An experimental study has been carried out on a noisy dissipative-driven ring lattice of units coupled via Morse potentials. An electronic circuit mimicking the lattice dynamics and noise sources is used. We show that inclusion of long range attractive forces facilitates clustering (at variance with the repulsive Toda ring) and van der Waals-like transition phenomena.
We use the model of interacting self-propelled particles as a rough model for the collective motions of cells and organisms. First we study self-propelled motion with linear attracting interactions. This way we develop the dynamics of swarms with self-confinement by global coupling in coordinate- and velocity-space. Further we study the model of Morse-type attracting forces and global velocity-coupling. We begin with pairs N=2; the attractors and distribution functions are discussed, then the case N>2 is discussed. Simulations for several dynamical modes of swarms of active Brownian particles are presented. In particular we study rotations, drift, fluctuations of shape and cluster formation. Finally we study the symmetry-breaking effects of hydrodynamic interactions of Oseen-type.
The problems studied here are relevant for an understanding of the functioning of hydrolytic enzyme molecules. These enzymes work like molecular machines breaking off the valence peptid bonds of substrates. In particular the role of Fermi resonance which is evident from a spectral lines of valence oscillations is studied. The influence of this resonance on valence splitting is discussed. It is shown that the breaking of these bonds has a higher probability, if the stochastic oscillations of atoms in catalytic groups at the active site have a large quality coefficient. We show that the corresponding low damping is essential for the Fermi resonance modes of these oscillations.
Based on earlier work on Toda rings we propose here a model for energy-rich excitations in molecules. Localization of energy may be due to the fusion of solitons at soft springs imbedded into a ring of hard springs. In thermal equilibrium an optimal temperature region exists, where the potential energy is concentrated at the soft sites. The energy distribution, the autocorrelation function and the spectrum of the forces is studied.
The issues about the behavior of variant test particles (TP) in 2D potential field with complex relief are studied. The cases with time-dependent parameters of potential field are considered. In particular the mathematical models that are discussed in this paper can describe either the process of penetration of TP (ligand) in active site of the enzyme or proton's transition from one potential pit to another.
KEYWORDS: Molecules, Energy transfer, Motion models, Chemical species, Life sciences, Laser applications, Complex systems, Modeling, Hydrogen, Molecular energy transfer
Influence of intramolecular dynamic structure on the process of energy transfer from the place of original localization to the active site and processes in the active site of enzyme is under consideration. The possibility of realization of `marked' degrees of freedom when the system motion occurs in a narrow area of phase space was considered within the framework of a simplest cluster model of an enzyme molecule. Under certain conditions the motion of the system becomes complex and perhaps stochastic and the spectrum of oscillations becomes more rich. the role of the interaction potential curve shapes of the system is discussed. Problems of spectral transformation and complexization and characteristic times determination are important for interpretation of the data obtained by the methods of laser spectroscopy and CARS, in particular. We discuss the problem of overcoming the potential energy barrier inside the active site in terms of the location and energy of definite parts of the substrate within the framework of a 2D model. The special role of fluctuations of atom groups and the substrate influence on the process are taken into account.
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