相关论文: Can re-entrance be observed in force induced trans…
We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
The pattern of isentropes in the vicinity of a first-order phase transition is proposed as a key for a sub-classification. While the confinement--deconfinement transition, conjectured to set in beyond a critical end point in the QCD phase…
We report on the onset of fluid entrainment when a contact line is forced to advance over a dry solid of arbitrary wettability. We show that entrainment occurs at a critical advancing speed beyond which the balance between capillary,…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
Monte Carlo simulations have been performed for aqueous charged colloidal suspensions as a function of charge density on the particles and salt concentration. We vary the charge density in our simulations over a range where a reentrant…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
Pairing reentrance phenomenon in the warm rotating $^{104}$Pd nucleus is studied within the Bardeen-Cooper-Schrieffer (BCS)-based approach (the FTBCS1). The theory takes into account the effect of quasiparticle number fluctuations on the…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
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…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
The effect of a diffusivity edge is studied in a system of scalar active matter confined by a periodic potential and driven by an externally applied force. We find that this system shows qualitatively distinct stationary regimes depending…
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…