Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/gamma for values from 1-10(-1)x that of water viscosity. However, for the regime between 10(-4)-10(-1)x that of water viscosity we observe power-law dependence of the form k approximately gamma(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.     

Gas-phase activation and reaction dynamics of chiral ion-dipole complexes

A family of enantiomerically pure oxonium ions, that is O-protonated 1-aryl-1-methoxyethanes, has been generated in the gas phase by the (CH(3))(2)Cl(+) methylation of the corresponding 1-arylethanols. Some information on their reaction dynamics was obtained from a detailed kinetic study of their inversion of configuration and dissociation. The activation parameters of the inversion reaction are found to obey two different isokinetic relationships depending upon the nature and the position of the substituents in the oxonium ions. In contrast, the activation parameters of the dissociation reaction obey a single isokinetic relationship. The inversion and dissociation rate constants do not follow simple linear free-energy relationships. This complicated kinetic picture has been rationalized in terms of different activation dynamics in gaseous CH(3)Cl, which, in turn, determine the reaction dynamics of the oxonium ion. When the predominant activation of the oxonium ion involves resonant energy exchange from the 1015 cm(-1) CH(3) rocking mode of unperturbed CH(3)Cl, the inversion reaction proceeds through the dynamically most favored TS, characterized by the unassisted C(alpha)bond;O bond elongation. When, instead, the activation of the oxonium ions requires the formation of an intimate encounter complex with CH(3)Cl, the inversion reaction takes place via the energetically most favored TS, characterized by multiple coordination of the CH(3)OH moiety with the H(alpha) and H(ortho) atoms of the benzylic residue. The activation dynamics operating in the intimate encounter complex with CH(3)Cl is also responsible for the dissociation of most selected oxonium ions.     

Jerk Influence Coefficients,via Screw Theory,of Closed Chains

In this paper a novel method for determining the kinematic influence coefficients up to the jerk analysis of closed chains with multiple degrees of freedom by means of screw theory, also known as motor algebra, is introduced. A closed chain is obtained by rigidly attaching the end-effector of a serial chain to the base link. This condition ensures that the velocity, acceleration, and jerk, both angular and of any point fixed to the end-effector are zero. Afterwards, a comparison between the kinematic equations of motion, up to the jerk analysis, obtained by traditional methods with those obtained by means of screw theory reveals the corresponding influence coefficients associated to the generalized coordinates employed to represent the motion of the closed chain. Finally, a numerical example is provided. Sommario. In questo lavoro viene proposto un nuovo metodo per la determinazione dei coefficienti che consentono di sviluppare l'analisi cinematica (jerk incluso) di catene chiuse a molti gradi di liberta' per mezzo della screw theory o algebra dei moti spaziali. La catena chiusa e' ottenuta attaccando rigidamente l'end-effector di una catena seriale al membro di base. Questa condizione assicura che velocita' accelerazione e jerk, sia nel moto angolare che per ciascun punto solidale con l'end-effector siano nulli. Un confronto tra le equazioni cinematiche del moto, inclusa l'analisi del jerk, ottenute con metodi tradizionali e quelle ottenute dalla screw theory, mostra i corrispondenti coefficienti di influenza associati alle coordinate generalizzate impiegate per descrivere il moto della catena chiusa. Un esempio numerico conclude il lavoro.     

Scaling behavior of a nonlinear oscillator with additive noise,white and colored

We study analytically and numerically the problem of a nonlinear mechanical oscillator with additive noise in the absence of damping. We show that the amplitude, the velocity and the energy of the oscillator grow algebraically with time. For Gaussian white noise, an analytical expression for the probability distribution function of the energy is obtained in the long-time limit. In the case of colored, Ornstein-Uhlenbeck noise, a self-consistent calculation leads to (different) anomalous diffusion exponents. Dimensional analysis yields the qualitative behavior of the prefactors (generalized diffusion constants) as a function of the correlation time. Received 10 October 2002 Published online 6 March 2003 RID="a" ID="a"e-mail: mallick@spht.saclay.cea.fr     

Electrodynamics of the vortex lattice in untwinned YBaCuO by complex impedance measurements

We report complex impedance measurements in an untwinned YBaCuO crystal. Our broad frequency range covers both the quasi static response and the resistive response of the vortex lattice. It allow us to characterize the irreversibility line without the need of any frequency dependent pinning parameters. We confirm the validity of the two modes model of vortex dynamic, and extract both the surface critical current and the flux flow resistivity around the first order transition T_m. This latter is identified by the abrupt loss of pinning and by an unexpected step of (T) at T_m. Received 22 November 2002 / Received in final form 17 February 2003 Published online 20 June 2003 RID="a" ID="a"e-mail: alain.pautrat@ismra.fr RID="b" ID="b"UMR 6508 associée au CNRS