12 research outputs found
Two-vibron bound states in alpha-helix proteins : the interplay between the intramolecular anharmonicity and the strong vibron-phonon coupling
The influence of the intramolecular anharmonicity and the strong
vibron-phonon coupling on the two-vibron dynamics in an -helix protein
is studied within a modified Davydov model. The intramolecular anharmonicity of
each amide-I vibration is considered and the vibron dynamics is described
according to the small polaron approach. A unitary transformation is performed
to remove the intramolecular anharmonicity and a modified Lang-Firsov
transformation is applied to renormalize the vibron-phonon interaction. Then, a
mean field procedure is realized to obtain the dressed anharmonic vibron
Hamiltonian. It is shown that the anharmonicity modifies the vibron-phonon
interaction which results in an enhancement of the dressing effect. In
addition, both the anharmonicity and the dressing favor the occurrence of two
different bound states which the properties strongly depend on the interplay
between the anharmonicity and the dressing. Such a dependence was summarized in
a phase diagram which characterizes the number and the nature of the bound
states as a function of the relevant parameters of the problem. For a
significant anharmonicity, the low frequency bound states describe two vibrons
trapped onto the same amide-I vibration whereas the high frequency bound states
refer to the trapping of the two vibrons onto nearest neighbor amide-I
vibrations.Comment: may 2003 submitted to Phys. Rev.
From Davydov solitons to decoherence-free subspaces: self-consistent propagation of coherent-product states
The self-consistent propagation of generalized [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 states reduces
to the disentangled evolution of the component states. The
self-consistency conditions for the latter amount to conditions for
decoherence-free propagation, which complement the 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
Relaxation channels of two-vibron bound states in \alpha-helix proteins
Relaxation channels for two-vibron bound states in an anharmonic alpha-helix
protein are studied. It is pointed out that the relaxation originates in the
interaction between the dressed anharmonic vibrons and the remaining phonons.
This interaction is responsible for the occurrence of transitions between
two-vibron eigenstates mediated by both phonon absorption and phonon emission.
At biological temperature, it is shown that the relaxation rate does not
significantly depends on the nature of the two-vibron state involved in the
process. Therefore, the lifetime for both bound and free states is of the same
order of magnitude and ranges between 0.1 and 1.0 ps for realistic parameters.
By contrast, the relaxation channels strongly depend on the nature of the
two-vibron states which is a consequence of the breather-like behavior of the
two-vibron bound states.Comment: octobre 2003 - soumis Phys. Rev.
Lattice Boltzmann Method Implementation on Multiple Devices using OpenCL
Scientific computing community has been in close connection with high performance computing (HPC),
which has been privilege of a limited group of scientists. Recently, with rapid development of
Graphics Processing Units (GPUs), the parallel processing power of high performance computers
has been brought up to every commodity desktop computer, reducing cost of scientific computations.
In this paper, we develop a general purpose Lattice Boltzmann code that runs on commodity
computer with multiple heterogeneous devices that support OpenCL specification. Different
approaches to Lattice Boltzmann code implementations on commodity computer with multiple
devices were explored. Simulation results for different code implementations on multiple
devices have been compared to each other, to results obtained for single device implementation
and with results from the literature. Simulation results for the commodity computer hardware
platforms with multiple devices implementation have showed significant speed improvement
compared to simulation implemented on single device
Implementation of the Lattice Boltzmann Method on Heterogeneous Hardware and Platforms using OpenCL
The Lattice Boltzmann method (LBM) has become an alternative method for computational fluid dynamics with a wide range of applications. Besides its numerical stability and accuracy, one of the major advantages of LBM is its relatively easy parallelization and, hence, it is especially well fitted to many-core hardware as graphics processing units (GPU). The majority of work concerning LBM implementation on GPU's has used the CUDA programming model, supported exclusively by NVIDIA. Recently, the open standard for parallel programming of heterogeneous systems (OpenCL) has been introduced. OpenCL standard matures and is supported on processors from most vendors. In this paper, we make use of the OpenCL framework for the lattice Boltzmann method simulation, using hardware accelerators - AMD ATI Radeon GPU, AMD Dual-Core CPU and NVIDIA GeForce GPU's. Application has been developed using a combination of Java and OpenCL programming languages. Java bindings for OpenCL have been utilized. This approach offers the benefits of hardware and operating system independence, as well as speeding up of lattice Boltzmann algorithm. It has been showed that the developed lattice Boltzmann source code can be executed without modification on all of the used hardware accelerators. Performance results have been presented and compared for the hardware accelerators that have been utilized