More Like this

1. Joint Grid Discretization for Biological Pattern Discovery

   https://doi.org/10.1145/3388440.3412415  

   Wang, Jiandong; Kumar, Sajal; Song, Mingzhou (September 2020, Proceedings. The 11th ACM Int'l Conf on Bioinform, Comput Biol and Health Inform)

   null (Ed.)

   The complexity, dynamics, and scale of data acquired by modern biotechnology increasingly favor model-free computational methods that make minimal assumptions about underlying biological mechanisms. For example, single-cell transcriptome and proteome data have a throughput several orders more than bulk methods. Many model-free statistical methods for pattern discovery such as mutual information and chi-squared tests, however, require discrete data. Most discretization methods minimize squared errors for each variable independently, not necessarily retaining joint patterns. To address this issue, we present a joint grid discretization algorithm that preserves clusters in the original data. We evaluated this algorithm on simulated data to show its advantage over other methods in maintaining clusters as measured by the adjusted Rand index. We also show it promotes global functional patterns over independent patterns. On single-cell proteome and transcriptome of leukemia and healthy blood, joint grid discretization captured known protein-to-RNA regulatory relationships, while revealing previously unknown interactions. As such, the joint grid discretization is applicable as a data transformation step in associative, functional, and causal inference of molecular interactions fundamental to systems biology. The developed software is publicly available at https://cran.r-project.org/package=GridOnClusters 

   more » « less
2. Active nematic fluids on Riemannian two-manifolds

   https://doi.org/10.1098/rspa.2024.0418  

   Zhu, Cuncheng; Saintillan, David; Chern, Albert (April 2025, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences)

   Recent advances in cell biology and experimental techniques using reconstituted cell extracts have generated significant interest in understanding how geometry and topology influence active fluid dynamics. In this work, we present a comprehensive continuum theory and computational method to explore the dynamics of active nematic fluids on arbitrary surfaces without topological constraints. The fluid velocity and nematic order parameter are represented as the sections of the complex line bundle of a two-manifold. We introduce the Levi–Civita connection and surface curvature form within the framework of complex line bundles. By adopting this geometric approach, we introduce a gauge-invariant discretization method that preserves the continuous local-to-global theorems in differential geometry. We establish a nematic Laplacian on complex functions that can accommodate fractional topological charges through the covariant derivative on the complex nematic representation. We formulate advection of the nematic field based on a unifying definition of the Lie derivative, resulting in a stable geometric semi-Lagrangian (sL) discretization scheme for transport by the flow. In general, the proposed surface-based method offers an efficient and stable means to investigate the influence of local curvature and global topology on the two-dimensional hydrodynamics of active nematic systems. 

   more » « less
3. Probing the conserved roles of cut in the development and function of optically different insect compound eyes

   https://doi.org/10.3389/fcell.2023.1104620  

   Rathore, Shubham; Meece, Michael; Charlton-Perkins, Mark; Cook, Tiffany A.; Buschbeck, Elke K. (March 2023, Frontiers in Cell and Developmental Biology)

   Astonishing functional diversity exists among arthropod eyes, yet eye development relies on deeply conserved genes. This phenomenon is best understood for early events, whereas fewer investigations have focused on the influence of later transcriptional regulators on diverse eye organizations and the contribution of critical support cells, such as Semper cells (SCs). As SCs in Drosophila melanogaster secrete the lens and function as glia, they are critical components of ommatidia. Here, we perform RNAi-based knockdowns of the transcription factor cut (CUX in vertebrates), a marker of SCs, the function of which has remained untested in these cell types. To probe for the conserved roles of cut , we investigate two optically different compound eyes: the apposition optics of D. melanogaster and the superposition optics of the diving beetle Thermonectus marmoratus . In both cases, we find that multiple aspects of ocular formation are disrupted, including lens facet organization and optics as well as photoreceptor morphogenesis. Together, our findings support the possibility of a generalized role for SCs in arthropod ommatidial form and function and introduces Cut as a central player in mediating this role. 

   more » « less
4. Generalized mechanics and dynamics of modulated turning

   https://doi.org/10.1016/j.jmatprotec.2022.117708  

   Eren, Bora; Nam, Soohyun; Sencer, Burak (October 2022, Journal of materials processing technology)

   Budak, Erhan (Ed.)

   This paper presents a generalized cutting force and regenerative chatter stability prediction for the modulated turning (MT) process. Uncut chip thickness is modeled by considering current tool kinematics and undulated (previously generated) surface topography for any given modulation condition in the feed direction. It is found that chip formation is governed by the undulated surface generated in multiple past spindle rotations. Uncut chip thickness is computed analytically in the form of trigonometric functions, and cutting forces are predicted by making use of orthogonal cutting mechanics. Regenerative chatter stability of the process is also modelled. Analytical semi-discretization-based solution is developed to accurately predict the stability lobe diagrams (SLDs) of the MT process. Predicted stability lobes are validated through numerical time-domain simulations and experimentally via orthogonal (plunge) turning tests. It is found that as compared to conventional single-point continuous turning, regenerative stability of MT exhibits multiple (3) regenerative delay loops and long out-of-cut duration in-between tool engagement stabilizes the process to reach up to 2x higher stable widths/depths as compared to the conventional continuous turning. 

   more » « less
5. Semi-Lagrangian Pressure Solver for Accurate, Consistent, and Conservative Volume-of-Fluid Simulations

   Fox, Julian; Owkes, Mark (June 2024, 16th Triennial International Conference on Liquid Atomization and Spray Systems,)

   In this work, a novel discretization of the incompressible Navier-Stokes equations for a gas-liquid flow is developed. Simulations of gas-liquid flows are often performed by discretizing time with a predictor → pressure → corrector approach and the phase interface is represented by a volume of fluid (VOF) method. Recently, unsplit, geometric VOF methods have been developed that use a semi-Lagrangian discretization of the advection term within the predictor step. A disadvantage of the current methods is that an alternative discretization (e.g. finite volume or finite difference) is used for the divergence operator in the pressure equation. Due to the inconsistency in discretizations, a flux-correction to the semi-Lagrangian advection term is required to achieve mass conservation, which increases the computational cost and reduces the accuracy. In this work, we explore the alternative of using a semi-Lagrangian discretization for the divergence operators in both the advection term and the pressure equation. The proposed discretization avoids the need to use a flux-correction to the semi-Lagrangian advection term as mass conservation is achieved through consistent discretization. Additionally, avoiding the flux-correction improves the accuracy while reducing the computational cost of the advection term semi-Lagrangian discretization. 

   more » « less