Related papers: Breathing dynamics based parameter sensitivity ana…
We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n) that depend on the size $n$ of the bubble…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
Recent papers that have studied variants of the Peyrard-Bishop model for DNA, have taken into account the long range interaction due to the dipole moments of the hydrogen bonds between base pairs. In these models the helicity of the double…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
We consider three different continuum polymer models, that all depend on a tunable parameter r that determines the strength of the excluded-volume interactions. In the first model chains are obtained by concatenating hard spherocylinders of…
The dynamic nature of air quality chemistry and transport makes it difficult to identify the mixture of air pollutants for a region. In this study of air quality in the Houston metropolitan area we apply dynamic principal component analysis…
In this paper we investigate the dynamical behavior of an interface or polymer, in interaction with a distant attractive substrate. The interface is modeled by the graph of a nearest neighbor path with non-negative integer coordinates, and…
The hydrogen-bond (H-bond) network of high-pressure water is investigated by neural-network-based molecular dynamics (MD) simulations with the first-principles accuracy. The static structure factors (SSFs) of water at three densities, i.e.,…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
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…
Pulmonary hypertension (PH), defined by a mean pulmonary arterial pressure (mPAP) $>$ 20 mmHg, is characterized by increased pulmonary vascular resistance and decreased pulmonary arterial compliance. There are few measurable biomarkers of…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free…
It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901…
This work presents an algorithm for determining the parameters of a nonlinear dynamic model of the respiratory system in patients undergoing assisted ventilation. Using the pressure and flow signals measured at the mouth, the model's…