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Register a new userNonlocal orientation-dependent dynamics of molecular strands
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Added by
Vakhtang Putkaradze Dr.
Publication date
2008
fields
Physics
and research's language is
English
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Time-dependent Hamiltonian dynamics is derived for a curve (molecular strand) in $mathbb{R}^3$ that experiences both nonlocal (for example, electrostatic) and elastic interactions. The dynamical equations in the symmetry-reduced variables are written on the dual of the semidirect-product Lie algebra $so(3) circledS (mathbb{R}^3oplusmathbb{R}^3oplusmathbb{R}^3oplusmathbb{R}^3)$ with three 2-cocycles. We also demonstrate that the nonlocal interaction produces an interesting new term deriving from the coadjoint action of the Lie group SO(3) on its Lie algebra $so(3)$. The new filament equations are written in conservative form by using the corresponding coadjoint actions.
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Euler-Poincare equations are derived for the dynamical folding of charged molecular strands (such as DNA) modeled as flexible continuous filamentary distributions of interacting rigid charge conformations. The new feature is that the equations of motion for the dynamics of such molecular strands are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges are included. These nonlocal dynamical equations are derived in the convective representation of continuum motion by using modified Euler-Poincare and Hamilton-Pontryagin variational formulations that illuminate the various approaches within the framework of symmetry reduction of Hamiltons principle for exact geometric rods. In the absence of nonlocal interactions, the equations recover the classical Kirchhoff theory of elastic rods in the spatial representation. The motion equations in the convective representation are shown to be affine Euler-Poincare equations relative to a certain cocycle. This property relates the geometry of the molecular strands to that of complex fluids. An elegant change of variables allows a direct passage from the infinite dimensional point of view to the covariant formulation in terms of Lagrange-Poincare equations. In another revealing perspective, the convective representation of the nonlocal equations of molecular strand motion is transformed into quaternionic form.
The gradient-flow dynamics of an arbitrary geometric quantity is derived using a generalization of Darcys Law. We consider flows in both Lagrangian and Eulerian formulations. The Lagrangian formulation includes a dissipative modification of fluid mechanics. Eulerian equations for self-organization of scalars, 1-forms and 2-forms are shown to reduce to nonlocal characteristic equations. We identify singular solutions of these equations corresponding to collapsed (clumped) states and discuss their evolution.
We discuss several models of the dynamics of interacting populations. The models are constructed by nonlinear differential equations and have two sets of parameters: growth rates and coefficients of interaction between populations. We assume that the parameters depend on the densities of the populations. In addition the parameters can be influenced by different factors of the environment. This influence is modelled by noise terms in the equations for the growth rates and interaction coefficients. Thus the model differential equations become stochastic. In some particular cases these equations can be reduced to a Foker-Plancnk equation for the probability density function of the densities of the interacting populations.
The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed to the X-ray beam, making the three dimensional reconstruction not trivial. Induced orientation of molecules prior to X-ray exposure can be highly beneficial, as it significantly reduces the number of collected diffraction patterns whilst improving the quality of the reconstructed structure. We present here the possibility of protein orientation using a time-dependent external electric field. We used ab initio simulations on Trp-cage protein to provide a qualitative estimation of the field strength required to break protein bonds, with 45 V/nm as a breaking point value. Furthermore, we simulated, in a classical molecular dynamics approach, the orientation of ubiquitin protein by exposing it to different time-dependent electric fields. The protein structure was preserved for all samples at the moment orientation was achieved, which we denote `orientation before destruction. Moreover, we find that the minimal field strength required to induce orientation within ten ns of electric field exposure, was of the order of 0.5 V/nm. Our results help explain the process of field orientation of proteins and can support the design of instruments for protein orientation.
We suggest kinetic models of dissipation for an ensemble of interacting oriented particles, for example, moving magnetized particles. This is achieved by introducing a double bracket dissipation in kinetic equations using an oriented Poisson bracket, and employing the moment method to derive continuum equations for magnetization and density evolution. We show how our continuum equations generalize the Debye-Hueckel equations for attracting round particles, and Landau-Lifshitz-Gilbert equations for spin waves in magnetized media. We also show formation of singular solutions that are clumps of aligned particles (orientons) starting from random initial conditions. Finally, we extend our theory to the dissipative motion of self-interacting curves.
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