Related papers: Sequence-dependent Three Interaction Site (TIS) Mo…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
Double excitations in organic molecules have garnered significant interest as a result of their importance in singlet fission and photophysics. These excitations play a crucial role in understanding the photoexcitation processes in…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
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…
We formulate and solve a two-state model for the elasticity of nicked, double-stranded DNA that borrows features from both the Worm Like Chain and the Bragg--Zimm model. Our model is computationally simple, and gives an excellent fit to…
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…
Molecular docking is a cornerstone of drug discovery to unveil the mechanism of ligand-receptor interactions. With the recent development of deep learning in the field of artificial intelligence, innovative methods were developed for…
We analyze structural and conformational properties in a simulated bead-spring model of a non-entangled, supercooled polymer melt. We explore the statics of the model via various structure factors, involving not only the monomers, but also…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…