Related papers: Entropic Penalties in Circular DNA Assembly
We present an experiment in which a horizontal quasi-2D granular system with a fixed neighbor network is cyclically compressed and decompressed over 1000 cycles. We remove basal friction by floating the particles on a thin air cushion, so…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
In this work, we consider two spins initially prepared in a product of coherent states and study their entanglement dynamics due to a general interacting Hamiltonian. We adopt an approach that allowed the derivation of a semiclassical…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We consider a Brownian particle confined by an external potential and subject to stochastic resetting to the origin. Motivated by the repetitive nature of the dynamics, we describe the process as a thermodynamic cycle of thermal expansion…
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
Entropic dynamics is a framework in which quantum theory is derived as an application of entropic methods of inference. Entropic dynamics on flat spaces has been extensively studied. The objective of this paper is to extend the entropic…
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
The depletion interaction mediated by non-adsorbing polymers promotes condensation and assembly of repulsive colloidal particles into diverse higher-order structures and materials. One example, with particularly rich emergent behaviors, is…
A one dimensional trap model for a thermally activated classical particle is introduced to simulate driven dynamics in presence of "ageing" effects. The depth of each trap increases with the time elapsed since the particle has fallen into…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
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…
Entropic Dynamics (ED) is a framework in which Quantum Mechanics is derived as an application of entropic methods of inference. In ED the dynamics of the probability distribution is driven by entropy subject to constraints that are codified…
We study numerically the induction mechanisms generated from an array of helical motions distributed along a cylinder. Our flow is a very idealized geometry of the columnar structure that has been proposed for the convective motion inside…