期刊
PHYSICAL REVIEW E
卷 106, 期 4, 页码 -出版社
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevE.106.044402
关键词
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资金
- NSF [DE-SC0019246]
- DOE [R37MH080046]
- NIH [DMR1720256]
- Goldwater Fellowship
- College of Creative Studies Summer Undergraduate Fellowship
- Nvidia
- UCSB Center for Scientific Computing [CNS- 1725797]
- UCSB MRL NSF
- [DMS-1616353]
- U.S. Department of Energy (DOE) [DE-SC0019246] Funding Source: U.S. Department of Energy (DOE)
In this study, we developed methods to investigate protein drift-diffusion dynamics in heterogeneous cell membranes and explore the roles of geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine discrete particle descriptions with continuum-level models, allowing us to track individual protein dynamics while coupled to continuum fields.
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine discrete particle descriptions with continuum-level models for tracking the individual protein drift-diffusion dynamics when coupled to continuum fields. We show how our approaches can be used to inves-tigate phenomena motivated by protein kinetics within dendritic spines. The spine geometry is hypothesized to play an important biological role regulating synaptic strength, protein kinetics, and self-assembly of clusters. We perform simulation studies for model spine geometries varying the neck size to investigate how phase-separation and protein organization is influenced by different shapes. We also show how our methods can be used to study the roles of geometry in reaction-diffusion systems including Turing instabilities. Our methods provide general approaches for investigating protein kinetics and drift-diffusion dynamics within curved membrane structures.
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