Physics Research Works
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- ItemSimulation source code for "Myosin and α-actinin regulation of stress fiber contractility under tensile stress"(2023) Ni, Haoran; Ni, Qin; Papoian, Garegin A.; Trache, Andreea; Jiang, Yi; Jiang, YiStress fibers are actomyosin bundles that regulate cellular mechanosensation and force transduction. Connecting to extracellular matrix through focal adhesion complexes, stress fibers actively generate contractile forces with myosin motors and crosslinking proteins. Under external mechanical stimuli such as tensile forces, the stress fiber remodels its architectures to adapt to the external cues, displaying properties of viscoelastic materials. How the structural remodeling of stress fibers is related to the generation of contractile force is not well understood. In this work, we simulate mechanochemical dynamics and force generation of stress fibers using the molecular simulation platform MEDYAN. We model stress fiber as two connecting bipolar bundles attached at the ends to focal adhesion complexes. The simulated stress fibers generate contractile force that is regulated by myosin motors and α-actinin crosslinkers. We find that stress fibers are able to enhance contractility by reducing the distance between actin filaments to increase crosslinker binding, while this structural remodeling ability depends on the crosslinker turnover rate. Under tensile pulling, the stress fiber shows an instantaneous increase of the contractile forces followed by a slow relaxation into a new steady state. While the new steady state contractility after pulling only depends on the overlap between actin bundles, the short term contractility enhancement is sensitive to the tensile pulling distance. We further show that this mechanical response is sensitive to the crosslinker turnover rate. Our results provide insights into the stress fiber mechanics that have significant implications for understanding the cellular adaptation to mechanical signaling.
- ItemData for "A tug of war between filament treadmilling and myosin induced contractility generates actin ring"(2022-06-23) Ni, Qin; Wagh, Kaustubh; Pathni, Aashli; Ni, Haoran; Vashisht, Vishavdeep; Upadhyaya, Arpita; Papoian, Garegin A.; Upadhyaya, Arpita; Papoian, Garegin A.In most eukaryotic cells, actin filaments assemble into a shell-like actin cortex under the plasma membrane, controlling cellular morphology, mechanics, and signaling. The actin cortex is highly polymorphic, adopting diverse forms such as the ring-like structures found in podosomes, axonal rings, and immune synapses. The biophysical principles that underlie the formation of actin rings and cortices remain unknown. Using a molecular simulation platform, called MEDYAN, we discovered that varying the filament treadmilling rate and myosin concentration induces a finite size phase transition in actomyosin network structures. We found that actomyosin networks condense into clusters at low treadmilling rates or high myosin concentration but form ring-like or cortex-like structures at high treadmilling rates and low myosin concentration. This mechanism is supported by our corroborating experiments on live T cells, which exhibit ring-like actin networks upon activation by stimulatory antibody. Upon disruption of filament treadmilling or enhancement of myosin activity, the pre-existing actin rings are disrupted into actin clusters or collapse towards the network center respectively. Our analyses suggest that the ring-like actin structure is a preferred state of low mechanical energy, which is, importantly, only reachable at sufficiently high treadmilling rates.
- ItemReorganizing Nothingness(2017) Misner, Charles WThis note is directed to scientists who intend to help wide audiences better understand current science progress. It sketches, in mostly qualitative descriptions, what is known about simple black holes. It describes black holes when they are no longer importantly interacting with other astronomical objects. Thus, it does not explore black holes seen to be currently acquiring mass by absorbing ordinary matter in accretion disks. Nor do I try to explain how matter just outside the black hole horizon can be expelled in violent jets powered by the energy stored in the gravitational fields of rotating black holes. Brief descriptions of simple black holes explain that BHs can be formed from ordinary matter in large stars that find no non-gravitational forces sufficient to overcome the intense gravity of extremely large masses at extreme densities. Where this note differs is when the simple descriptions suggest that, after forming and entering beyond the BH horizon, the collapsing matter is crushed beyond the scope of current physics nearly into a point, inside the BH, that we can’t observe. I insist that, instead, the matter is crushed and then disposed of by being flushed out of our universe in a tube of huge and increasing spatial length. A mathematical appendix explores this idea in a little detail. I suggest that many low curvature spacetime regions inside the BH are very robust consequences of Einstein’s equations and require a new vocabulary in their description. There I choose analog words to present my viewpoint. I find a use for phrases such as: nothingness; enzymatic matter; phase transitions; recuse; autonomic spacetime creation.
- ItemEvanescent Laws(2012-04-23) Misner, Charles WThe invited talk (not recorded) for which these slides were prepared discusses the properties of a physics law which suggest it should be called 'Evanescent'. This occurs when, in some domain, either – It becomes irrelevant or useless; – It is indefinable or misleading; – Its normal consequences can be evaded; or – It (rarely) is incorrect in some domain. Also I will make the evanescence case for energy and entropy on the cosmological scale.
- ItemDynamical symmetry indicators for Floquet crystals(Springer Nature, 2021-10-13) Yu, Jiabin; Zhang, Rui-Xing; Song, Zhi-DaVarious exotic topological phases of Floquet systems have been shown to arise from crystalline symmetries. Yet, a general theory for Floquet topology that is applicable to all crystalline symmetry groups is still in need. In this work, we propose such a theory for (effectively) non-interacting Floquet crystals. We first introduce quotient winding data to classify the dynamics of the Floquet crystals with equivalent symmetry data, and then construct dynamical symmetry indicators (DSIs) to sufficiently indicate the inherently dynamical Floquet crystals. The DSI and quotient winding data, as well as the symmetry data, are all computationally efficient since they only involve a small number of Bloch momenta. We demonstrate the high efficiency by computing all elementary DSI sets for all spinless and spinful plane groups using the mathematical theory of monoid, and find a large number of different nontrivial classifications, which contain both first-order and higher-order 2+1D anomalous Floquet topological phases. Using the framework, we further find a new 3+1D anomalous Floquet second-order topological insulator (AFSOTI) phase with anomalous chiral hinge modes.