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The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
We develop an irregular lattice mass-spring-model (MSM) to simulate and study the deformation modes of a thin elastic ribbon as a function of applied end-to-end twist and tension. Our simulations reproduce all reported experimentally…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
In this paper, we seek to model the deformation of nucleated cells by single diode-laser bar optical stretchers. We employ a recently developed computational model, the Dynamic Ray-Tracing method, to determine the stress distribution…
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
Neural network compression methods have enabled deploying large models on emerging edge devices with little cost, by adapting already-trained models to the constraints of these devices. The rapid development of AI-capable edge devices with…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
The shear-induced deformation of a capsule with a stiff nucleus, a model of eukaryotic cells, is studied numerically. The membrane of the cell and of its nucleus are modelled as a thin and impermeable elastic material obeying a Neo-Hookean…
We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Computational models have become an essential part of exploratory protocols in cell biology, as a complement to in vivo or in vitro experiments. These virtual models have the twofold advantage of enabling access to new types of data and…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
We give a new approach to coding sequence (CDS) density estimation in genomic analysis based on the topological pressure, which we develop from a well known concept in ergodic theory. Topological pressure measures the "weighted information…
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…