Related papers: The recombinase protein is a torque sensitive mole…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
In combining DNA nanotechnology and high-bandwidth single-molecule detection in nanopipettes, we demonstrate an all-electric, label-free hybridisation sensor for short DNA sequences (< 100 nt). Such short fragments are known to occur as…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
The recA/RAD51 gene family encodes a diverse set of recombinase proteins that effect homologous recombination, DNA-repair, and genome stability. The recA gene family is expressed in almost all species of Eubacteria, Archaea, and Eukaryotes,…
Recent results from the ATLAS and the CMS experiments at the Large Hadron Collider indicate the presence of a top-quark pair bound state near the threshold region. We present a way to reconstruct a toponium state at the $t\bar{t}$ threshold…
Understanding the relationship between protein sequences and their functions is fundamental to protein engineering, but this task is hindered by the combinatorially vast sequence space and the experimental noise inherent in fitness…
Most proteins involved in processing DNA accomplish their activities as a monomer or as a component of a multimer containing a relatively small number of other elements. They generally act locally, binding to one or a few small regions of…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m))…
Proteins are the active working horses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
In this project, we present a deep neural network (DNN)-based biophysics model that uses multi-scale and uniform topological and electrostatic features to predict protein properties, such as Coulomb energies or solvation energies. The…
Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory…
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA…
In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…