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In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
Hydrogen is the most abundant element in the universe, and its properties under conditions of high temperature and pressure are crucial to understand the interior of of large gaseous planets and other astrophysical bodies. At ultra high…
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…
We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the…
Cooling simulations of neutron stars and their comparison with the data from thermally emitting x-ray sources put constraints on the properties of axions, and by extension of any light pseudoscalar dark matter particles, whose existence has…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
In the present work we develop a Monte Carlo algorithm of the carbon chains ordered into 2D hexagonal array. The chemical bond of the chained carbon is computed from 1K to 1300K. Our model confirms that the beta phase is more energetic…
Annealing Mg-implanted homoepitaxial GaN at temperatures at or above 1400 {\deg}C eliminates the formation of inversion domains and leads to improved dopant activation efficiency. Extended defects in the form of inversion domains contain…
We present a quantitative analysis of superfluidity and superconductivity in dense matter from observations of isolated neutron stars in the context of the minimal cooling model. Our new approach produces the best fit neutron triplet…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $\varphi$ between neighboring base pairs stacked along the molecule backbone.…
The study of primordial chemistry of molecules adresses a number of interesting questions pertaining to the thermal balance of collapsing molecular protoclouds. In numerous astrophysical cases molecular cooling and heating influence…
Molecular dynamics simulations are utilized to study the microwave heating of methane hydrate by the five-body rotation coordinate system with the TIP5P-Ewald model. The structure I of methane hydrate is constructed, and the ice and free…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
We investigate the nucleation of carbon dioxide (CO$_2$) hydrates from carbon dioxide aqueous solutions by means of molecular dynamics simulations using the TIP4P/Ice and the TraPPE models for water and CO$_2$ respectively. We work at 400…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
We report on the detection of deuterated molecular hydrogen, HD, at $z = 0.18$. HD and H$_{\rm 2}$ are detected in HST/COS data of a low metallicity ($Z \sim 0.07Z_\odot$) damped Ly$\alpha$ system at $z = 0.18562$ toward QSO B0120$-$28,…
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…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Equilibrium properties of hydrogen-helium mixtures under conditions similar to the interior of giant gas planets are studied by means of first principle density functional molecular dynamics simulations. We investigate the molecular and…