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Dusanka Janezic

Publications and source records attributed to Dusanka Janezic.

14 recordsLinked to original sources
PubMed2006

New force field for calcium binding sites in annexin-membrane complexes.

For accurate classical molecular dynamics (MD) simulations of the calcium mediated bound complexes of annexin and membrane we have developed new force-field parameters correctly describing the interaction of the Ca ion with its environment. We have used quantum chemical calculations to investigate the potential energy surface experienced by the Ca ion within the three different binding sites found in domain 1 of annexin V (ANX V/1). Based on these calculations we were able to quantify the charge polarization of atoms within the binding sites, and to determine the geometry and force constants of harmonic restraints between the Ca ion and its coordinating oxygen atoms. Harmonic restraints were introduced to compensate for the deviations between the quantum mechanical potential energy surface and that of the classical force field. Our analysis has shown that using the refined force field for the Ca binding sites enables long-time MD simulations that conserve the initial structure of ANX V/1 significantly better than MD simulations using the standard force field.

Annexin A5↗
PubMed2005

Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators.

New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of molecular vibrations to solve the Hamiltonian equations of motion. The presented integrators analytically resolve the internal high-frequency molecular vibrations by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The translation and rotation of a molecule are treated as vibrational motions with the vibrational frequency zero. All types of motion are thus described in terms of the normal coordinates. The method's time reversibility requirement was used to determine the equations of motion for internal coordinate system of a molecule. The calculation of long-range forces is performed numerically within the generalized second-order leap-frog scheme, in the same way as in standard second-order symplectic methods. The new methods for integrating classical equations of motion using normal mode analysis allow us to use a long integration step and are applicable to any system of molecules with one equilibrium configuration.

Journal Article↗
PubMed2005

Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules.

A series of molecular dynamics (MD) simulations of nonlinear molecules has been performed to test the efficiency of newly introduced semianalytical second-order symplectic time-reversible MD integrators that combine MD and the standard theory of molecular vibrations. The simulation results indicate that for the same level of accuracy, the new algorithms allow significantly longer integration time steps than the standard second-order symplectic leap-frog Verlet method. Since the computation cost per integration step using new MD integrators with longer time steps is approximately the same as for the standard method, a significant speed-up in MD simulation is achieved.

Journal Article↗
PubMed2005

Molecular dynamics integration and molecular vibrational theory. III. The infrared spectrum of water.

The new symplectic molecular dynamics (MD) integrators presented in the first paper of this series were applied to perform MD simulations of water. The physical properties of a system of flexible TIP3P water molecules computed by the new integrators, such as diffusion coefficients, orientation correlation times, and infrared (IR) spectra, are in good agreement with results obtained by the standard method. The comparison between the new integrators' and the standard method's integration time step sizes indicates that the resulting algorithm allows a 3.0 fs long integration time step as opposed to the standard leap-frog Verlet method, a sixfold simulation speed-up. The accuracy of the method was confirmed, in particular, by computing the IR spectrum of water in which no blueshifting of the stretching normal mode frequencies is observed as occurs with the standard method.

Journal Article↗
PubMed2002

Some multiple-time-scale problems in molecular dynamics.

Many physical problems, particularly in chemical and biological systems, involve processes that occur over widely varying time scales. Such problems have motivated the development of new methods for treating multiple-time-scale problems in molecular dynamics (MD). Methods have been developed for determining the vibrational frequencies and normal modes of large systems in full and reduced conformational space. A method is given for quasiharmonic analysis and reduced quasiharmonic analysis.

Animals↗
PubMed2002

CROW for large scale macromolecular simulations.

CROW (Columns and Rows Of Workstations - http://www.sicmm.org/crow/) is a parallel computer cluster based on the Beowulf (http://www.beowulf.org/) idea, modified to support a larger number of processors. Its architecture is based on point-to-point network architecture, which does not require the use of any network switching equipment in the system. Thus, the cost is lower, and there is no degradation in network performance even for a larger number of processors.

Computational Biology↗
PubMedDate not supplied

Molecular dynamics integration time step dependence of the split integration symplectic method on system density.

This paper shows that the maximal size of the integration time step of the Split Integration Symplectic Method (SISM) for molecular dynamics (MD) integration, a combination of the analytical solution of the high-frequency harmonic part of the Hamiltonian and the numerical solution of the low-frequency remaining part, depends on the system density. This approach was tested on a system of linear chain molecules. The numerical results indicate that the integration time step used by the SISM is limited by atoms' motion generated by the electrostatic and Lennard-Jones interactions in the system. As the density of the system increases, the size of the integration time step allowed by the SISM thus becomes smaller but remains significantly larger than possible by standard methods of the same order and complexity.

Journal Article↗
PubMedDate not supplied

Enumeration of conjugated circuits in nanotubes.

The resonance energy of (1,1)n "armchair" carbon nanotubes and (n,n)1 nanoribbons was determined by enumerating the conjugated circuits (CC) and the Kekulé structures. The lower indices denote the number of hexagon layers. It was found that the resonance energy per carbon atom is equal to 0.160 eV in (1,1)n tubes and 0.142 eV in (n,n)1 tubes.

Journal Article↗
PubMedDate not supplied

Improving the performance of molecular dynamics simulations on parallel clusters.

In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds.

Journal Article↗
PubMedDate not supplied

Periodic cages.

Various cages are constructed by using three types of caps: f-cap (derived from spherical fullerenes by deleting zones of various size), kf-cap (obtainable by cutting off the polar ring, of size k), and t-cap ("tubercule"-cap). Building ways are presented, some of them being possible isomerization routes in the real chemistry of fullerenes. Periodic cages with ((5,7)3) covering are modeled, and their constitutive typing enumeration is given. Spectral data revealed some electronic periodicity in fullerene clusters. Semiempirical and strain energy calculations complete their characterization.

Journal Article↗
PubMedDate not supplied

Molecular dynamics integration meets standard theory of molecular vibrations.

An iterative SISM (split integration symplectic method) for molecular dynamics (MD) integration is described. This work explores an alternative for the internal coordinate system prediction in the SISM introduced by JaneZic et al. (J. Chem. Phys. 2005, 122, 174101). The SISM, which employs a standard theory of molecular vibrations, analytically resolves the internal high-frequency molecular vibrations. This is accomplished by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The Eckart frame, which is usually used in the standard theory of molecular vibrations as an internal coordinate system of a molecule, is adopted to be used within the framework of the second order generalized leapfrog scheme. In the presented MD integrator the internal coordinate frame at the end of the integration step is predicted halfway through the integration step using a predictor-corrector type iterative approach thus ensuring the method's time reversibility. The iterative SISM, which is applicable to any system of molecules with one equilibrium configuration, was applied here to perform all-atom MD simulations of liquid CO2 and SO2. The simulation results indicate that for the same level of accuracy, this algorithm allows significantly longer integration time steps than the standard second-order leapfrog Verlet (LFV) method.

Journal Article↗
PubMedDate not supplied

Symplectic molecular dynamics simulations on specially designed parallel computers.

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Algorithms↗
PubMedDate not supplied

Retro-leapfrog and related retro map operations.

Operations on maps are well-known theoretical tools for transforming a given polyhedral tessellation. Several theoretical investigations of fullerenes, such as their pi-electronic structure and stability, need information on the original map which was transformed into a larger molecular structure. In this respect, retro-operations, particularly those of the most used leapfrog, chamfering, and capra operations, appear particularly useful in searching the associate graphs of fullerenes. A series of analyzed cages proved to be leapfrog transforms of smaller cages. This information was useful in understanding their closed pi-electronic structure and related properties including the local aromaticity. An index based on the optimized geometries enabled the evaluation of aromaticity of their various substructures. Pictorial images of the pi-electron distribution as the main Kekulé valence structures have been performed by the aid of the JSCHEM software package.

Carbon↗