Related papers: A Single Nucleotide Resolution Model for Large-Sca…
In this paper, we present Reed-Solomon coded single-stranded representation learning (RSRL), a novel end-to-end model for learning representations for multi-modal lossless DNA storage. In contrast to existing learning-based methods, the…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
It is well known that during homology recognition and strand exchange the double stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
Something about structure of the water shell of DNA and how it can help to design of novel biologically-active molecules and potential drugs with sequence-specific binding to nucleic acids.
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random…
Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…
The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores…
DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…