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  1. Free, publicly-accessible full text available August 1, 2024
  2. Abstract Motivation

    Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this cross-species transfer, sequence similarity does not imply functional similarity, and thus, several current approaches incorporate protein–protein interactions to help map findings between species. Existing transfer methods either formulate the alignment problem as a matching problem which pits network features against known orthology, or more recently, as a joint embedding problem.


    We propose a novel state-of-the-art joint embedding solution: Embeddings to Network Alignment (ETNA). ETNA generates individual network embeddings based on network topological structure and then uses a Natural Language Processing-inspired cross-training approach to align the two embeddings using sequence-based orthologs. The final embedding preserves both within and between species gene functional relationships, and we demonstrate that it captures both pairwise and group functional relevance. In addition, ETNA’s embeddings can be used to transfer genetic interactions across species and identify phenotypic alignments, laying the groundwork for potential opportunities for drug repurposing and translational studies.

    Availability and implementation

  3. We study p -Laplacians and spectral clustering for a recently proposed hypergraph model that incorporates edge-dependent vertex weights (EDVW). These weights can reflect different importance of vertices within a hyperedge, thus conferring the hypergraph model higher expressivity and flexibility. By constructing submodular EDVW-based splitting functions, we convert hypergraphs with EDVW into submodular hypergraphs for which the spectral theory is better developed. In this way, existing concepts and theorems such as p -Laplacians and Cheeger inequalities proposed under the submodular hypergraph setting can be directly extended to hypergraphs with EDVW. For submodular hypergraphs with EDVW-based splitting functions, we propose an efficient algorithm to compute the eigenvector associated with the second smallest eigenvalue of the hypergraph 1-Laplacian. We then utilize this eigenvector to cluster the vertices, achieving higher clustering accuracy than traditional spectral clustering based on the 2-Laplacian. More broadly, the proposed algorithm works for all submodular hypergraphs that are graph reducible. Numerical experiments using real-world data demonstrate the effectiveness of combining spectral clustering based on the 1-Laplacian and EDVW.
    Free, publicly-accessible full text available February 21, 2024
  4. We present a numerical investigation of the modes of adhesion and endocytosis of two spherocylindrical nanoparticles (SCNPs) on planar and tensionless lipid membranes, using systematic molecular dynamics simulations of an implicit-solvent model, with varying values of the SCNPs' adhesion strength and dimensions. We found that at weak values of the adhesion energy per unit of area, ξ , the SCNPs are monomeric and adhere to the membrane in the parallel mode. As ξ is slightly increased, the SCNPs dimerize into wedged dimers, with an obtuse angle between their major axes that decreases with increasing ξ . However, as ξ is further increased, we found that the final adhesion state of the two SCNPs is strongly affected by the initial distance, d 0 , between their centers of mass, upon their adhesion. Namely, the SCNPs dimerize into wedged dimers, with an acute angle between their major axes, if d 0 is relatively small. However, for relatively high d 0 , they adhere individually to the membrane in the monomeric normal mode. For even higher values of ξ and small values of d 0 , the SCNPs cluster into tubular dimers. However, they remain monomeric if d 0 is high. Finally, themore »SCNPs endocytose either as a tubular dimer, if d 0 is low or as monomers for large d 0 , with the onset value of ξ of dimeric endocytosis being lower than that of monomeric endocytosis. Dimeric endocytosis requires that the SCNPs adhere simultaneously at nearby locations.« less
    Free, publicly-accessible full text available February 22, 2024
  5. Since many advanced applications require specific assemblies of nanoparticles (NPs), considerable efforts have been made to fabricate nanoassemblies with specific geometries. Although nanoassemblies can be fabricated through top-down approaches, recent advances show that intricate nanoassemblies can also be obtained through guided self-assembly, mediated for example by DNA strands. Here, we show, through extensive molecular dynamics simulations, that highly ordered self-assemblies of NPs can be mediated by their adhesion to lipid vesicles (LVs). Specifically, Janus NPs are considered so that the amount by which they are wrapped by the LV is controlled. The specific geometry of the nanoassembly is the result of effective curvature-mediated repulsion between the NPs and the number of NPs adhering to the LV. The NPs are arranged on the LV into polyhedra which satisfy the upper limit of Euler’s polyhedral formula, including several deltahedra and three Platonic solids, corresponding to the tetrahedron, octahedron, and icosahedron.
    Free, publicly-accessible full text available February 24, 2024
  6. Abstract We develop a framework for incorporating edge-dependent vertex weights (EDVWs) into the hypergraph minimum s - t cut problem. These weights are able to reflect different importance of vertices within a hyperedge, thus leading to better characterized cut properties. More precisely, we introduce a new class of hyperedge splitting functions that we call EDVWs-based, where the penalty of splitting a hyperedge depends only on the sum of EDVWs associated with the vertices on each side of the split. Moreover, we provide a way to construct submodular EDVWs-based splitting functions and prove that a hypergraph equipped with such splitting functions can be reduced to a graph sharing the same cut properties. In this case, the hypergraph minimum s - t cut problem can be solved using well-developed solutions to the graph minimum s - t cut problem. In addition, we show that an existing sparsification technique can be easily extended to our case and makes the reduced graph smaller and sparser, thus further accelerating the algorithms applied to the reduced graph. Numerical experiments using real-world data demonstrate the effectiveness of our proposed EDVWs-based splitting functions in comparison with the all-or-nothing splitting function and cardinality-based splitting functions commonly adopted in existingmore »work.« less
    Free, publicly-accessible full text available December 1, 2023
  7. Free, publicly-accessible full text available November 1, 2023
  8. Using molecular dynamics simulations of a coarse-grained model, in conjunction with the weighted histogram analysis method, the adhesion modes of two spherical Janus nanoparticles (NPs) on the outer or inner side of lipid vesicles are explored. In particular, the effects of the area fraction, J , of the NPs that interact attractively with lipid head groups, the adhesion strength and the size of the NPs on their adhesion modes are investigated. The NPs are found to exhibit two main modes of adhesion when adhered to the outer side of the vesicle. In the first mode, which occurs at relatively low values of J , the NPs are apart from each other. In the second mode, which occurs at higher values of J , the NPs form an in-plane dimer. Janus NPs, which adhere to the inner side of the vesicle, are always found to be apart from each other, regardless of the value of J and their diameter.
  9. The adhesion modes and endocytosis pathway of spherocylindrical nanoparticles (NPs) are investigated numerically using molecular dynamics simulations of a coarse-grained implicit-solvent model. The investigation is performed systematically with respect to the adhesion energy density ξ, NP’s diameter D, and NP’s aspect ratio α. At weak ξ, the NP adheres to the membrane through a parallel mode, i.e., its principal axis is parallel to the membrane. However, for relatively large ξ, the NP adheres through a perpendicular mode, i.e., the NP is invaginated, such as its principal axis is nearly perpendicular to the membrane. The value of ξ at the transition from the parallel to the perpendicular mode decreases with increasing the D or α, in agreement with theoretical arguments based on the Helfrich Hamiltonian. As ξ is further increased, the NP undergoes endocytosis, with the value of ξ at the endocytosis threshold that is independent of the aspect ratio but decreases with increasing D. The kinetics of endocytosis depends strongly on ξ and D. While for low values of D, the NP first rotates to a parallel orientation then to a perpendicular orientation. At high values of ξ or D, the NP is endocytosed while in the parallel orientation.