Under certain conditions, RNA repeat sequences phase separate, yielding protein-free biomolecular condensates. Importantly, have also been implicated in neurological disorders, such as Huntington's disease. Thus, mapping to their behavior, functions, and dysfunctions is an active area of research. However, despite several advances, it remains challenging characterize the behavior at a submolecular resolution. Here, we implemented residue-resolution coarse-grained model LAMMPS─that...

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

Magnesium ion dependent RNA liquid-liquid phase separation with lower critical solution temperatures is driven by the phosphate backbone and modulated solvation property of nucleobases. Here, we report a key role 2'-OH group ribose sugar in condensation presence divalent cations. We show that 2'-deoxyribose inhibits nucleic acid suppresses intra-condensate networking transition, known as percolation, underlies condensate dynamical arrest. All-atom simulations reveal increased compaction...

Biomolecular condensates are typically maintained by networks of molecular interactions, with canonical examples including those formed prion-like low complexity domains (LCDs) proteins. Single-component LCD have been predicted to exhibit small-world network topologies and spatial inhomogeneities in protein compaction. Here, we systematically characterize underlying investigate the relationship between single molecule properties topologies. We employ a chemically specific coarse-grained...

<title>Abstract</title> Magnesium ion-dependent RNA liquid-liquid phase separation with lower critical solution temperatures is driven by the phosphate backbone and modulated solvation property of nucleobases. Here, we report a key role 2’-OH group ribose sugar in condensation presence divalent cations. We show that 2’-deoxyribose inhibits nucleic acid suppresses intra-condensate networking transition, known as percolation, underlies condensate dynamical arrest. All-atom simulations reveal...

Cells must limit RNA-RNA interactions to avoid irreversible RNA entanglement. may prevent deleterious by genome organization complementarity however, viruses generate long, perfectly complementary antisense during replication. How do viral RNAs entanglement? One possibility is sequestration into biomolecular condensates. To test this, we reconstituted critical SARS-CoV-2 in Nucleocapsid We observed that with low propensity resulted more round, liquid-like condensates while those high...

Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we systematically investigate the effect stiffness on ground-state conformations generic coarse-grained model for polymers. This possesses multiple transition barriers. Therefore, employ advanced generalized-ensemble Monte Carlo methods to search lowest-energy...

Cells must limit RNA-RNA interactions to avoid irreversible RNA entanglement. may prevent deleterious by genome organization complementarity however, viruses generate long, perfectly complementary antisense during replication. How do viral RNAs entanglement? One possibility is sequestration into biomolecular condensates. To test this, we reconstituted critical SARS-CoV-2 in Nucleocapsid We observed that with low propensity resulted more round, liquid-like condensates while those high...

We employ the recently introduced generalized microcanonical inflection point method for statistical analysis of phase transitions in flexible and semiflexible polymers study impact bending stiffness upon character order between random-coil, globules, pseudocrystalline conformations. The high-accuracy estimates entropy its derivatives required this were obtained by extensive replica-exchange Monte Carlo simulations. observe that transition behavior into compact phases changes qualitatively...

Biomolecular condensates are complex droplets comprising many different types of 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 such opposing interactions suppress coarsening so equal size coexist at equilibrium. This control depends strongly on the charge asymmetry between constituents, while...

Canonical analysis has long been the primary 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 only enables systematic identification and classification transitions systems any size, but it can also distinguish that standard canonical cannot resolve. By applying to a generic coarse-grained model semiflexible polymers, we identify...

Under certain conditions, RNA repeat sequences phase separate yielding protein-free biomolecular condensates. Importantly, have also been implicated in neurological disorders, such as Huntington’s Disease. Thus, mapping to their behavior, functions, and dysfunctions is an active area of research. However, despite several advances, it remains challenging characterize the behavior at submolecular resolution. Here, we implemented a residue-resolution coarse-grained model LAMMPS – that...