Collective motion of bacteria and their dynamic assembly behavior

The system-plus-bath model is an important tool to understand nonadiabatic dynamics for large molecular systems. The understanding of the collective motion of a huge number of bath modes is essential to reveal their key roles in the overall dynamics. We apply the principal component analysis (PCA) to investigate the bath motion based on the massive data generated from the MM-SQC (symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian) nonadiabatic dynamics of the excited-state energy transfer dynamics of Frenkel-exciton model. The PCA method clearly clarifies that two types of bath modes, which either display the strong vibronic couplings or have the frequencies close to electronic transition, are very important to the nonadiabatic dynamics. These observations are fully consistent with the physical insights. This conclusion is obtained purely based on the PCA understanding of the trajectory data, without the large involvement of pre-defined physical knowledge. The results show that the PCA approach, one of the simplest unsupervised machine learning methods, is very powerful to analyze the complicated nonadiabatic dynamics in condensed phase involving many degrees of freedom.

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REGULAR STRUCTURE OF LOW-LYING STATES FOR ATOMIC NUCLEI UNDER RANDOM INTERACTIONS

International Journal of Modern Physics E ◽

10.1142/s021830130801194x ◽

2008 ◽

Vol 17 (supp01) ◽

pp. 304-317

Author(s):

Y. M. ZHAO

Keyword(s):

Ground State ◽

Collective Motion ◽

Regular Structure ◽

Positive Parity ◽

Many Body ◽

Random Interactions ◽

Atomic Nuclei ◽

Many Body Systems

In this paper we review regularities of low-lying states for many-body systems, in particular, atomic nuclei, under random interactions. We shall discuss the famous problem of spin zero ground state dominance, positive parity dominance, collective motion, odd-even staggering, average energies, etc., in the presence of random interactions.

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Swarm shedding in networks of self-propelled agents

Scientific Reports ◽

10.1038/s41598-021-92748-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jason Hindes ◽

Victoria Edwards ◽

Klimka Szwaykowska Kasraie ◽

George Stantchev ◽

Ira B. Schwartz

Keyword(s):

Network Topology ◽

Collective Motion ◽

Mean Field Theory ◽

Mean Field ◽

Interaction Strength ◽

Central Question ◽

Agent Interaction ◽

Sparse Networks ◽

Swarm Pattern ◽

Limited Sensing

AbstractUnderstanding swarm pattern formation is of great interest because it occurs naturally in many physical and biological systems, and has artificial applications in robotics. In both natural and engineered swarms, agent communication is typically local and sparse. This is because, over a limited sensing or communication range, the number of interactions an agent has is much smaller than the total possible number. A central question for self-organizing swarms interacting through sparse networks is whether or not collective motion states can emerge where all agents have coherent and stable dynamics. In this work we introduce the phenomenon of swarm shedding in which weakly-connected agents are ejected from stable milling patterns in self-propelled swarming networks with finite-range interactions. We show that swarm shedding can be localized around a few agents, or delocalized, and entail a simultaneous ejection of all agents in a network. Despite the complexity of milling motion in complex networks, we successfully build mean-field theory that accurately predicts both milling state dynamics and shedding transitions. The latter are described in terms of saddle-node bifurcations that depend on the range of communication, the inter-agent interaction strength, and the network topology.

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Probing bacterial cell wall growth by tracing wall-anchored protein complexes

Nature Communications ◽

10.1038/s41467-021-22483-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yi-Jen Sun ◽

Fan Bai ◽

An-Chi Luo ◽

Xiang-Yu Zhuang ◽

Tsai-Shun Lin ◽

...

Keyword(s):

Cell Wall ◽

Cell Shape ◽

Bernoulli Shift ◽

Protein Complexes ◽

Axial Direction ◽

Cell Wall Growth ◽

Flagellar Motors ◽

Shift Map ◽

Dynamic Assembly ◽

Wall Growth

AbstractThe dynamic assembly of the cell wall is key to the maintenance of cell shape during bacterial growth. Here, we present a method for the analysis of Escherichia coli cell wall growth at high spatial and temporal resolution, which is achieved by tracing the movement of fluorescently labeled cell wall-anchored flagellar motors. Using this method, we clearly identify the active and inert zones of cell wall growth during bacterial elongation. Within the active zone, the insertion of newly synthesized peptidoglycan occurs homogeneously in the axial direction without twisting of the cell body. Based on the measured parameters, we formulate a Bernoulli shift map model to predict the partitioning of cell wall-anchored proteins following cell division.

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