Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length...

Pulsed helium ion beam induced deposition: A means to high growth rates

The sub-nanometer beam of a helium ion microscope was used to study and optimize helium-ion beam induced deposition of PtC nanopillars with the (CH3)3Pt(CPCH3) precursor. The beam current, beam dwell time, precursor refresh time, and beam focus have been independently varied. Continuous beam exposure resulted in narrow but short pillars, while...

Model for nanopillar growth by focused helium ion-beam-induced deposition

An analytical model for the growth of nanopillars by helium ion-beam-induced deposition is presented and compared to experimental data. This model describes the competition between pillar growth in vertical and lateral directions. It assumes that vertical growth is induced by incident primary ions and type-1 secondary electrons, whereas lateral...

The persistence length of double stranded DNA determined using dark field tethered particle motion

The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are...

Percolation transitions in two dimensions

We investigate bond- and site-percolation models on several two-dimensional lattices numerically, by means of transfer-matrix calculations and Monte Carlo simulations. The lattices include the square, triangular, honeycomb kagome, and diced lattices with nearest-neighbor bonds, and the square lattice with nearest- and next-nearest-neighbor bonds...

Application of the optimized Baxter model to the hard-core attractive Yukawa system

We perform Monte Carlo simulations on the hard-core attractive Yukawa system to test the optimized Baxter model that was introduced by Prinsen and Odijk [J. Chem. Phys. 121, 6525 (2004) ] to study a fluid phase of spherical particles interacting through a short-range pair potential. We compare the chemical potentials and pressures from the...

Computing the starting state for Gibbs-Duhem integration

Gibbs-Duhem integration implies the numerical integration of a Clapeyron equation. To start the numerical integration, an initial coexistence point and a corresponding initial slope of the Clapeyron equation are needed. In order to apply Gibbs-Duhem integration to all kinds of systems at diverse physical conditions, one has to investigate and...

Three-dimensional Ising model confined in low-porosity aerogels: A Monte Carlo study

Role of elasticity forces in thermodynamics of intercalation compounds: Self-consistent mean-field theory and Monte Carlo simulations

We propose a self-consistent mean-field lattice-gas theory of intercalation compounds based on effective interactions between interstitials in the presence of the host atoms. In addition to short-range screened Coulomb repulsions, usually discussed in the lattice gas models, the present theory takes into account long-range effective attractions...

The effect of Coulomb interactions on the ac mobility of charges in quasi-one-dimensional systems. Example: Discotic liquid crystals

Using Monte Carlo simulations we calculate the frequency dependence of the diffusive mobility of a group of carriers on a short one-dimensional chain. We allow the carriers to interact with each other through weakly screened long-range Coulomb potentials. We consider both doped systems with discrete immobile counterions and gated systems with...

Estimation of detector responses by midway forward and adjoint Monte Carlo coupling in nuclear systems