Biomedical subjects

Alexey L Kaledin

Publications and source records attributed to Alexey L Kaledin.

4 recordsLinked to original sources

PubMed2006

Vibrational analysis of the H5O2+ infrared spectrum using molecular and driven molecular dynamics.

Standard molecular and driven molecular dynamics are used to analyze prominent spectral features in the H5O2+ infrared spectrum. In the driven method, the molecular Hamiltonian is augmented with a time-dependent term, mu x epsilon(0) sin(omegat), where mu is the dipole moment of H5O2+, epsilon0 is the electric field, and omega is the frequency. The magnitude of the electric field determines whether the driving is mild (the harmonic limit) or strong (anharmonic motion and mode coupling). We analyze the spectrum in the wavenumber range from 600 to 1900 cm(-1), where recent experimental measurements are available for H5O2+. On the basis of the simulations, we have assigned the broad feature around 1000 cm(-1) to the proton transfer coupled with the torsion motion. Intense absorption near 1780 cm(-1) is assigned to the H2O monomer bend coupled with proton transfer.

Models, Chemical↗

PubMed2005

Gradient-based direct normal-mode analysis.

A formulation of a direct, iterative method for obtaining the lowest eigenvalues and eigenvectors of a Hessian matrix is presented. Similar to the iterative schemes in electronic structure configuration interaction calculations (methods due to Lanczos, Davidson, and others), the mass-weighted Hessian matrix K is not constructed explicitly; instead, its operation on a basis vector (a direction in the 3N Cartesian configuration space of the atoms) is computed based on the principles of dynamical equations of motion. By noting that the time derivative of the gradient vector in the harmonic force field is related to the particles' momenta via dg/dt = Kp, a Hessian-vector product can be computed on the fly by finite differentiation of the gradient along the direction specified by the p vector. Thus, only two evaluations of the gradient are required per Davidson-like iteration per root, which leads to a linear scaling behavior of the computational effort with the number of atoms (provided that the evaluation of the gradient scales linearly). Preliminary results are presented for a 27,000-atom 4He nanodroplet.

Journal Article↗

PubMed2004

Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.

The driven molecular-dynamics (DMD) method, recently proposed by Bowman, Zhang, and Brown [J. Chem. Phys. 119, 646 (2003)], has been implemented into the TINKER molecular modeling program package. The DMD method yields frequencies and normal modes without evaluation of the Hessian matrix. It employs an external harmonic driving term that can be used to scan the spectrum and determine resonant absorptions. The molecular motions, induced by driving at resonant frequencies, correspond to the normal-mode vibrations. In the current work we apply the method to a 20-residue protein, Trp-cage, that has been reported by Neidigh, Fesinmeyer, and Andersen [Nature Struct. Biol. 9, 425 (2002)]. The structural and dynamical properties of this molecule, such as B-factors, root-mean square fluctuations, anisotropies, vibrational entropy, and cross-correlations coefficients, are calculated using the DMD method. The results are in very good agreement with ones calculated using standard normal-mode analysis method. Thus, the DMD method provides a viable alternative to the standard Hessian-based method and has considerable potential for the study of large systems, where the Hessian-based method is not feasible.

Algorithms↗

PubMed2004

An application of error reduction and harmonic inversion schemes to the semiclassical calculation of molecular vibrational energy levels.

A singular value decomposition based harmonic inversion signal processing scheme is applied to the semiclassical initial value representation (IVR) calculation of molecular vibrational states. Relative to usual IVR procedure of Fourier analysis of a signal made from the Monte Carlo evaluation of the phase space integral in which many trajectories are needed, the new procedure obtains acceptable results with many fewer trajectories. Calculations are carried out for vibrational energy levels of H2O to illustrate the overall procedure.

Journal Article↗