Related papers: Modeling of two-dimensional DNA display
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
Building on the remarkable achievements in generative sampling of natural images, we propose an innovative challenge, potentially overly ambitious, which involves generating samples of entire multivariate time series that resemble images.…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
We propose a new approach for constructing a 3D representation from a 2D wireframe drawing. A drawing is simply a parallel projection of a 3D object onto a 2D surface; humans are able to recreate mental 3D models from 2D representations…
Two-dimensional spectroscopy (2DS) is a powerful ultrafast technique for probing electronic and vibrational dynamics in complex microscopic systems. Extracting detailed information on system dynamics and system-bath interactions from 2DS…
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…
The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems. Understanding these avalanches of high-dimensional data -- by distilling underlying principles and mechanisms --…
Domain decomposition is a technique used to reduce memory overhead on large neutron transport problems. Currently, the optimal load-balanced processor allocation for these domains is typically determined through small-scale simulations of…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Nearly all 3D displays need calibration for correct rendering. More often than not, the optical elements in a 3D display are misaligned from the designed parameter setting. As a result, 3D magic does not perform well as intended. The…
Numerical simulations are commonly used to understand the parameter dependence of given spatio-temporal phenomena. Sampling a multi-dimensional parameter space and running the respective simulations leads to an ensemble of a large number of…
Dynamic mode decomposition (DMD) is a versatile approach that enables the construction of low-order models from data. Controller design tasks based on such models require estimates and guarantees on predictive accuracy. In this work, we…
We focus on an important yet challenging problem: using a 2D deep network to deal with 3D segmentation for medical image analysis. Existing approaches either applied multi-view planar (2D) networks or directly used volumetric (3D) networks…
We review recent advances in the DNA sequencing based on the measurement of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major…
Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway…
Anatomical landmark correspondences in medical images can provide additional guidance information for the alignment of two images, which, in turn, is crucial for many medical applications. However, manual landmark annotation is…
Two-dimensional (2D) spectroscopy combines high temporal and spectral resolution, allowing the observation of ultrafast energy transfer and the separation of homogeneous and inhomogeneous broadening. Typically, 2D spectroscopy is dominated…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…