Related papers: The evaluation of directionally writhing polymers
We demonstrate the use of multiscale polymer modelling to quantitatively predict DNA linear dichroism (LD) in shear flow. LD is the difference in absorption of light polarised along two perpendicular axes, and has long been applied to study…
In this paper we continue our recent analysis [K. Haydukivska et al., J. Mol. Liq., 2021, 328, 115456] of complex molecules with two branching points at both ends of the linear backbone with $f_1$ and $f_2$ side arms starting from them,…
In this paper, we take a fresh look at using spectral analysis for assessing locking phenomena in finite element formulations. We propose to "measure" locking by comparing the difference between eigenvalue and mode error curves computed on…
Understanding looping probabilities, including the particular case of ring-closure or cyclization, of fluctuating polymers (eg DNA) is important in many applications in molecular biology and chemistry. In a continuum limit the configuration…
We calculate the energy and wave functions of two particles confined to two spatial dimensions interacting via arbitrary anisotropic potentials with negative or zero net volume. The general rigorous analytic expressions are given in the…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
We investigate the tight packing of nematic polymers inside a confining hard sphere. We model the polymer {\sl via} the continuum Frank elastic free energy augmented by a simple density dependent part as well as by taking proper care of the…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
Previous work shows that a net directed motion arises from a system of individual particles undergoing run-and-tumble dynamics in the presence of an array of asymmetric barriers. Here, we show that when the individual particle is replaced…
Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled…
Probabilistic models of directed polymers in random environment have received considerable attention in recent years. Much of this attention has focused on integrable models. In this paper, we introduce some new computational tools that do…