Related papers: How adsorption influences DNA denaturation
We analyse the effects of the environment (solvent quality, presence of extended structures - crowded environment) that may have impact on the order of the transition between denaturated and bounded DNA states and lead to changes in the…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
A new scenario of thermalization process of the adsorbate attached at solid surfaces is proposed. The scenario is based on existence of electric dipole layer in which the electron wavefunctions extend over the positive ions. Thus the strong…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
Low-energy structures of a hybrid system consisting of a polymer and an attractive nanowire substrate as well as the thermodynamics of the adsorption transition are studied by means of Monte Carlo computer simulations. Depending on…
For the DNA denaturation transition in the presence of random contact energies, or equivalently the disordered wetting transition, we introduce a Strong Disorder Renewal Approach to construct the optimal contacts in each disordered sample…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
We compare the thermodynamic behavior of a finite single nongrafted polymer near an attractive substrate with that of a polymer grafted to that substrate. After we recently found first-order-like signatures in the microcanonical entropy at…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
When a noble gas atom approaches a solid surface, it is adsorbed via the Van der Waals force, which is called physisorption. In this thesis, several experimental results concerning physisorbed atoms at surfaces are presented. First, photon…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
When two or more atoms bind to a solid surface, the substrate can mediate an interaction between them. In this paper, we use density-functional theory to quantify the substrate-mediated pair interaction between two adatoms on 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…
We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
A kinetic theory is proposed to elucidate complex nature of adsorption and desorption on surface and to calculate the adsorption and desorption rates in a practically simple way. This theory provides decomposition of the energy barriers and…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…
We study a system consisting of a particle adsorbed on a carbon nanotube resonator. The particle is allowed to diffuse along the resonator, in order to enable study of e.g. room temperature mass sensing devices. The system is initialized in…
Many experimental studies of protein deposition on solid surfaces involve alternating adsorption/desorption steps. In this paper, we investigate the effect of a desorption step (separating two adsorption steps) on the kinetics, the…