Related papers: A stitch in time: Efficient computation of genomic…
With recent advances in sequencing technologies, large amounts of epigenomic data have become available and computational methods are contributing significantly to the progress of epigenetic research. As an orthogonal approach to methods…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
Most real-world dynamic systems are composed of different components that often evolve at very different rates. In traditional temporal graphical models, such as dynamic Bayesian networks, time is modeled at a fixed granularity, generally…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
Upcoming many core processors are expected to employ a distributed memory architecture similar to currently available supercomputers, but parallel pattern mining algorithms amenable to the architecture are not comprehensively studied. We…
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…
One of the main challenges in modeling massive stars to the onset of core collapse is the computational bottleneck of nucleosynthesis during advanced burning stages. The number of isotopes formed requires solving a large set of…
We discuss the performance of direct summation codes used in the simulation of astrophysical stellar systems on highly distributed architectures. These codes compute the gravitational interaction among stars in an exact way and have an…
We propose a deep hashing framework for sketch retrieval that, for the first time, works on a multi-million scale human sketch dataset. Leveraging on this large dataset, we explore a few sketch-specific traits that were otherwise…
Genetic algorithms are a powerful tool in optimization for single and multi-modal functions. This paper provides an overview of their fundamentals with some analytical examples. In addition, we explore how they can be used as a parameter…
Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent…
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
We describe in detail a new and highly efficient algorithm for studying site or bond percolation on any lattice. The algorithm can measure an observable quantity in a percolation system for all values of the site or bond occupation…
This paper presents an effective normal estimation method adopting multi-patch stitching for an unstructured point cloud. The majority of learning-based approaches encode a local patch around each point of a whole model and estimate the…
In topologically-protected quantum computation, quantum gates can be carried out by adiabatically braiding two-dimensional quasiparticles, reminiscent of entangled world lines. Bonesteel et al. [Phys. Rev. Lett. 95, 140503 (2005)], as well…