Related papers: ChromRec: Self-Assembly of Nucleosomes Driven by D…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
Based on experimental and simulation methods we helped develop, we are advancing mechanistic understanding of how self-assembled NC metamaterials can produce distinctive near- and far-field optical properties not readily achievable in…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
Deep neural networks (DNNs) have witnessed great successes in semantic segmentation, which requires a large number of labeled data for training. We present a novel learning framework called Uncertainty guided Cross-head Co-training (UCC)…
Deep learning, especially convolutional neural networks (CNNs) and Transformer architectures, have become the focus of extensive research in medical image segmentation, achieving impressive results. However, CNNs come with inductive biases…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
We investigated the high-order harmonic generation (HHG) process of diatomic molecular ion $\mathrm{H}_2^+$ in non-Born-Oppenheimer approximations. The corresponding three-dimensional time-dependent Schr\"odinger equation is solved with…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
Capturing the interplay between electronic correlations and many-particle entanglement requires a unified framework for Hamiltonian and eigenbasis renormalization. In this work, we apply the unitary renormalization group (URG) scheme…
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential…
Neutron/gamma discrimination has been intensively researched in recent years, due to its unique scientific value and widespread applications. With the advancement of detection materials and algorithms, nowadays we can achieve fairly good…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
Selective configuration control of plasmonic nanostructures using either top-down or bottom-up approaches has remained challenging in the field of active plasmonics. We demonstrate the realization of DNA-assembled reconfigurable plasmonic…
We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains…
Taxonomic classification in biodiversity research involves organizing biological specimens into structured hierarchies based on evidence, which can come from multiple modalities such as images and genetic information. We investigate whether…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…