Related papers: Bubbles, clusters and denaturation in genomic DNA:…
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
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…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
3D-Particle Tracking (3D-PTV) and Phase Sensitive Constant Temperature Anemometry in pseudo-turbulence--i.e., flow solely driven by rising bubbles-- were performed to investigate bubble clustering and to obtain the mean bubble rise…
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the…
Dynamical properties of a Lennard-Jones binary mixture embedded in an off lattice matrix of soft spheres are studied in the direct space upon supercooling by molecular dynamics simulations. On lowering temperature the smaller particles tend…
Systematic microstructure design requires reliable thermodynamic descriptions of each and all microstructure elements. While such descriptions are well established for most bulk phases, thermodynamic assessment of crystal defects is…
Bosonic condensates offer exciting prospects for studies of non-equilibrium quantum dynamics. Understanding the dynamics is particularly challenging in the sub-picosecond timescales typical for room temperature luminous driven-dissipative…
The behavior of nuclear matter is studied at low densities and temperatures using classical molecular dynamics with three different sets of potentials with different compressibility. Nuclear matter is found to arrange in crystalline…
Heat conduction has been found a plausible solution to explain discrepancies between expected and measured temperatures in hot bubbles of planetary nebulae (PNe). While the heat conduction process depends on the chemical composition, to…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
We briefly review some of the models used to describe DNA denaturation dynamics, focusing on the value of the dynamical exponent $z$, which governs the scaling of the characteristic time $\tau\sim L^z$ as a function of the sequence length…
We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
High-throughput ab-initio calculations, cluster expansion techniques and thermodynamic modeling have been synergistically combined to characterize the binodal and the spinodal decompositions features in the pseudo-binary lead chalcogenides…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
We present a phenomenological model of the dynamics of buoyant bubbles in the atmosphere of a cluster of galaxies. The derived equations describe velocity, size, mass, temperature and density of the buoyant bubbles as functions of time…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…