相关论文: Single-Molecule Morphology of Topologically Digest…

We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…

X-ray computed tomography (CT) reconstructs cross-sectional images from projection data. However, ionizing X-ray radiation associated with CT scanning might induce cancer and genetic damage. Therefore, the reduction of radiation dose has…

Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…

Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for understanding health and disease, yet their scale and…

Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…

We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…

One important question in neuroscience is how global behavior in a brain network emerges from the interplay between network connectivity and the neural dynamics of individual nodes. To better understand this theoretical relationship, we…

Hierarchically modular organization is a canonical network topology that is evolutionarily conserved in the nervous systems of animals. Within the network, neurons form directional connections defined by the growth of their axonal…

We analytically describe the architecture of randomly damaged uncorrelated networks as a set of successively enclosed substructures -- k-cores. The k-core is the largest subgraph where vertices have at least k interconnections. We find the…

We showed in this paper that similarity network can be used as an powerful tools to study the relationship of tRNA genes. We constructed a network of 3719 tRNA gene sequences using simplest alignment and studied its topology, degree…

Complex distribution networks are pervasive in biology. Examples include nutrient transport in the slime mold \emph{Physarum polycephalum} as well as mammalian and plant venation. Adaptive rules are believed to guide development of these…

Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…

In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…

The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…

A single protein molecule is regarded as a contact network of amino-acid residues. Some studies have indicated that this network is a small world network (SWN), while other results have implied that this is a fractal network (FN). However,…

Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…

Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches…

A construction method for duplex cage structures with icosahedral sym- metry made out of single-stranded DNA molecules is presented and applied to an icosidodecahedral cage. It is shown via a mixture of analytic and computer techniques that…

The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…

Biomolecular graph analysis has recently gained much attention in the emerging field of geometric deep learning. Here we focus on organizing biomolecular graphs in ways that expose meaningful relations and variations between them. We…