Biomedical subjects

Volodymyr Babin

Publications and source records attributed to Volodymyr Babin.

5 recordsLinked to original sources

PubMed2006

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections.

There is considerable interest in developing methodologies for the accurate evaluation of free energies, especially in the context of biomolecular simulations. Here, we report on a reexamination of the recently developed metadynamics method, which is explicitly designed to probe "rare events" and areas of phase space that are typically difficult to access with a molecular dynamics simulation. Specifically, we show that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques. As test cases, we have studied the folding free energy landscape of two prototypical peptides: Ace-(Gly)(2)-Pro-(Gly)(3)-Nme in vacuo and trialanine solvated by both implicit and explicit water. The method has been implemented in the classical biomolecular code AMBER and is to be distributed in the next scheduled release of the code.

Algorithms↗

PubMed2006

Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure.

We have investigated to what extent molecular dynamics (MD) simulations can reproduce DNA sequence-specific features, given different electrostatic descriptions and different cell environments. For this purpose, we have carried out multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2. With respect to the electrostatic descriptions, two different force fields are studied: a traditional description based on atomic point charges and a polarizable force field. With respect to the cell environment, the difference between crystal and solution environments is emphasized, as well as the structural importance of divalent ions. By imposing the correct experimental unit cell environment, an initial configuration with two ideal B-DNA duplexes in the unit cell is shown to converge to the crystallographic structure. This convergence is measured by the appearance of sequence-dependent features that very closely resemble the crystallographic ones as well as by the decay of the all-atom root-mean-squared coordinates deviations (RMSD) with respect to the crystallographic structure. Given the appropriate crystallographic constraints, this is the first example of multiple nanosecond molecular dynamics trajectory that shows an ideal B-DNA model converging to an experimental structure, with a significant decay of RMSD.

Base Sequence↗

PubMed2006

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations.

The deprotonation of solvated formic acid was investigated theoretically with ab initio simulations. With the Car-Parrinello method, deprotonation and reprotonation by means of a proton wire were observed. The microscopics of these reactions were analyzed, and reveal the key role played by nearby water molecules in catalyzing the reactions. A constrained molecular dynamics calculation was carried out to estimate the dissociation free energy. Deprotonation of formic acid was further investigated with the recently developed metadynamics method using the formic acid oxygen coordination numbers as the collective variables. The determined free-energy landscape gives barriers similar to that obtained with the constrained free-energy calculation.

Computational Biology↗

PubMed2005

Pattern formation in nonextensive thermodynamics: selection criterion based on the Renyi entropy production.

We analyze a system of two different types of Brownian particles confined in a cubic box with periodic boundary conditions. Particles of different types annihilate when they come into close contact. The annihilation rate is matched by the birth rate, thus the total number of each kind of particles is conserved. When in a stationary state, the system is divided by an interface into two subregions, each occupied by one type of particles. All possible stationary states correspond to the Laplacian eigenfunctions. We show that the system evolves towards those stationary distributions of particles which minimize the Renyi entropy production. In all cases, the Renyi entropy production decreases monotonically during the evolution despite the fact that the topology and geometry of the interface exhibit abrupt and violent changes.

Journal Article↗

PubMed2004

Minimization of the Renyi entropy production in the stationary states of the Brownian process with matched death and birth rates.

We analyze the Fleming-Viot process. The system is confined in a box, whose boundaries act as a sink of Brownian particles. The death rate at the boundaries is matched by the branching (birth) rate in the system and thus the number of particles is kept constant. We show that such a process is described by the Renyi entropy whose production is minimized in the stationary state. The entropy production in this process is a monotonically decreasing function of time irrespective of the initial conditions. The first Laplacian eigenvalue is shown to be equal to the Renyi entropy production in the stationary state. As an example we simulate the process in a two-dimensional box.

Journal Article↗