相关论文: Effective interaction between helical bio-molecule…

We present a detailed analysis of the effective force between two smooth spherical colloids floating at a fluid interface due to deformations of the interface. The results hold in general and are applicable independently of the source of…

The classical Debye-Huckel (DH) theory clearly accounts for the origin of screening in electrolyte solutions and works rather well for dilute electrolyte solutions. While the Debye screening length decreases with the ion concentration and…

We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…

DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…

The interactions between atoms and molecules may be described by a potential energy function of the nuclear coordinates. Non-bonded interactions are dominated by repulsive forces at short range and attractive dispersion forces at long…

The hydrodynamic interactions among bacterial cell bodies, flagella, and surrounding boundaries are essential for understanding bacterial motility in complex environments. In this study, we demonstrate that each slender flagellum can be…

Interparticle interactions in charge-stabilized colloidal suspensions, of arbitrary salt concentration, are described at the level of effective interactions in an equivalent one-component system. Integrating out from the partition function…

Computer simulations and theory are used to systematically investigate how the effective force between two big colloidal spheres in a sea of small spheres depends on the basic (big-small and small-small) interactions. The latter are modeled…

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…

Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…

We introduce a test for the overall effect of interaction between DNA methylation and a set of single nucleotide polymorphisms (SNPs) on a quantitative phenotype. The developed inference procedure is based on a functional approach that…

Molecular Dynamics simulations are used to study the effective interactions in charged stabilized colloidal suspensions. For not too high macroion charges and sufficiently large screening, the concept of the potential of mean force is known…

A numerical study within the framework of the Poisson-Nernst-Planck equations is conducted to investigate electrostatic screening of charged bio-molecules within synthetic pores having diameters of at least 10 Debye lengths. We show that…

Using a non-contact atomic force microscope we track and manipulate the position of single electrons confined to atomic structures engineered from silicon dangling bonds (DBs) on the hydrogen terminated silicon surface. By varying the…

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…

We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…

The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is…

An effective interaction approach is used to describe the interactions between the spin 0 or spin 1/2 dark matter particle and the degrees of freedom of the standard model. This approach is applicable to those models in which the dark…

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…

An effective nucleon-nucleon interaction calculated in nuclear matter from the Bonn potential has been parametrized in terms of a local density- and energy-dependent two-body interaction. This allows to calculate the real part of the…