Related papers: Two-dimensional chemical mapping for non-coding RN…
Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design. One of the major approaches in such a study is inverse quantitative structure…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Two-dimensional crystals, single sheets of layered materials, often show distinct properties desired for optoelectronic applications, such as larger and direct band gaps, valley- and spinorbit effects. Being atomically thin, the low amount…
Heterogeneous information network (HIN) embedding aims to embed multiple types of nodes into a low-dimensional space. Although most existing HIN embedding methods consider heterogeneous relations in HINs, they usually employ one single…
This paper tackles the pressing challenge of mutagenicity prediction by introducing three ground-breaking approaches. First, it showcases the superior performance of 2D scattering coefficients extracted from molecular images, compared to…
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
Some experimental evidences for methane are produced that the simple transition from frequency scanning of nonlinear-optical resonances to magnetic one may be accompanied with transition from sub-Doppler collisionally broadened structure to…
Work function-mediated charge transfer in graphene/$\alpha$-RuCl$_3$ heterostructures has been proposed as a strategy for generating highly-doped 2D interfaces. In this geometry, graphene should become sufficiently doped to host surface and…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Assignment of protein backbone resonances is most routinely carried out using triple resonance three dimensional NMR experiments involving amide 1H and 15N resonances. However for intrinsically unstructured proteins, alpha-helical proteins…
An unambiguous crystallographic structure solution for the observed phases II-VI of high pressure hydrogen does not exist due to the failure of standard structural probes at extreme pressure. In this work we propose that nuclear magnetic…
The Affymetrix U95 and U133 Latin Square spike-in datasets are reanalysed, together with a dataset from a version of the U95 spike-in experiment without a complex non-specific background. The approach uses a physico-chemical model which…
Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality…
More than twenty coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
A simple Mathematica code based on the differential realization of hard-core boson operators for finding exact solutions of the periodic-N spin-1/2 systems with or beyond nearest neighbor interactions is proposed, which can easily be used…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…