Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles

We present a new theory for modeling forced indentation spectral lineshapes of biological particles, which considers non-linear Hertzian deformation due to an indenter-particle physical contact and bending deformations of curved beams modeling the particle structure. The bending of beams beyond the critical point triggers the particle dynamic transition to the collapsed state, an extreme event leading to the catastrophic force drop as observed in the force (F)-deformation (X) spectra. The theory interprets fine features of the spectra: the slope of the FX curves and the position of force-peak signal, in terms of mechanical characteristics --- the Young's moduli for Hertzian and bending deformations E_H and E_b, and the probability distribution of the maximum strength with the strength of the strongest beam F_b^* and the beams' failure rate m. The theory is applied to successfully characterize the $FX$ curves for spherical virus particles --- CCMV, TrV, and AdV

Ionization in a laser assisted ion-ion collision

The ionization of a hydrogen-like heavy ion by impact of a charged projectile under simultaneous irradiation by a short laser pulse is investigated within the non-perturbative approach, based on numerical solutions of the time-dependent Dirac equation. Special emphasis is placed on the question of whether the laser- and impact-ionization channels interfere with each other, and how this intereference affects the ionization probability. To answer this question we performed detailed calculations for the laser-assisted collisions between hydrogen-like $Pb^{81+}$ and alpha particles. The results of the calculations clearly indicate that for the experimentally relevant set of (collision and laser) parameters, the interference contribution can reach 10% and can be easily controlled by varying the laser frequency.Comment: 9 pages, 10 figure

K-shell ionization of heavy hydrogen-like ions

A theoretical study of the K-shell ionization of hydrogen-like ions, colliding with bare nuclei, is performed within the framework of the time-dependent Dirac equation. Special emphasis is placed on the ionization probability that is investigated as a function of impact parameter, collision energy and nuclear charge. To evaluate this probability in a wide range of collisional parameters we propose a simple analytical expression for the transition amplitude. This expression contains three fitting parameters that are determined from the numerical calculations, based on the adiabatic approximation. In contrast to previous studies, our analytical expression for the transition amplitude and ionization probability accounts for the full multipole expansion of the two-center potential and allows accurate description of nonsymmetric collisions of nuclei with different atomic numbers, $Z_1 \neq Z_2$. The calculations performed for both symmetric and asymmetric collisions indicate that the ionization probability is reduced when the difference between the atomic numbers of ions increases.Comment: 8 pages, 6 figure

Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico

Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral non-covalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physico-chemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force-deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the reversible dissociation of lateral bonds followed by irreversible dissociation of the longitudinal bonds. We have determined the free energies of dissociation of the lateral (6.9+/-0.4 kcal/mol) and longitudinal (14.9+/-1.5 kcal/mol) tubulin-tubulin bonds. These values in conjunction with the large flexural rigidity of tubulin protofilaments obtained (18,000-26,000 pN*nm^2), support the idea that the disassembling microtubule is capable of generating a large mechanical force to move chromosomes during cell division. Our computational modeling offers a comprehensive quantitative platform to link molecular tubulin characteristics with the physiological behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration of biomechanical properties of other cytoskeletal and multiprotein assemblie