Related papers: RNA-RNA interaction prediction: partition function…
We compare the results obtained in the framework of the quasiparticle random phase approximation (QRPA) on top of a Hartree-Fock-Bogoliubov (HFB) with the most recent experiments on giant monopole resonances in Pb, Sn, Zr, Sm, Mo and Cd.…
When belief propagation (BP) converges, it does so to a stationary point of the Bethe free energy $F$, and is often strikingly accurate. However, it may converge only to a local optimum or may not converge at all. An algorithm was recently…
In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…
In the present paper a newer application of Artificial Neural Network (ANN) has been developed i.e., predicting response-function results of electrical-mechanical system through ANN. This method is specially useful to complex systems for…
An artificial neural network (ANN) is investigated as a tool for estimating rate coefficients for the collisional excitation of molecules. The performance of such a tool can be evaluated by testing it on a dataset of collisionally-induced…
We develop the spacetime aspects of the computation of partition functions for string/M-theory on AdS(3) xM. Subleading corrections to the semi-classical result are included systematically, laying the groundwork for comparison with CFT…
We consider the problem of signal estimation (denoising) from a statistical-mechanical perspective, in continuation to a recent work on the analysis of mean-square error (MSE) estimation using a direct relationship between optimum…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
Biomedical research has revealed the crucial role of miRNAs in the progression of many diseases, and computational prediction methods are increasingly proposed for assisting biological experiments to verify miRNA-disease associations…
Ions are critical to the structure and stability of polyelectrolytes such as nucleic acids. In this work, we systematically calculated the potentials of mean force between two like-charged nanoparticles in salt solutions by Monte Carlo…
We study two interacting particle systems, both modeled as a system of $N$ stochastic differential equations driven by Brownian motions with singular kernels and moderate interaction. We show a quantitative result where the convergence rate…
The partition function of the two-dimensional Ising model on a square lattice with nearest-neighbour interactions and periodic boundary conditions is investigated. Kaufman [Phys. Rev. 76, 1232--1243 (1949)] gave a solution for this function…
Assemblies of interacting quantum particles often surprise us with properties that are difficult to predict. One of the simplest quantum many-body systems is the spin 1/2 Heisenberg antiferromagnetic chain, a linear array of interacting…
Probabilistic inference in pairwise Markov Random Fields (MRFs), i.e. computing the partition function or computing a MAP estimate of the variables, is a foundational problem in probabilistic graphical models. Semidefinite programming…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
This paper proposes to apply the Ultra-Relativistic Quantum Molecular Dynamic (UrQMD) approach to implement the PANDA project (GSI). Modeling of $\bar{p}$A-interactions has been performed at antiproton energies from 1 GeV to 200 GeV by…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes$-$molecular complexes that translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the poles. We study…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…