相关论文: Stacking Interactions in Denaturation of DNA Fragm…
Mesoscopic-scale stacking reconfigurations are investigated when van der Waals films are stacked. We have developed a method to visualize complicated stacking structures and mechanical distortions simultaneously in stacked atom-thick films…
Tailoring the nanomorphology of organic photoactive layers through a specialized chain of processing steps is an imperative challenge on the path towards reliable and performant organic electronic manufacturing. This hurdle generally proves…
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian,…
Polymer-grafted nanoparticles (PGNPs) can provide property profiles than cannot be obtained individually by polymers or nanoparticles (NPs). Here, we have studied the mixing--demixing transition of symmetric copolymer melts of…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
Two roads are presently being followed in order to establish the existence of a liquid-gas phase transition in finite nuclear systems from nuclear reactions at high energy. The clean experiment of observing the thermodynamic properties of a…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…
The phase diagram of a stack of tensionless membranes with nonlinear curvature energy and vertical harmonic interaction is calculated exactly in a large number of dimensions of configuration space. At low temperatures, the system forms a…
In frameworks of the phenomenological approach we analyze of the phase diagram of mixed compounds. We obtain space groups of symmetry of the real structures as result of phase transition from close-packed degenerate structure. The theory of…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
We analyze different microscopic RNA models at zero temperature. We discuss both the most simple model, that suffers a large degeneracy of the ground state, and models in which the degeneracy has been remove, in a more or less severe…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
Configuration interaction method is used to calculate transition amplitudes and other properties of the low states of dysprosium which are used in cooling and in study of the time variation of the fine structure constant and violation of…
The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we…