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pro vyhledávání: '"Dinner, Aaron"'
Active nematics, formed from a liquid crystalline suspension of active force dipoles, are a paradigmatic active matter system whose study provides insights into how chemical driving produces the cellular mechanical forces essential for life. Recent a
Externí odkaz:
http://arxiv.org/abs/2411.09588
Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specific knowledge. Here, we introduce geom2vec, in which pretrained graph ne
Externí odkaz:
http://arxiv.org/abs/2409.19838
Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as "biological hardware." In this context, it is important to understand the inherent limi
Externí odkaz:
http://arxiv.org/abs/2409.05827
Fitting models to data to obtain distributions of consistent parameter values is important for uncertainty quantification, model comparison, and prediction. Standard Markov Chain Monte Carlo (MCMC) approaches for fitting ordinary differential equatio
Externí odkaz:
http://arxiv.org/abs/2408.15505
An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation, direct simu
Externí odkaz:
http://arxiv.org/abs/2404.19653
Standard approaches to controlling dynamical systems involve biologically implausible steps such as backpropagation of errors or intermediate model-based system representations. Recent advances in machine learning have shown that "imperfect" feedback
Externí odkaz:
http://arxiv.org/abs/2404.03798
Many chemical reactions and molecular processes occur on timescales that are significantly longer than those accessible by direct simulation. One successful approach to estimating dynamical statistics for such processes is to use many short time seri
Externí odkaz:
http://arxiv.org/abs/2311.07881
Autor:
Qiu, Yuqing, White, Elizabeth D., Munro, Edwin M., Vaikuntanathan, Suriyanarayanan, Dinner, Aaron R.
Cell polarization relies on long-range cortical flows, which are driven by active stresses and resisted by the cytoskeletal network. While the general mechanisms that contribute to cortical flows are known, a quantitative understanding of the factors
Externí odkaz:
http://arxiv.org/abs/2310.10819
Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to computational challeng
Externí odkaz:
http://arxiv.org/abs/2310.01704
Autor:
Redford, Steven A., Colen, Jonathan, Shivers, Jordan L., Zemsky, Sasha, Molaei, Mehdi, Floyd, Carlos, Ruijgrok, Paul V., Vitelli, Vincenzo, Bryant, Zev, Dinner, Aaron R., Gardel, Margaret L.
In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in knowledge conce
Externí odkaz:
http://arxiv.org/abs/2308.16831