A Dynamically Correlated Network Model for the Collective Dynamics in Glass-Forming Molecular Liquids and Polymers

The non-Arrhenius behavior of segmental dynamics in glass-forming liquids is one of the most profound mysteries in soft matter physics. In this article, we propose a dynamically correlated network (DCN) model to understand the growing behavior of dynamically correlated regions during cooling, which leads to the viscous slowdown of supercooled liquids. The fundamental concept of the model is that the cooperative region of collective motions has a network structure that consists of string-like parts, and networks of various sizes interpenetrate each other. Each segment undergoes dynamical coupling with its neighboring segments via a finite binding energy. Monte Carlo simulations showed that the fractal dimension of the DCNs generated at different temperatures increased and their size distribution became broader with decreasing temperature. The segmental relaxation time was evaluated based on a power law with four different exponents for the activation energy of rearrangement with respect to the DCN size. The results of the present DCN model are consistent with the experimental results for various materials of molecular and polymeric liquids.

Conformational Spread Drives the Evolution of the Calcium-calmodulin Protein Kinase II

The calcium calmodulin (Ca2+CAM) dependent protein kinase II (CaMKII) decodes Ca2+ frequency oscillations. It has a central role in learning. I matched residue and organismal evolution to collective motions deduced from the atomic structure of the human CaMKIIa holoenzyme. Protein dynamic simulations and bioinformatic analysis showed its stacked ring architecture conformationally couples kinase domains (KDs) via its central hub. The simulations revealed underlying b-sheet collective motions in the hub ab association domain (AD) map onto a coevolved residue network and partition it into two distinct sectors. The holoenzyme evolved in metazoans by stabilization of ancient enzyme dimers and fold elongation to create a second, metastable sector for ring assembly. Continued evolution targeted the ring contacts for lateral conformational spread. The a isoform, predominantly expressed in the brain, emerged last and evolved rapidly in sync with the poikilotherm-homeotherm jump in the evolution of memory. The correlation between CaMKII dynamics and phylogenetics argues single residue evolution fine-tunes hub conformational spread. The central role of CaMKII ringed architecture In the brain could be to increase Ca2+ frequency response range for complex learning functions.

Large-scale vortices with dynamic rotation emerged from monolayer collective motion of gliding Flavobacteria

A collective motion of self-driven particles has been a fascinating subject in physics and biology. Sophisticated macroscopic behavior emerges through a population in thousands or millions of bacterial cells, propelling itself by flagellar rotation and its chemotactic response. Here we found a series of collective motions accompanying successive phase-transitions in a non-flagellated rod-shaped soil bacterium, Flavobacterium johnsoniae, which was driven by a surface cell movement known as gliding motility. When we spot the cells on an agar plate with a low level of nutrients, the bacterial community exhibited vortex patterns that spontaneously appeared as lattice and integrated into a large-scale circular plate. All patterns exhibit with monolayer of bacteria, which enable to visualize an individual cell with a high resolution among a wide-range pattern two-dimensionally. The single cells moved at random orientation, but the cells connected with one another showed left-turn biased trajectories in starved environment. This feature is possibly due to the collision of cells inducing a nematic alignment of dense cells as self-propelled rods. Subsequently, each vortex oscillated independently, and then transformed to the rotating mode as an independent circular plate. Notably, the rotational direction of the circular plate was counterclockwise without exception. The plates developed accompanying rotation with constant angular velocity, suggesting that the mode is an efficient strategy for bacterial survival. Importance Self-propelled bacteria propelled by flagella rotation often display highly organized dynamic patterns at high cell densities. Here we found a new mode of collective motion in non-flagellated bacteria: vortex patterns were spontaneously appeared as lattice and integrated into a large-scale circular plate comprising hundreds of thousands of cells, which exhibited unidirectional rotation in a counterclockwise manner and expanded in size on agar. A series of collective motions was driven by gliding motility of the rod-shaped soil bacterium Flavobacterium johnsoniae. In a low nutrient environment, single cells moved at random orientation while cells at high density moved together as a unitary cluster. This might be an efficient strategy for cells of this species to find nutrients.

Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2

The number of confirmed COVID-19 cases is rapidly increasing with no direct treatment for the disease. Few repurposed drugs, such as Remdesivir, Chloroquine, Hydroxychloroquine, Lopinavir, and Ritonavir, are being tested against SARS-CoV-2. Remdesivir is the drug of choice for Ebola virus disease and has been authorized for emergency use. This drug acts against SARS-CoV-2 by inhibiting the RNA-dependent-RNA-polymerase (RdRp) of SARS-CoV-2. RdRp of viruses is prone to mutations that confer drug resistance. A recent study by Pachetti et al. in 2020 identified the P323L mutation in the RdRp protein of SARS-CoV-2. In this study, we aimed to determine the potency of lead compounds similar to Remdesivir, which can be used as an alternative when variants of SARS-CoV-2 develop resistance due to RdRp mutations. The initial screening yielded 704 compounds that were 90% similar to the control drug, Remdesivir. On further evaluation through drugability and antiviral inhibition percentage analyses, we shortlisted 32 and seven compounds, respectively. These seven compounds were further analyzed for their molecular interactions, which revealed that all seven compounds interacted with RdRp with higher affinity than Remdesivir under native conditions. However, three compounds failed to interact with the mutant protein with higher affinity than Remdesivir. Dynamic cross-correlation matrix (DCCM) and vector field collective motions analyses were performed to identify the precise movements of docked complexes' residues. Furthermore, the compound SCHEMBL20144212 showed a high affinity for native and mutant proteins and might provide an alternative against SARS-CoV-2 variants that might confer resistance to Remdesivir. Further validations by in vitro and in vivo studies are needed to confirm the efficacy of our lead compounds for their inhibition against SARS-CoV-2.

Volatility Co-Movement in Stock Markets

The volatility and log-price collective movements among stocks of a given market are studied in this work using co-movement functions inspired by similar functions in the physics of many-body systems, where the collective motions are a signal of structural rearrangement. This methodology is aimed to identify the cause of coherent changes in volatility or price. The function is calculated using the product of the variations in volatility (or price) of a pair of stocks, averaged over all pair particles. In addition to the global volatility co-movement, its distribution according to the volatility of the stocks is also studied. We find that stocks with similar volatility tend to have a greater co-movement than stocks with dissimilar volatility, with a general decrease in co-movement with increasing volatility. On the other hand, when the average volatility (or log-price) is subtracted from the stock volatility (or log-price), the co-movement decreases notably and becomes almost zero. This result, interpreted within the background of many body physics, allows us to identify the index motion as the main source for the co-movement. Finally, we confirm that during crisis periods, the volatility and log-price co-movement are much higher than in calmer periods.

Mechanistic underpinning of nonuniform collective motions in swarming bacteria

Self-propelled bacteria can exhibit a large variety of non-equilibrium self-organized phenomena. Swarming is one such fascinating dynamical scenario where a number of motile individuals grouped into clusters and move in synchronized flows and vortices. While precedent investigations in rod-like particles confirm that increased aspect-ratio promotes alignment and order, recent experimental studies in bacteria Bacillus subtilis show a non-monotonic dependence of cell-aspect ratio on their swarming motion. Here, by computer simulations of an agent-based model of selfpropelled, mechanically interacting, rod-shaped bacteria in overdamped condition, we explore the collective dynamics of bacterial swarm subjected to a variation of cell-aspect ratio. When modeled with an identical self-propulsion speed across a diverse range of cell aspect ratio, simulations demonstrate that both shorter and longer bacteria exhibit slow dynamics whereas the fastest speed is obtained at an intermediate aspect ratio. Our investigation highlights that the origin of this observed non-monotonic trend of bacterial speed and vorticity with cell-aspect ratio is rooted in the cell-size dependence of motility force. The swarming features remain robust for a wide range of surface density of the cells, whereas asymmetry in friction attributes a distinct effect. Our analysis identifies that at an intermediate aspect ratio, an optimum cell size and motility force promote alignment, which reinforces the mechanical interactions among neighboring cells leading to the overall fastest motion. Mechanistic underpinning of the collective motions reveals that it is a joint venture of the short-range repulsive and the size-dependent motility forces, which determines the characteristics of swarming.

Mechanistic underpinning of cell aspect ratio-dependent emergent collective motions in swarming bacteria

Self-propelled bacteria can exhibit a large variety of non-equilibrium self-organized phenomena. Swarming is one such fascinating dynamical scenario where a number of motile individuals group into dynamical clusters and move...

Dynamical arrest of topological defects in 2D hyperuniform disk packings

We investigate collective motions of points in 2D systems, orchestrated by Lloyd algorithm. The algorithm iteratively updates a system by minimising the total quantizer energy of the Voronoi landscape of the system. As a result of a tradeoff between energy minimisation and geometric frustration, we find that optimised systems exhibit a defective landscape along the process, where strands of 5- and 7-coordinated dislocations are embedded in the hexatic phase. In particular, dipole defects, each of which is the simplest possible pair of a pentagon and a heptagon, come into the picture of dynamical arrest, as the system freezes down to a disordered hyperuniform state. Moreover, we explore the packing fractions of 2D disk packings associated to the obtained hyperuniform systems by considering the maximum inscribed disks in their Voronoi cells.