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Three-nucleon forces are an essential ingredient for an accurate description of nuclear few- and many-body systems. However, implementing them directly in many-body calculations is technically very challenging. Thus, there is a need for an…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
Phase and time delays of atomic above-threshold ionization were recently experimentally explored in an $\omega -2\omega$ setting [Zipp et al, Optica 1, 361 (2014)]. The phases of wavepackets ejected from argon by a strong $2\omega$ pulse…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided…
We present results of a systematic study of the capture process through the barrier penetration model. The nucleus-nucleus interaction potential is calculated using the double-folding model (DFM) with the M3Y Paris NN forces. The nucleon…
We investigate further the recent proposal for the form of the Matrix theory action in weak background fields. We perform DVV reduction to the multiple D0-brane action in order to find the Matrix string theory action for multiple…
The description of forces across confined complex fluids still holds many challenges due to the possible overlap of different contributions. Here, an attempt is made to untangle the interaction between charged surfaces across nanoparticle…
The interaction of swift, free-space electrons with confined optical near fields has recently sparked much interest. It enables a new type of photon-induced near-field electron microscopy, mapping local optical near fields around…
Using the GAEA semi-analytic model, we analyse the connection between Damped Lyman-$\alpha$ systems (DLAs) and HI in galaxies. Our state-of-the-art semi-analytic model is tuned to reproduce the local galaxy HI mass function, and that also…
In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under…
This work assesses a classical density functional theory (DFT) model for predicting macroscopic static contact angles of pure substances and mixtures by comparison to own experimental data. We employ a DFT with a Helmholtz energy functional…
Force field have for decades proven to be an indispensable tool for molecular simulations which are out of reach for ab-initio methods. Recent efforts to improve the accuracy of these simulations have focused on the inclusion of many-body…
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and…
Solid-state materials have recently emerged as a new stage of strong-field physics and attosecond science. The mechanism of the electron dynamics driven by an ultrashort intense laser pulse is under intensive discussion. Here we…
Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using current laboratory techniques, and prior…
We show experimentally that a cheap glass microcapillary can accumulate {\lambda}-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop…