Related papers: Sequence matching algorithms and pairing of noncod…
We report multipronged progress on the stochastic averaging approach to numerical analytic continuation of quantum Monte Carlo data. With the sampled spectrum parametrized with delta-functions in continuous frequency space, a calculation of…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
In this article, the reproducing kernel Hilbert space [0, 1] is employed for solving a class of third-order periodic boundary value problem by using fitted reproducing kernel algorithm. The reproducing kernel function is built to get fast…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism $\mbox{$\bR \rightarrow \bGamma$}$ between two relational…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
We study the non restoration of symmetries with a local order parameter in field theory at finite temperature. After giving an interpretation of the phenomenon, we show that hierarchy problems are a necessary condition for its realization…
Low rank tensor learning, such as tensor completion and multilinear multitask learning, has received much attention in recent years. In this paper, we propose higher order matching pursuit for low rank tensor learning problems with a convex…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two…
We address the problem of recovering multiple structures of different classes in a dataset contaminated by noise and outliers. In particular, we consider geometric structures defined by a mixture of underlying parametric models (e.g. planes…
We aim to investigate relationships between select processing parameters or inputs (composition, temperature, annealing time) and two structural parameters, specifically, the mean radius and volume fraction of the Fe$_3$Si nanocrystals. To…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
In this article we consider the graph alignment problem from the perspective of high-dimensional statistics: we aim to estimate an unknown permutation $\pi^*$ from the observation of two correlated random adjacency matrices $A_1$, $A_2$. We…
This work proposes a hierarchical clustering algorithm for high-dimensional datasets using the cyclic space of reversible finite cellular automata. In cellular automaton (CA) based clustering, if two objects belong to the same cycle, they…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…