Related papers: Folding 3-noncrossing RNA pseudoknot structures
In this paper we present an algorithm for enumerating without repetitions all the non-crossing generically minimally rigid bar-and-joint frameworks under edge constraints (also called constrained non-crossing Laman frameworks) on a given…
We present a formal and constructive simulation framework for nondeterministic finite automata (NFAs) using time-shared, depth-unrolled feedforward networks (TS-FFNs), i.e., acyclic unrolled computations with shared parameters that are…
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…
The electronic structure of NaFeAs is studied with angle resolved photoemission spectroscopy on high quality single crystals. Large portions of the band structure start to shift around the structural transition temperature, and smoothly…
We find that the fractal scaling in a class of scale-free networks originates from the underlying tree structure called skeleton, a special type of spanning tree based on the edge betweenness centrality. The fractal skeleton has the…
In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan {\it et al.} (Alkan {\it et al.}, J. Comput. Biol., Vol:267--282, 2006). Our main results are the derivation of the…
Many biological networks grow by elongation of filaments that can branch and fuse -- typical examples include fungal mycelium or slime mold. These networks must simultaneously perform multiple tasks such as transport, exploration, and…
By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem DFT has recently emerged as a powerful tool for reducing the computational scaling of Kohn--Sham DFT. To date,…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
DNA minicircles are closed double-stranded DNA (dsDNA) fragments that have been demonstrated to be an important experimental tool to understand supercoiled, or stressed, DNA mechanics, such as nucleosome positioning and DNA-protein…
We employ several unsupervised machine learning techniques, including autoencoders, random trees embedding, and t-distributed stochastic neighboring ensemble (t-SNE), to reduce the dimensionality of, and therefore classify, raw (auxiliary)…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…
RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for…
The three-nucleon force (3NF) is crucial in shaping the shell structure of atomic nuclei, particularly impacting the enhancement of spin-orbit (SO) splitting, especially in nuclei with significant deviations from stability. Despite its…
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…
The spin crossover properties and the domains of existence of the different phases for the [Fe(PM-BIA)2(NCS)2] complex are obtained from combining DFT and classical molecular dynamics (MD). The potential energy surfaces expressed in the…
Networks of silicon nanowires possess intriguing electronic properties surpassing the predictions based on quantum confinement of individual nanowires. Employing large-scale atomistic pseudopotential computations, as yet unexplored branched…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…