics.comp-ph↗

arXiv2020

The impact of magnetic field on the conformations of supracolloidal polymer-like structures with super-paramagnetic monomers

We investigate the properties of magnetic supracolliodal polymers -- magnetic filaments (MFs) -- with super-paramagnetic monomers, with and without Van der Waals (VdW) attraction between them. We employ molecular dynamics (MD) simulations to elucidate the impact of crosslinking mechanism on the structural and magnetic response of MFs to an applied external homogeneous magnetic field. We consider two models: plain crosslinking, which results in a flexible backbone; and constrained crosslinking, which provides significant stiffens against bending. We find that for plain crosslinking, even a slight increase of the central attraction leads to collapsed MF conformations. Structures that initially exhibit spherical symmetry evolve into cylindrically symmetric ones, with growing magnetic field strength. Plain crosslinking also allows for conformational bistability. MFs with constrained crosslinking tend to, instead, unravel in field. In both crosslinking scenarios, central attraction is able to hinder low-field magnetic response of MFs, albeit the bistability of plainly crosslinked MFs manifests itself also in the high-field region.

cond-mat.soft↗

arXiv2019

The influence of crosslinkers and magnetic particle distribution along the filament backbone on the magnetic properties of supracolloidal linear polymer-like chains

Diverse polymer crosslinking techniques allow the synthesis of linear polymer-like structures whose monomers are colloidal particles. In the case where all or part of these colloidal particles are magnetic, one can control the behaviour of these supracolloidal polymers, known as magnetic filaments (MFs), by applied magnetic fields. However, the response of MFs strongly depends on the crosslinking procedure. In the present study, we employ Langevin dynamics simulations to investigate the influence of the type of crosslinking and the distribution of magnetic particles within MFs on their response to an external magnetic field. We found that if the rotation of the dipole moment of particles is not coupled to the backbone of the filament, the impact of the magnetic content is strongly decreased.

cond-mat.soft↗