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When treated with antibiotics below the minimum inhibitory concentration, bacterial cell division turns off, but cell growth does not. Thus, rod-like bacteria, including E. coli, can elongate many times their length without increasing their…
We study single cell E.coli chemotaxis in a spatio-temporally varying attractant environment. Modeling the attractant concentration in the form of a traveling sine wave, we measure in our simulations, the chemotactic drift velocity of the…
TMDs are a new family of 2D materials with features that make them appealing for potential applications in nanomaterials science and engineering. Although, the edges of the 2D TMDs show excellent electrocatalytic performance, their basal…
The Escherichia coli chemoreceptors form an extensive array that achieves cooperative and adaptive sensing of extracellular signals. The receptors control the activity of histidine kinase CheA, which drives a nonequilibrium…
Lines of exceptional points are robust in the 3-dimensional non-Hermitian parameter space without requiring any symmetry. However, when more elaborate exceptional structures are considered, the role of symmetry becomes critical. One such…
We formulate an active-gel theory for multicellular migration in the extra-cellular matrix (ECM). The cells are modeled as an active, polar solvent, and the ECM as a viscoelastic solid. Our theory enables to analyze the dynamic reciprocity…
A pathway-based mean-field theory (PBMFT) was recently proposed for E. coli chemotaxis in [G. Si, T. Wu, Q. Quyang and Y. Tu, Phys. Rev. Lett., 109 (2012), 048101]. In this paper, we derived a new moment system of PBMFT by using the moment…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Cellular decision-making under stress involves rapid pathway selection despite energy scarcity. Here we demonstrate that thermodynamic constraints actively drive energy-efficient sporulation, where continuous metabolic sources enable system…
Single-cell RNA sequencing technologies have revolutionized our understanding of cellular heterogeneity, yet computational methods often struggle to balance performance with biological interpretability. Embedded topic models have been…
We study a novel class of open-loop control protocols constructed to perform arbitrary nontrivial single-qubit logic operations robust against time-dependent non-Markovian noise. Amplitude and phase modulation protocols are crafted…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
We have studied structure formation in a confined block copolymer melt by means of dynamic density functional theory (DDFT). The confinement is two-dimensional, and the confined geometry is that of a cylindrical nanopore. Although the…
This is a comprehensive review of the strong-interaction limit of density functional theory. It covers the derivation of the limiting strictly correlated electrons (SCE) functional from exact Hohenberg-Kohn DFT, basic aspects of SCE physics…
Singlet fission (SF) is a multi-exciton generation process that could be harnessed to improve the efficiency of photovoltaic devices. Experimentally, systems derived from the pentacene molecule have been shown to exhibit ultrafast SF with…
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…
Recently, there has been a lot of effort in understanding sRNA mediated regulation of gene expression and how this mode of regulation differs from transcriptional regulation.In E.coli, in the presence of oxidative stress, the synthesis of…
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…
Hypothesis: Bacterial contamination of surfaces poses a major threat to public health. Designing effective antibacterial or self-cleaning surfaces requires understanding how bacteria-laden droplets interact with solid substrates and how…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…