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Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We investigate the motion of a run-and-tumble particle (RTP) in one dimension. We find the exact probability distribution of the particle with and without diffusion on the infinite line, as well as in a finite interval. In the infinite…
While it is very common to model diffusion as a random walk by assuming memorylessness of the trajectory and diffusive step lengths, these assumptions can lead to significant errors. This paper describes the extent to which a physical…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical…
Using computer simulations in two dimensions we investigate the dynamics and structure of passive polymeric tracer with different topologies immersed in a low-density active particle bath. One of the key observations is that polymer exhibit…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…
In recent experiments [T. Basta et al., Proc. Natl. Acad. Sci. U.S.A. 111, 670 (2014)] lipids and membrane proteins were observed to self-assemble into membrane protein polyhedral nanoparticles (MPPNs) with a well-defined polyhedral protein…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
The precise tracking of micron sized colloidal particles - held in the vicinity of each other using optical tweezers - is an elegant way to gain information about the particle-particle pair interaction potential. The accuracy of the method,…
Coherent transition radiation (CTR) from relativistic electron beam interaction with an overdense plasma foil is investigated by making use of two-dimensional particle-in-cell simulations. Well-defined single electron beam either of uniform…
Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…
The production of two double strand breaks in spatially separated locations on the DNA molecule can cause the loss of a whole DNA loop, which can be of substantial length depending on the geometrical position of the two damaged sites and…
Motion in bounded domains is a fundamental concept in various fields, including billiard dynamics and random walks on finite lattices, with important applications in physics, ecology and biology. An important universal property related to…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
As quantum computers and simulators begin to produce results that cannot be verified classically, it becomes imperative to develop a variety of tools to detect and diagnose experimental errors on these devices. While state or process…