Related papers: Hydrodynamic interactions in DNA thermophoresis
The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model…
Surface tension plays a ubiquitous role in phase transitions including condensation or evaporation of atmospheric liquid droplets. Especially, understanding of interfacial thermodynamics of the critical nucleus of 1 nm scale is important…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
In this work we study thermoelectric properties of graphene nanoribbons with side-attached organic molecules. By adopting a single-band tight binding Hamiltonian and the Green's function formalism, we calculated the transmission and Seebeck…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
We propose a simple model to study resonant tunneling through an organic molecule between to conducting leads, taking into account the vibrational modes of the molecule. We solve the model approximately analytically in the weak coupling…
The application of a temperature gradient to an extended system generates an electromotive force that induces an electric current in conductors and a macroscopic polarization in insulators. The ratio of the electromotive force to the…
Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond…
Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…
Hydrodynamics is known to have strong effects on the kinetics of phase separation. There exist open questions on how such effects manifest in systems under confinement. Here, we have undertaken extensive studies of the kinetics of phase…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…
Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B transitions in DNA observed in silico in a simulated…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Swimming droplets are a class of active particles whose motility changes as a function of time due to shrinkage and self-avoidance of their trail. Here we combine experiments and theory to show that our non-Markovian droplet (NMD) model,…
Thermoelectric properties of GdBaCo_{2}O_{5+x} and NdBaCo_{2}O_{5+x} single crystals have been studied upon continuous doping of CoO_2 planes with either electrons or holes. The thermoelectric response and the resistivity behavior reveal a…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…