Related papers: ATP-Dependent Mismatch Recognition in DNA Replicat…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
DNA mismatch repair (MMR) is the essential mechanism for preserving genomic integrity in various living organisms. In this process, MutS homologs (MSH) play crucial roles in identifying mismatched basepairs and recruiting downstream MMR…
We present a comprehensive and systematic study of thermal rectification in a prototypical low-dimensional quantum system -- a non-linear resonator: we identify necessary conditions to observe thermal rectification and we discuss strategies…
The increasing use of deep neural networks (DNNs) in safety-critical systems has raised concerns about their potential for exhibiting ill-behaviors. While DNN verification and testing provide post hoc conclusions regarding unexpected…
Automatic defect detection for 3D printing processes, which shares many characteristics with change detection problems, is a vital step for quality control of 3D printed products. However, there are some critical challenges in the current…
Adenosine triphosphate (ATP) is the universal chemical energy currency for cellular activities provided mainly by the membrane enzyme FoF1-ATP synthase in bacteria, chloroplasts and mitochondria. Synthesis of ATP is accompanied by subunit…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Retrosynthesis plays a crucial role in the fields of organic synthesis and drug development, where the goal is to identify suitable reactants that can yield a target product molecule. Although existing methods have achieved notable success,…
Particle identification is one of the core tasks in the data analysis pipeline at the Large Hadron Collider (LHC). Statistically, this entails the identification of rare signal events buried in immense backgrounds that mimic the properties…
Tomography is an imaging technique that works by reconstructing a scene from acquired data in the form of line integrals of the imaging domain. A fundamental underlying assumption in the reconstruction procedure is the precise alignment of…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
Kernel matching is a widely used technique for estimating treatment effects, particularly valuable in observational studies where randomized controlled trials are not feasible. While kernel-matching approaches have demonstrated practical…
Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for…
The model for cAMP-dependent synaptic plasticity relates the characterization of a noradrenaline-stimulated adenylyl cyclase with DNA unzipping. Specific proteins condition cAMP insertion in specific sites of the DNA structure to direct…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. Performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal…
Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…