Related papers: Reversible B/A Transitions in Single DNA Molecule …
Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational…
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…
Achieving a coherent understanding of the many thermodynamic and dynamic anomalies of water is among the most important unsolved puzzles in physics, chemistry, and biology. One hypothesized explanation imagines the existence of a line of…
Relying on symmetry considerations appropriate for helical biopolymers such as DNA and filamentous actin, we argue that crystalline packings of mutually repulsive helical macromolecules fall principally into two categories: unfrustrated…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
We discern hydration geometries around the sugar-phosphate-backbone of an RNA double helix at the molecular level. RNA disordering upon melting is connected with a transition from ordered water structures towards local phosphate group…
The osmotic coefficient of B-DNA in water may, in moderately dilute solutions, deviate as much as 100 % from predictions based on a simple 'counterion condensation' theory. We determine the results for osmotic properties via a cell model…
We present a comprehensive study of water drops sliding down chemically heterogeneous surfaces formed by a periodic pattern of alternating hydrophobic and hydrophilic stripes. Drops are found to undergo a stick-slip motion whose average…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
A liquid droplet is fragmented by a sudden pressurized-gas blow, and the resulting droplets, adhered to the window of a flatbed scanner, are counted and sized by computerized means. The use of a scanner plus image recognition software…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
For the first time, an ab initio molecular dynamics simulation was performed to describe the C$_3$S/water interface. The simulation shows that oxides with favorable environment are protonated at first, creating very stable hydroxide groups.…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined…
In the modern world, the focus of natural science research thought has shifted mainly to the molecular level, including the study of water. Water is considered as a mixture of interacting H2O molecules and their clusters based on the data…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…