相关论文: Coarse-grained modelling of strong DNA bending I: …
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a much broader range of forces, salt concentrations and contour lengths than previous approaches. Our theory…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA…
We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Long range charge transfer experiments in DNA oligomers and the subsequently measured -- and very diverse -- transport response of DNA wires in solid state experiments exemplifies the need for a thorough theoretical understanding of charge…