相关论文: Linear Polycatenanes from Kinetoplast Edge Loops
We set up an evolutionary algorithm combined with density functional tight-binding (DFTB) calculations to investigate hydrogen adsorption on flat graphene and graphene monolayers curved over substrate steps. During the evolution, candidates…
Linear and nonlinear optical lineshapes reveal details of excitonic structure in semiconductor polymers. We implement absorption, photoluminescence, and transient absorption spectroscopies in DPP-DTT, an electron push-pull copolymer, to…
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we…
Numerical modeling of electrodynamic aggregation is carried out for a random ensemble of magnetized nanodust taken as a many body system of strongly magnetized thin rods (i.e., one-dimensional static magnetic dipoles), which possess…
Quantification of microscopy time-series of in vitro reconstituted motor driven microtubule (MT) transport in 'gliding assays' is typically performed using computational object tracking tools. However, these are limited to non-intersecting…
Confined thin structures are ubiquitous in nature. Spatial and length constraints have led to a number of novel packing strategies at both the micro-scale, as when DNA packages inside a capsid, and the macro-scale, seen in plant root…
Dissipative Particle Dynamics (DPD) is becoming a popular particle based method to study flow through microchannels due to the ease with which the presence of biological cells or DNA chains can be modeled. Many Lab-On-Chip (LOC) devices…
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…
Recent studies introduced biased (degree-dependent) edge percolation as a model for failures in real-life systems. In this work, such process is applied to networks consisting of two types of nodes with edges running only between nodes of…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
Organic molecular crystals are appealing for next-generation optoelectronic applications, most notably due to their multiexciton generation process that can increase the efficiency of photovoltaic devices. However, a general understanding…
Convolutional Neural Networks (CNN) are widely used in many computer vision tasks. Yet, their increasing size and complexity pose significant challenges for efficient deployment on resource-constrained platforms. Hence, network pruning has…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
We develop a minimal system to study the stochastic formation of Borromean links within topologically entangled networks without requiring the use of knot invariants. Borromean linkages may form in entangled solutions of open polymer chains…