arXiv subjects

Dilimulati Aierken

Publications and source records attributed to Dilimulati Aierken.

6 recordsLinked to original sources

arXiv2026

Roadmap for Condensates in Cell Biology

Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants, clarifies key concepts for researchers, funding bodies, and journals. After unifying terminology that often separates disciplines, we outline the core physics of condensate formation, review their biological roles, and identify outstanding challenges in nonequilibrium theory, multiscale simulation, and quantitative in-cell measurements. We close with a forward-looking outlook to guide coordinated efforts toward predictive, experimentally anchored understanding and control of biomolecular condensates.

physics.bio-ph↗

arXiv2025

Condensate Size Control by Net Charge

Biomolecular condensates are complex droplets comprising diverse molecules that interact using various mechanisms. Condensation is often driven by short-ranged attraction, but net charges can also mediate long-ranged repulsion. Using molecular dynamics simulations and an equilibrium field theory, we show that such opposing interactions can suppress coarsening so that many droplets of equal size coexist at equilibrium. This size control depends strongly on the charge asymmetry between constituents, while the strength of the short-ranged attractions has a weak influence. Essentially, droplets expel ions, so they cannot screen electrostatics effectively, implying droplets acquire a net charge and cannot grow indefinitely. Our work reveals how electrostatic effects control droplet size, which is relevant for understanding biomolecular condensates and creating synthetic patterns in chemical engineering.

cond-mat.soft↗

arXiv2023

Secondary-Structure Phase Formation for Semifelxible Polymers by Bifurcation in Hyperphase Space

Canonical analysis has long been the primary analysis method for studies of phase transitions. However, this approach is not sensitive enough if transition signals are too close in temperature space. The recently introduced generalized microcanonical inflection-point analysis method not only enables the systematic identification and classification of transitions in systems of any size, but it can also distinguish transitions that standard canonical analysis cannot resolve. By applying this method to a generic coarse-grained model for semiflexible polymers, we identify a mixed structural phase dominated by secondary structures such as hairpins and loops that originates from a bifurcation in the hyperspace spanned by inverse temperature and bending stiffness. This intermediate phase, which is embraced by the well-known random-coil and toroidal phases, is testimony to the necessity of balancing entropic variability and energetic stability in functional macromolecules under physiological conditions.

cond-mat.soft↗

arXiv2023

Impact of bending stiffness on ground-state conformations for semiflexible polymers

Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we systematically investigate the effect of the bending stiffness on ground-state conformations of a generic coarse-grained model for semiflexible polymers. This model possesses multiple transition barriers. Therefore, we employ advanced generalized-ensemble Monte Carlo methods to search for the lowest-energy conformations. As the formation of distinct versatile ground-state conformations, including compact globules, rod-like bundles, and toroids, strongly depends on the strength of the bending restraint, we also performed a detailed analysis of contact and distance maps.

cond-mat.soft↗

arXiv2023

Stable intermediate phase of secondary structures for semiflexible polymers

Systematic microcanonical inflection-point analysis of precise numerical results obtained in extensive generalized-ensemble Monte Carlo simulations reveals a bifurcation of the coil-globule transition line for polymers with a bending stiffness exceeding a threshold value. The region, enclosed by the toroidal and random-coil phases, is dominated by structures crossing over from hairpins to loops upon lowering the energy. Conventional canonical statistical analysis is not sufficiently sensitive to allow for the identification of these separate phases.

cond-mat.soft↗

arXiv2022

Comparison of Conformational Phase Behavior for Flexible and Semiflexible Polymers

We employ the recently introduced generalized microcanonical inflection point method for the statistical analysis of phase transitions in flexible and semiflexible polymers and study the impact of the bending stiffness upon the character and order of transitions between random-coil, globules, and pseudocrystalline conformations. The high-accuracy estimates of the microcanonical entropy and its derivatives required for this study were obtained by extensive replica-exchange Monte Carlo simulations. We observe that the transition behavior into the compact phases changes qualitatively with increasing bending stiffness. Whereas the $Θ$ collapse transition is less affected, the first-order liquid-solid transition characteristic for flexible polymers ceases to exist once bending effects dominate over attractive monomer-monomer interactions.

cond-mat.soft↗