The ves hypothesis and protein misfolding

Proteins function by changing conformation. These conformational changes, which involve the concerted motion of a large number of atoms are classical events but, in many cases, the triggers are quantum mechani- cal events such as chemical reactions. Here the initial quantum states after the chemical reaction are assumed to be vibrational excited states, something that has been designated as the VES hypothesis. While the dynamics under classical force fields fail to explain the relatively lower structural stability of the proteins associated with misfolding diseases, the application of the VES hy- pothesis to two cases can provide a new explanation for this phenomenon. This explanation relies on the transfer of vibrational energy from water molecules to proteins, a process whose viability is also examined

From Davydov solitons to decoherence-free subspaces: self-consistent propagation of coherent-product states

The self-consistent propagation of generalized $D_{1}$ [coherent-product] states and of a class of gaussian density matrix generalizations is examined, at both zero and finite-temperature, for arbitrary interactions between the localized lattice (electronic or vibronic) excitations and the phonon modes. It is shown that in all legitimate cases, the evolution of $D_{1}$ states reduces to the disentangled evolution of the component $D_{2}$ states. The self-consistency conditions for the latter amount to conditions for decoherence-free propagation, which complement the $D_{2}$ Davydov soliton equations in such a way as to lift the nonlinearity of the evolution for the on-site degrees of freedom. Although it cannot support Davydov solitons, the coherent-product ansatz does provide a wide class of exact density-matrix solutions for the joint evolution of the lattice and phonon bath in compatible systems. Included are solutions for initial states given as a product of a [largely arbitrary] lattice state and a thermal equilibrium state of the phonons. It is also shown that external pumping can produce self-consistent Frohlich-like effects. A few sample cases of coherent, albeit not solitonic, propagation are briefly discussed.Comment: revtex3, latex2e; 22 pages, no figs.; to appear in Phys.Rev.E (Nov.2001

Stochastic Lagrangian Particle Approach to Fractal Navier-Stokes Equations

In this article we study the fractal Navier-Stokes equations by using stochastic Lagrangian particle path approach in Constantin and Iyer \cite{Co-Iy}. More precisely, a stochastic representation for the fractal Navier-Stokes equations is given in terms of stochastic differential equations driven by L\'evy processes. Basing on this representation, a self-contained proof for the existence of local unique solution for the fractal Navier-Stokes equation with initial data in \mW^{1,p} is provided, and in the case of two dimensions or large viscosity, the existence of global solution is also obtained. In order to obtain the global existence in any dimensions for large viscosity, the gradient estimates for L\'evy processes with time dependent and discontinuous drifts is proved.Comment: 19 page

Multi-soliton energy transport in anharmonic lattices

We demonstrate the existence of dynamically stable multihump solitary waves in polaron-type models describing interaction of envelope and lattice excitations. In comparison with the earlier theory of multihump optical solitons [see Phys. Rev. Lett. {\bf 83}, 296 (1999)], our analysis reveals a novel physical mechanism for the formation of stable multihump solitary waves in nonintegrable multi-component nonlinear models.Comment: 4 pages, 4 figure

Global Existence and Regularity for the 3D Stochastic Primitive Equations of the Ocean and Atmosphere with Multiplicative White Noise

The Primitive Equations are a basic model in the study of large scale Oceanic and Atmospheric dynamics. These systems form the analytical core of the most advanced General Circulation Models. For this reason and due to their challenging nonlinear and anisotropic structure the Primitive Equations have recently received considerable attention from the mathematical community. In view of the complex multi-scale nature of the earth's climate system, many uncertainties appear that should be accounted for in the basic dynamical models of atmospheric and oceanic processes. In the climate community stochastic methods have come into extensive use in this connection. For this reason there has appeared a need to further develop the foundations of nonlinear stochastic partial differential equations in connection with the Primitive Equations and more generally. In this work we study a stochastic version of the Primitive Equations. We establish the global existence of strong, pathwise solutions for these equations in dimension 3 for the case of a nonlinear multiplicative noise. The proof makes use of anisotropic estimates, $L^{p}_{t}L^{q}_{x}$ estimates on the pressure and stopping time arguments.Comment: To appear in Nonlinearit

Burgers' Flows as Markovian Diffusion Processes

We analyze the unforced and deterministically forced Burgers equation in the framework of the (diffusive) interpolating dynamics that solves the so-called Schr\"{o}dinger boundary data problem for the random matter transport. This entails an exploration of the consistency conditions that allow to interpret dispersion of passive contaminants in the Burgers flow as a Markovian diffusion process. In general, the usage of a continuity equation $\partial_t\rho =-\nabla (\vec{v}\rho)$, where $\vec{v}=\vec{v}(\vec{x},t)$ stands for the Burgers field and $\rho$ is the density of transported matter, is at variance with the explicit diffusion scenario. Under these circumstances, we give a complete characterisation of the diffusive transport that is governed by Burgers velocity fields. The result extends both to the approximate description of the transport driven by an incompressible fluid and to motions in an infinitely compressible medium. Also, in conjunction with the Born statistical postulate in quantum theory, it pertains to the probabilistic (diffusive) counterpart of the Schr\"{o}dinger picture quantum dynamics.Comment: Latex fil

Energy localization and shape transformations in semiflexible polymer rings

Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the internal excitations and the bending degrees of freedom of the chain modifies the local bending rigidity of the chain. In the absence of driving the array takes a circular shape.When the energy pumped into the system exceeds some critical value the chain undergoes a nonequilibrium phase transition: The circular shape of the aggregate becomes unstable and the chain takes the shape of an ellipse or, in general, of a polygon. The excitation energy distribution becomes spatially nonuniform: It localizes in such places where the chain is more flat. The weak interaction of the chain with a flat surface restricts the dynamics to a flat manifold.Y.B.G. acknowledges partial financial support from a special program of the National Academy of Sciences of Ukraine, and is thankful to the Department of Applied Mathematics and Computer Science and the Department of Physics, Technical University of Denmark as well as the University of Seville for hospitality. J.F.R.A acknowledges Grant No. 2011/FQM-280 from CEICE, Junta de Andalucia Spain. J.F.R.A. and V.J.S.-M. acknowledge financial support from Project No. FIS2015-65998-C2-2-P from MINECO, Spain.Gaididei, YB.; Archilla, JFR.; Sánchez Morcillo, VJ.; Gorria, C. (2016). Energy localization and shape transformations in semiflexible polymer rings. Physical Review E. 93(6):062227-1-062227-9. https://doi.org/10.1103/PhysRevE.93.062227S062227-1062227-993

Natural boundaries for the Smoluchowski equation and affiliated diffusion processes

The Schr\"{o}dinger problem of deducing the microscopic dynamics from the input-output statistics data is known to admit a solution in terms of Markov diffusions. The uniqueness of solution is found linked to the natural boundaries respected by the underlying random motion. By choosing a reference Smoluchowski diffusion process, we automatically fix the Feynman-Kac potential and the field of local accelerations it induces. We generate the family of affiliated diffusions with the same local dynamics, but different inaccessible boundaries on finite, semi-infinite and infinite domains. For each diffusion process a unique Feynman-Kac kernel is obtained by the constrained (Dirichlet boundary data) Wiener path integration.As a by-product of the discussion, we give an overview of the problem of inaccessible boundaries for the diffusion and bring together (sometimes viewed from unexpected angles) results which are little known, and dispersed in publications from scarcely communicating areas of mathematics and physics.Comment: Latex file, Phys. Rev. E 49, 3815-3824, (1994