Cooperative Origin of Low-Density Domains in Liquid Water

We study the size of clusters formed by water molecules possessing large enough tetrahedrality with respect to their nearest neighbors. Using Monte Carlo simulation of the SPC/E model of water, together with a geometric analysis based on Voronoi tessellation, we find that regions of lower density than the bulk are formed by accretion of molecules into clusters exceeding a minimum size. Clusters are predominantly linear objects and become less compact as they grow until they reach a size beyond which further accretion is not accompanied by a density decrease. The results suggest that the formation of "ice-like" regions in liquid water is cooperative.Comment: 16 pages, 6 figure

Physics of the liquid-liquid critical point

Within the inherent structure (IS) thermodynamic formalism introduced by Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys. Rev. A {\bf 25}, 978 (1982)] we address the basic question of the physics of the liquid-liquid transition and of density maxima observed in some complex liquids such as water by identifying, for the first time, the statistical properties of the potential energy landscape (PEL) responsible for these anomalies. We also provide evidence of the connection between density anomalies and the liquid-liquid critical point. Within the simple (and physically transparent) model discussed, density anomalies do imply the existence of a liquid-liquid transition.Comment: Physical Review Letters, in publicatio

High frequency longitudinal and transverse dynamics in water

High-resolution, inelastic x-ray scattering measurements of the dynamic structure factor S(Q,\omega) of liquid water have been performed for wave vectors Q between 4 and 30 nm^-1 in distinctly different thermodynamic conditions (T= 263 - 420 K ; at, or close to, ambient pressure and at P = 2 kbar). In agreement with previous inelastic x-ray and neutron studies, the presence of two inelastic contributions (one dispersing with Q and the other almost non-dispersive) is confirmed. The study of their temperature- and Q-dependence provides strong support for a dynamics of liquid water controlled by the structural relaxation process. A viscoelastic analysis of the Q-dispersing mode, associated with the longitudinal dynamics, reveals that the sound velocity undergoes the complete transition from the adiabatic sound velocity (c_0) (viscous limit) to the infinite frequency sound velocity (c_\infinity) (elastic limit). On decreasing Q, as the transition regime is approached from the elastic side, we observe a decrease of the intensity of the second, weakly dispersing feature, which completely disappears when the viscous regime is reached. These findings unambiguously identify the second excitation to be a signature of the transverse dynamics with a longitudinal symmetry component, which becomes visible in the S(Q,\omega) as soon as the purely viscous regime is left.Comment: 28 pages, 12 figure

Adsorption-desorption kinetics in nanoscopically confined oligomer films under shear

The method of molecular dynamics computer simulations is employed to study oligomer melts confined in ultra-thin films and subjected to shear. The focus is on the self-diffusion of oligomers near attractive surfaces and on their desorption, together with the effects of increasing energy of adsorption and shear. It is found that the mobility of the oligomers near an attractive surface is strongly decreased. Moreover, although shearing the system forces the chains to stretch parallel to the surfaces and thus increase the energy of adsorption per chain, flow also promotes desorption. The study of chain desorption kinetics reveals the molecular processes responsible for the enhancement of desorption under shear. They involve sequences of conformations starting with a desorbed tail and proceeding in a very fast, correlated, segment-by-segment manner to the desorption of the oligomers from the surfaces.

Supercooled confined water and the Mode Coupling crossover temperature

We present a Molecular Dynamics study of the single particle dynamics of supercooled water confined in a silica pore. Two dynamical regimes are found: close to the hydrophilic substrate molecules are below the Mode Coupling crossover temperature, $T_C$, already at ambient temperature. The water closer to the center of the pore (free water) approaches upon supercooling $T_C$ as predicted by Mode Coupling Theories. For free water the crossover temperature and crossover exponent $\gamma$ are extracted from power-law fits to both the diffusion coefficient and the relaxation time of the late $\alpha$ region.Comment: To be published, Phys. Rev. Lett., 4 pages, 3 figures, revTeX, minor changes in the figures, references added, changes in the tex

Origin of entropy convergence in hydrophobic hydration and protein folding

An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy convergence follows from the weak temperature dependence of occupancy fluctuations for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior between water and common organic solvents is the relative temperature insensitivity of the water isothermal compressibility. The information theory model provides a quantitative description of small molecule hydration and predicts a negative entropy at convergence. Interpretations of entropic contributions to protein folding should account for this result.Comment: Phys. Rev. Letts. (in press 1996), 3 pages, 3 figure

Molecular dynamics simulation of polymer helix formation using rigid-link methods

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under gradual cooling are followed until each reaches a state from which no further change is possible. The interactions are chosen so that the true ground state is a helix, and a high proportion of simulation runs succeed in reaching this state; the fraction that manage to form defect-free helices is a function of both chain length and cooling rate. In order to demonstrate behavior analogous to the formation of protein tertiary structure, additional attractive interactions are introduced into the model, leading to the appearance of aligned, antiparallel helix pairs. The simulations employ a computational approach that deals directly with the internal coordinates in a recursive manner; this representation is able to maintain constant bond lengths and angles without the necessity of treating them as an algebraic constraint problem supplementary to the equations of motion.Comment: 15 pages, 14 figure

Secondary-Structure Design of Proteins by a Backbone Torsion Energy

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both phi and psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the alpha-helix-forming-tendencies by lowering/raising the torsion-energy surface in the alpha-helix region and likewise increase/decrease the beta-sheet-forming tendencies by lowering/raising the surface in the beta-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming-tendencies by performing folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure

Hydrogen Bond Dynamics Near A Micellar Surface: Origin of the Universal Slow Relaxation at Complex Aqueous Interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than a hundred picosecond. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5kcal/mole.Comment: 12 pages. Phys. Rev. Lett. (Accepted) (2002

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes

The biological function of chaperone complexes is to assist the folding of non-native proteins. The widely studied GroEL chaperonin is a double-barreled complex that can trap non-native proteins in one of its two barrels. The ATP-driven binding of a GroES cap then results in a major structural change of the chamber where the substrate is trapped and initiates a refolding attempt. The two barrels operate anti-synchronously. The central region between the two barrels contains a high concentration of disordered protein chains, the role of which was thus far unclear. In this work we report a combination of atomistic and coarse-grained simulations that probe the structure and dynamics of the equatorial region of the GroEL/GroES chaperonin complex. Surprisingly, our simulations show that the equatorial region provides a translocation channel that will block the passage of folded proteins but allows the passage of secondary units with the diameter of an alpha-helix. We compute the free-energy barrier that has to be overcome during translocation and find that it can easily be crossed under the influence of thermal fluctuations. Hence, strongly non-native proteins can be squeezed like toothpaste from one barrel to the next where they will refold. Proteins that are already fairly close to the native state will not translocate but can refold in the chamber where they were trapped. Several experimental results are compatible with this scenario, and in the case of the experiments of Martin and Hartl, intra chaperonin translocation could explain why under physiological crowding conditions the chaperonin does not release the substrate protein