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Yury Polyachenko

Publications and source records attributed to Yury Polyachenko.

2 recordsLinked to original sources

Co-condensation and multivalency enable acetylation-sensitive, concentration-robust assembly of BRD4 condensates

Biomolecular condensates must assemble at specific locations and times inside living cells to perform their biological functions. However, it remains unclear how condensate formation achieves high spatiotemporal precision, responding sensitively to local chemical modifications while remaining robust to fluctuations in protein concentration. Here we study chromatin-associated BRD4 condensates to identify a physical mechanism that enables this combination of sensitivity and robustness. Using an ultra-coarse-grained molecular-dynamics model, we show that co-condensation of BRD4 with chromatin enables rapid assembly below the bulk coexistence concentration, thereby suppressing off-chromatin condensation and enhancing spatial selectivity. Multivalent binding between BRD4 and acetylated histone tails sharpens the dependence of co-condensation on acetylation density through combinatorial effects, increasing contrast between highly acetylated regions and weakly acetylated background chromatin. This mechanism explains how co-condensation and multivalent binding jointly enable sensitive yet robust spatiotemporal targeting by chromatin-associated condensates.

physics.bio-ph

Transition Metal Dichalcogenide MoS${}_2$: oxygen and fluorine functionalization for selective plasma processing

Low-temperature plasma processing is a promising technique for tailoring transition metal dichalcogenides (TMDs). For chalcogen substitution processing, a key challenge is to identify the ion energy window that enables selective chalcogen removal while preserving the metal lattice. Using ab-initio molecular dynamics (AIMD), we demonstrate that oxygen and fluorine functionalization widen the processing window by significantly lowering the sulfur sputtering energy threshold ($E_{\text{sputt,S}}$) of MoS${}_2$ from $\sim 30$ eV to $\sim 10$ eV via formation of sputtering products such as SO${}_2$ and SF${}_n$. Additionally, we show that experimentally relevant cryogenic temperatures strongly affect $E_{\text{sputt,S}}$. The dependence is confirmed via AIMD and also predicted by a mechanistic parameter-free theory, suggesting that $E_{\text{sputt}}(T)$ generalizes to other TMDs, functionalization, and surface impacts in general. Our results highlight oxygen/fluorine functionalization, ionic impact angle, and material temperature to be key control parameters for selective, damage-controlled chalcogen removal in TMD processing.

cond-mat.mtrl-sci