Related papers: Model for processive nucleotide and repeat additio…
Recently proposed encoder-decoder structures for modeling Hawkes processes use transformer-inspired architectures, which encode the history of events via embeddings and self-attention mechanisms. These models deliver better prediction and…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
As a secondary structure of DNA, DNA tetrahedra exhibit intriguing charge transport phenomena and provide a promising platform for wide applications like biosensors, as shown in recent electrochemical experiments. Here, we study charge…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
Cell membranes interact via anchored receptor and ligand molecules. Central questions on cell adhesion concern the binding affinity of these membrane-anchored molecules, the mechanisms leading to the receptor-ligand domains observed during…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
We present a simple description on the electrophoretic dynamics of polyelectrolytes going through designed channels with narrow constrictions of slit geometry. By analyzing rheological behaviours of the stuck chain, which is coupled to the…
We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular…
We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of propagating front of…
Replica-mean-field models have been proposed to decipher the activity of neural networks via a multiply-and-conquer approach. In this approach, one considers limit networks made of infinitely many replicas with the same basic neural…
An efficient numerical framework is presented for modeling viscoelasticity and permanent set of polymers. It is based on the hereditary integral form of transient network theory, in which polymer chains belong to distinct networks each with…
Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad of…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…