相关论文: Effective interaction between helical bio-molecule…
Charge-stabilized colloidal suspensions display a rich variety of microstructural and thermodynamic properties, which are determined by electro-steric interactions between all ionic species. The large size asymmetry between molecular-scale…
This paper concentrates on relationships of formal systems with biology. The paper is based on previous papers by the author. We have freely used texts of those papers where the formulations are of use, and we have extended the concepts and…
By a combination of Monte Carlo simulations and analytical calculations, we investigate the effective interactions between highly charged planar interfaces, neutralized by mobile counterions (salt-free system). While most previous analysis…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
Dual mechanical braiding experiments provide a useful tool with which investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
Contact probabilities between loci, separated by arbitrary genomic distance, for a number of cell types have been reported using genome-wide chromosome conformation capture (Hi-C) experiments. How to extract the effective interaction…
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension…
We show that two-particle interferences can be used to probe the nuclear motion in a doubly-excited hydrogen molecule. The dissociation of molecular hydrogen by electron impact involves several decay channels, associated to different…
We have performed single molecule stretching experiments and dynamic light scattering (DLS) in order to characterize the interaction between the DNA molecule and the fluorescent stain GelRed. The results from single molecule stretching show…
Recent laboratory experiments have measured fusion cross sections at center-of-mass energies low enough for the effects of atomic and molecular electrons to be important. To extract the cross section for bare nuclei from these data (as…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We investigate, for the first time, the thermal signature of a single-stranded helical molecule that is described beyond usual nearest-neighbor electron hopping, by analyzing electronic specific heat. Depending on the hopping of electrons,…
Electric double layers (EDL) with counterions only, say electrons with the elementary charge $-e$, in thermal equilibrium at the inverse temperature $\beta$ are considered. In particular, we study the effect of the surface charge modulation…
Molecular transport of biomolecules plays a pivotal role in the machinery of life. Yet, this role is poorly understood due the lack of quantitative information. Here, the role and properties of the C-terminal region of Escherichia coli Hfq…
We study unzipping of a complementary RNA-DNA helix applied to an external force, focusing on the force-force correlations. While at the microscopic level these are given by the sequence, the experiment measures effective, macroscopic…
Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a…
The effective interaction between spherical colloids in nematic liquid crystals is investigated in the framework of the Landau-de Gennes theory. The colloids differ through their interaction with the nematic. While both particles induce…
Very recently the Wood-Saxon (WS) type interaction in the single-folding potential approach are constructed to simulate the $ \phi{\text -}\alpha $ potentials. One set of the $ \phi{\text -}\alpha $ potentials are based on the first…