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Register a new userModels for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS
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An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.
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Aggregation of amphiphiles through the action of hydrophobic interactions is a common feature in soft condensed matter systems and is of particular importance in the context of biophysics as it underlies both the generation of functional biological machinery as well as the formation of pathological misassembled states of proteins. Here we explore the aggregation behaviour of amphiphilic polymers using lattice Monte-Carlo calculations and show that the distribution of hydrophobic residues within the polymer sequence determines the facility with which dry/wet interfaces can be created and that such interfaces drive the aggregation process.
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this melting transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.
The determination of a patients DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design personalized medicine [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-of-the-art density functional theory together with the non-equilibrium Greens Function method, leads to current responses that differ by at least one order of magnitude for different bases and can thus provide a much more robust read-out of the base sequence. The implementation of our proposed setup could thus lead to a viable protocol for rapid DNA sequencing with significant consequences for the future of genome related research in particular and health care in general.
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 force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the finite worm-like chain (FWLC) theory, which takes into account these effects. We show the FWLC predictions diverge from the classic WLC solution for molecules with contour lengths a few times the persistence length. Thus the FWLC will allow more accurate experimental calibration for relatively short molecules, facilitating future discoveries in single-molecule force microscopy.
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here, the effect of $G$ on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness $C_text{eff}$ for small twist-bend coupling. We find that the bare $G$ is screened by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with $G=0$, but with long-wavelength bending and twisting rigidities that are shifted by $G$-dependent amounts. Using results for torsional and bending rigidities for freely-fluctuating DNA, we show how our perturbative results can be extended to a non-perturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo triad and molecular dynamics oxDNA models, characterized by different degrees of coarse-graining, validating the perturbative and non-perturbative analyses. While our theory is in generally-good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely-used coarse-grained models.
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