相关论文: Large-scale chromosome folding versus genomic DNA …

In many processes, the variations in underlying characteristics can be approximated by noisy multi-periodic patterns. If large-scale patterns are superimposed by a noise with long-range correlations, the detection of multi-periodic patterns…

Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…

Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…

We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT…

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…

In the past two decades, many research groups worldwide have tried to understand and categorize simple regimes in the charge transfer of such biological systems as DNA. Theoretically speaking, the lack of exact theories for electron-nuclear…

Linear scaling density functional theory approaches to electronic structure are often based on the tendency of electrons to localize even in large atomic and molecular systems. However, in many cases of actual interest, for example in…

Many media are divided into elementary units with irregular shape and size, as exemplified by domains in magnetic materials, bubbles in foams, or cells in biological tissues. Such media are essentially characterized by geometrical disorder…

Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…

Fourier transform (FT) plays a crucial role in a broad range of applications, from enhancement, restoration and analysis through to security, compression and manipulation. The Fourier transform (FT) is a process that converts a function…

Dynamical density functional theory (DDFT) is a powerful variational framework to study the nonequilibrium properties of colloids by only considering a time-dependent one-body number density. Despite the large number of recent successes,…

The discrete Fourier transform (DFT) is of fundamental interest in photonic quantum information, yet the ability to scale it to high dimensions depends heavily on the physical encoding, with practical recipes lacking in emerging platforms…

The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…

Two-dimensional mixtures of dipolar colloidal particles with different dipole moments exhibit extremely rich self-assembly behaviour and are relevant to a wide range of experimental systems, including charged and super-paramagnetic colloids…

In this work, we introduce a definition of the Discrete Fourier Transform (DFT) on Euclidean lattices in $\R^n$, that generalizes the $n$-th fold DFT of the integer lattice $\Z^n$ to arbitrary lattices. This definition is not applicable for…

Large-scale density functional theory (DFT) calculations provide a powerful tool to investigate the atomic and electronic structure of materials with complex structures. This article reviews a large-scale DFT calculation method, the…

In this paper a novel data embedding technique in frequency domain has been proposed using Discrete Fourier Transform (DFT) for image authentication and secured message transmission based on hiding a large volume of data into gray images.…

Density-functional theory (DFT) has revolutionized computer simulations in chemistry and material science. A faithful implementation of the theory requires self-consistent calculations. However, this effort involves repeatedly diagonalizing…

We give a fairly comprehensive review of wavelets and of their application to density-functional theory (DFT) and to our recent application of a wavelet-based version of linear-response time-dependent DFT (LR-TD-DFT). Our intended audience…

Linear-scaling implementations of density functional theory (DFT) reach their intended efficiency regime only when applied to systems having a physical size larger than the range of their Kohn-Sham density matrix (DM). This causes a problem…