Related papers: Three-Dimensional Loop Extrusion
It is difficult to intuit how electronic structure features$-$such as band gap magnitude, location of band extrema, effective masses, etc.$-$arise from the underlying crystal chemistry of a material. Here we present a strategy to distill…
We identify occlusion reasoning as a fundamental yet overlooked aspect for 3D layout-conditioned generation. It is essential for synthesizing partially occluded objects with depth-consistent geometry and scale. While existing methods can…
Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static…
The scattering patterns near the primary rainbow of oblate drops are simulated by extending the vectorial complex ray model (VCRM) [1] to three-dimensional (3D) calculations. With the curvature of wavefront as intrinsic property of a ray,…
Predicting protein functional characteristics from structure remains a central problem in protein science, with broad implications from understanding the mechanisms of disease to designing novel therapeutics. Unfortunately, current machine…
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale…
Linear and nonlinear optical lineshapes reveal details of excitonic structure in semiconductor polymers. We implement absorption, photoluminescence, and transient absorption spectroscopies in DPP-DTT, an electron push-pull copolymer, to…
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs or catalytic sites. Here we explore methods to generate template libraries and algorithms to query…
Graph convolutions have gained popularity due to their ability to efficiently operate on data with an irregular geometric structure. However, graph convolutions cause over-smoothing, which refers to representations becoming more similar…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
Three pomerons are known to couple via the gluon loop and interactions of this kind which are responsible for high-mass diffraction are described in terms of the gluonic structure function of the QCD pomeron. We show that the triple-pomeron…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…
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…
Trajectory segmentation refers to dividing a trajectory into meaningful consecutive sub-trajectories. This paper focuses on trajectory segmentation for 3D rigid-body motions. Most segmentation approaches in the literature represent the…
A general method for describing magnetic reconnection in arbitrary three-dimensional magnetic configurations is proposed. The method is based on the field-line mapping technique previously used only for the analysis of magnetic structure at…
A theory of fractional kinetics of glial cancer cells is presented. A role of the migration-proliferation dichotomy in the fractional cancer cell dynamics in the outer-invasive zone is discussed an explained in the framework of a continuous…
Micro-scale flow in cylindrical geometries can harness chaotic advection to perform complex thermally activated biochemical reactions such as the polymerase chain reaction (PCR). We have applied a 3D computational fluid dynamics model to…
When injected through a contraction, high molecular weight polymer solutions exhibit a sharp increase of apparent viscosity which originates from stretching polymer chains above a critical extension rate. This chain stretching can also…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…