Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion DOI Creative Commons
Baicheng Mei, Gary S. Grest,

Songyue Liu

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(31)

Опубликована: Июль 23, 2024

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure intermolecular organization. Synthetic rings are hybrid objects with conformations that both ideal random walk globular features, which can serve models of genomic DNA. To date, emphasis has been placed on the effect ring molecular weight unusual behaviors. Here, we combine simulations a microscopic force-level theory build unified understanding for how key aspects dynamics depend different tunable properties including backbone rigidity, monomer concentration, degree traditional entanglement, weight. Our large-scale melts very stiffnesses reveal unanticipated agree well our generalized theory. This includes universal master curve center-of-mass diffusion constants function scaled by chemistry thermodynamic state-dependent critical generalizes concept an entanglement cross-over linear chains. The physics is rigidity concentration induced changes length, interring packing, interpenetration, liquid compressibility slow down space-time dynamic-force correlations macromolecular scales. A power law decay constant inverse squared first consequence, followed ultraslow activated hopping transport regime. results set stage address kinetic arrest in families synthetic biological systems.

Язык: Английский

Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations DOI Creative Commons
Dinesh Sundaravadivelu Devarajan, Jiahui Wang, Beata Szała-Mendyk

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Март 1, 2024

Abstract Material properties of phase-separated biomolecular condensates, enriched with disordered proteins, dictate many cellular functions. Contrary to the progress made in understanding sequence-dependent phase separation little is known about sequence determinants condensate material properties. Using hydropathy scale and Martini models, we computationally decipher these relationships for charge-rich protein condensates. Our computations yield dynamical, rheological, interfacial condensates that are quantitatively comparable experimentally characterized Interestingly, find model natural proteins respond similarly charge segregation, despite different compositions. Molecular interactions within closely resemble those single-chain ensembles. Consequently, strongly correlate molecular contact dynamics structural We demonstrate potential harness characteristics predicting engineering functional insights from dilute

Язык: Английский

Процитировано

48
Sequence-Dependent Material Properties of Biomolecular Condensates and their Relation to Dilute Phase Conformations DOI Creative Commons
Dinesh Sundaravadivelu Devarajan, Jiahui Wang, Beata Szała-Mendyk

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Май 12, 2023

Material properties of phase-separated biomolecular assemblies, enriched with disordered proteins, dictate their ability to participate in many cellular functions. Despite the significant effort dedicated understanding how sequence protein drives its phase separation form condensates, little is known about determinants condensate material properties. Here, we computationally decipher these relationships for charged proteins using model sequences comprised glutamic acid and lysine residues as well naturally occurring LAF1's RGG domain DDX4's N-terminal domain. We do so by delineating arrangement oppositely within influences dynamical, rheological, interfacial condensed through equilibrium non-equilibrium molecular simulations hydropathy scale Martini models. Our computations yield that are quantitatively comparable experimentally characterized systems. Interestingly, find both natural respond similarly segregation charges, despite very different compositions. Condensates highly charge-segregated exhibit slower dynamics than uniformly charge-patterned sequences, because comparatively long-lived contacts between residues. Surprisingly, interactions similar those a single-chain all sequences. Consequently, strongly correlated dense contact structural findings demonstrate potential harness characteristics predicting engineering functional insights from dilute

Язык: Английский

Процитировано

10
Regional population and social welfare from the perspective of sustainability: Evaluation indicator, level measurement, and interaction mechanism DOI Creative Commons
Xueyi Wang, Mingchun Li, Taiyi He

и другие.

PLoS ONE, Год журнала: 2024, Номер 19(1), С. e0296517 - e0296517

Опубликована: Янв. 11, 2024

Key to regional sustainable development are the and interplay of population dynamics social welfare, each playing a significant role. As representative region with demographic characteristics such as negative growth large labor outflow, interaction between welfare in Nanchong deserve in-depth exploration. This article takes research object, constructs an evaluation indicator system through backtracking, uses entropy method coupling coordination model measure level interactive effect from 2010 2021. The results show that: Firstly, comprehensive shows linear upward trend, which indicates stable positive structure distribution, gradual improvement quality effectively compensate for weakening quantity, thus achieving population. Secondly, exponential has maintained rapid momentum various dimensions long-term effects have completely absorbed effects, welfare. Thirdly, during sample period, consistently high strength, factors diffusing integrating. On this basis, diffusion theory is used empirical reference construct three mechanisms implications inferred results.

Язык: Английский

Процитировано

4
Liquid state theory of the structure of model polymerized ionic liquids DOI
Ankita Das, Baicheng Mei, Alexei P. Sokolov

и другие.

The Journal of Chemical Physics, Год журнала: 2024, Номер 161(6)

Опубликована: Авг. 13, 2024

We employ polymer integral equation theory to study a simplified model of semiflexible polymerized ionic liquids (PolyILs) that interact via hard core repulsions and short range screened Coulomb interactions. The multi-scale structure in real Fourier space PolyILs (ions chosen mimic Li, Na, K, Br, PF6, TFSI) are determined as function melt density, interaction strength, ion size. Comparisons with homopolymer melt, neutral polymer–solvent-like athermal mixture, an atomic liquid carried out elucidate the distinct manner ions mediate changes packing, role excluded volume effects, influence chain connectivity, respectively. effect strength depends rich on size reflecting interplay steric adsorption, charge layering. Ion-mediated bridging monomers is found, which intensifies for larger ions. Intermediate layering correlations characterized by many-body screening length grows PolyIL cooling, disagreement Debye–Hückel theory, but accord experiments. Qualitative differences collective structure, including ion-size-dependent bifurcation factor peak pair correlation function, predicted. monomer cage order parameter increases significantly, its counterpart decreases, become smaller. Such behaviors allow one categorize into two broad classes small large Dynamical implications predicted structural results qualitatively discussed.

Язык: Английский

Процитировано

2
Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion DOI Creative Commons
Baicheng Mei, Gary S. Grest,

Songyue Liu

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(31)

Опубликована: Июль 23, 2024

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure intermolecular organization. Synthetic rings are hybrid objects with conformations that both ideal random walk globular features, which can serve models of genomic DNA. To date, emphasis has been placed on the effect ring molecular weight unusual behaviors. Here, we combine simulations a microscopic force-level theory build unified understanding for how key aspects dynamics depend different tunable properties including backbone rigidity, monomer concentration, degree traditional entanglement, weight. Our large-scale melts very stiffnesses reveal unanticipated agree well our generalized theory. This includes universal master curve center-of-mass diffusion constants function scaled by chemistry thermodynamic state-dependent critical generalizes concept an entanglement cross-over linear chains. The physics is rigidity concentration induced changes length, interring packing, interpenetration, liquid compressibility slow down space-time dynamic-force correlations macromolecular scales. A power law decay constant inverse squared first consequence, followed ultraslow activated hopping transport regime. results set stage address kinetic arrest in families synthetic biological systems.

Язык: Английский

Процитировано

1