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We present a new multistage method to study the N-Methyl-D-Aspartate (NMDA) neuroreceptor starting from the reconstruction of its crystallographic structure. Thanks to the combination of Homology Modelling, Molecular Dynamics and Lattice Boltzmann simulations, we analyse the allosteric transition of NDMA upon ligand binding and compute the receptor response to ionic passage across the membrane. [ABSTRACT FROM AUTHOR]

Protein folding, vital to life and death, is the basis of biological physics. The information about the protein folding process and dynamics is of tremendous significance in the protein-folding field, and the research about protein folding pathways has attracted considerable attention. Here, four protein systems (1HOD, 2AJJ, 2DX3, 2RLG) are performed the folding simulation starting from the linear structures in order to investigate their folding mechanisms using the classical molecular dynamics (MD) and the self-guided Langevin dynamics (SGLD), respectively. The latter can increase the low-frequency motion, which is particularly related to the folding process of protein. Compared with MD, there is a significant improvement through SGLD method, such as the evolution of the radius of gyration, root mean square deviation, cluster analysis, native contact, helix content, process of the protein folding and the free energy landscape. This research shows that the extended states successfully fold into the corresponding native structures within 95 ns using SGLD. Furthermore, the result of multiple trajectories again supports the above conclusion. However, classical MD ultimately fails to show any stable helix formation at the same simulation time. The detailed folding pathway and mechanism of these proteins are elucidated using the SGLD method in this report. [ABSTRACT FROM AUTHOR]

This paper discusses the nature of heavy Rydberg states, i.e. quantum states in molecular systems that are bound by the almost pure Coulomb potential between pairs of ions. A theoretical framework is developed in terms of mass–scaling laws for heavy Rydberg systems of certain reduced mass, so that the physics of electronic Rydberg states can be straightforwardly applied to heavier ion–pair systems, or any other system bound by a 1/ r potential. The general description of such quantum systems is supported by an experimental investigation of the energy region near the H + H - ion–pair dissociation limit, using a 1 XUV?+?1 UV laser excitation scheme. Such a scheme allows for preparation of a single intermediate rovibrational quantum state, from which the ion–pair threshold region can be explored with a narrowband Fourier–transform limited laser. Field–induced lowering of the H + H - dissociation limit was observed in the presence of an electric field. Using a combination of DC and pulsed electric fields two–photon induced threshold ion–pair production spectroscopy (TIPPS) was performed for a variety of field strengths. Below the field–dissociation limit coherent wave packets of bound heavy Rydberg states are excited in an electric field. The coherent evolution of the Stark states, giving rise to oscillations in angular momentum space, can be quantitatively understood in terms of the linear Stark effect in the hydrogen atom, where the light electron is replaced by the heavier H - particle. The dynamics of wave packets of heavy Rydberg states is slower than in ordinary electronic Rydberg states, according to their larger mass. For a wide variety of binding energy and external electric field, the observed oscillation frequencies of the Stark wave packets match this model. An important parameter describing the specific properties of the H + H - Rydberg states is the scaled lifetime, which may be considered as a material constant, and it is determined att= (5.8±2.0)×10 -21 s n 4 . [ABSTRACT FROM AUTHOR]

A systematic approach for the derivation of the exact translational–rovibronic (non-relativistic) Hamiltonian for a polyatomic molecule consisting of N nuclei and n electrons is presented. All coupling terms which contribute to the total energy are identified. The Hamiltonian is greatly simplified by taking the internal coordinates (bond lengths and bond angles) as the vibrational variables. The translational–rovibronic Hamiltonian of triatomic molecules are considered as an application for this general formulation. [ABSTRACT FROM AUTHOR]

Detailed molecular dynamics simulations are carried out to investigate the translation–rotation coupling in linear molecules. We calculated the moment of inertia ratio dependence of the self–diffusion coefficients D , the so–called dynamic isotope effect on the self–diffusion, in pure fluids. Our model systems consist of linear homonuclear pseudo–triatomic rigid molecules for three different molecular sizes over a wide range of density for a given temperature. For a compact representation of our results an exponential approach is employed, which demonstrates a strong translation–rotation coupling on the self–diffusion coefficient in a linear molecule. We find as a main result that in contrast to the low density behaviour at high densities the change of the rotation–translation coupling as a function of the moments of inertia is quite similar for all investigated molecules and we could explain this finding by a careful inspection of the corresponding velocity autocorrelation functions. Finally we present a comparison of experimental data for 20 neat molecular liquids and the corresponding theoretical predictions based on our findings for linear molecules. The good overall agreement indicates that our approach can be generalized and is therefore not only a compact representation of the calculated data but has also large predictive capabilities. [ABSTRACT FROM AUTHOR]

The relation between the dielectric constant and the particle polarizability for a polarizable liquid composed of Lennard-Jones particles carrying a saturable induced dipole is studied by computer simulations. It is shown that the widely accepted Clausius-Mossotti relation is only valid for low polarizabilities and fails for high polarizabilities. The results can be fitted accurately by an Onsager-like relation using an effective particle radius measured in the simulations which is larger than the equivalent hard-sphere radius defined conventionally. Furthermore, the orientational ordering transition found at high polarizabilities is shown to be of anti-ferroelectric type. [ABSTRACT FROM AUTHOR]

Editorial. Discusses the role of the "Molecular Physics" periodical in covering a wide spectrum of theoretical and experimental aspects of molecular systems. Topics on molecular systems for research consideration and publication; Generalization of statistical mechanics concepts and methods to investigate structural, interfacial and dynamic properties; Interest in the study of gelation and glass transition in complex fluids.