Proton strings and rings in atypical nucleation of ferroelectricity in ice.

Ordinary ice has a proton-disordered phase which is kinetically metastable, unable to reach, spontaneously, the ferroelectric (FE) ground state at low temperature where a residual Pauling entropy persists. Upon light doping with KOH at low temperature, the transition to FE ice takes place, but its microscopic mechanism still needs clarification. We introduce a lattice model based on dipolar interactions plus a competing, frustrating term that enforces the ice rule (IR). In the absence of IR-breaking defects, standard Monte Carlo (MC) simulation leaves this ice model stuck in a state of disordered proton ring configurations with the correct Pauling entropy. A replica exchange accelerated MC sampling strategy succeeds, without open path moves, interfaces, or off-lattice configurations, in equilibrating this defect-free ice, reaching its low-temperature FE order through a well-defined first-order phase transition. When proton vacancies mimicking the KOH impurities are planted into the IR-conserving lattice, they enable standard MC simulation to work, revealing the kinetics of evolution of ice from proton disorder to partial FE order below the transition temperature. Replacing ordinary nucleation, each impurity opens up a proton ring generating a linear string, an actual FE hydrogen bond wire that expands with time. Reminiscent of those described for spin ice, these impurity-induced strings are proposed to exist in doped water ice too, where IRs are even stronger. The emerging mechanism yields a dependence of the long-time FE order fraction upon dopant concentration, and upon quenching temperature, that compares favorably with that known in real-life KOH doped ice.

A Markov state modeling analysis of sliding dynamics of a 2D model.

Non-equilibrium Markov State Modeling (MSM) has recently been proposed by Pellegrini et al. [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach builds a small set of collective variables, which obey a transition-matrix-based equation of motion, faithfully describing the slow motions of the system. A crucial question is whether this approach can be extended from the original 1D small size demo to larger and more realistic size systems, without an inordinate increase of the number and complexity of the collective variables. Here we present a direct application of the MSM scheme to the sliding of an island made of over 1000 harmonically bound particles over a 2D periodic potential. Based on a totally unprejudiced phase space metric and without requiring any special doctoring, we find that here too the scheme allows extracting a very small number of slow variables, necessary and sufficient to describe the dynamics of island sliding.

Markov state modeling of sliding friction.

Markov state modeling (MSM) has recently emerged as one of the key techniques for the discovery of collective variables and the analysis of rare events in molecular simulations. In particular in biochemistry this approach is successfully exploited to find the metastable states of complex systems and their evolution in thermal equilibrium, including rare events, such as a protein undergoing folding. The physics of sliding friction and its atomistic simulations under external forces constitute a nonequilibrium field where relevant variables are in principle unknown and where a proper theory describing violent and rare events such as stick slip is still lacking. Here we show that MSM can be extended to the study of nonequilibrium phenomena and in particular friction. The approach is benchmarked on the Frenkel-Kontorova model, used here as a test system whose properties are well established. We demonstrate that the method allows the least prejudiced identification of a minimal basis of natural microscopic variables necessary for the description of the forced dynamics of sliding, through their probabilistic evolution. The steps necessary for the application to realistic frictional systems are highlighted.

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/molecular mechanics Car-Parrinello study of key steps of the enzymatic reaction for a representative member of this family, caspase-3. The hydrolysis of the acyl-enzyme complex is described at the density functional (BLYP) level of theory while the protein frame and solvent are treated using the GROMOS96 force field. These calculations show that the attack of the hydrolytic water molecule implies an activation free energy of ca. DeltaF(A) approximately equal 19 +/- 4 kcal/mol in good agreement with experimental data and leads to a previously unrecognized gem-diol intermediate that can readily (DeltaF(A) approximately equal 5 +/- 3 kcal/mol) evolve to the enzyme products. Our findings assist in elucidating the striking difference in catalytic activity between caspases and other structurally well-characterized cysteine proteases (papains and cathepsins) and may help design novel transition-state analog inhibitors.

Physical origin of selectivity in ionic channels of biological membranes.

This paper shows that the selectivity properties of monovalent cation channels found in biological membranes can originate simply from geometrical properties of the inner core of the channel without any critical contribution from electrostatic interactions between the permeating ions and charged or polar groups. By using well-known techniques of statistical mechanics, such as the Langevin equations and Kramer theory of reaction rates, a theoretical equation is provided relating the permeability ratio PB/PA between ions A and B to simple physical properties, such as channel geometry, thermodynamics of ion hydration, and electrostatic interactions between the ion and charged (or polar) groups. Diffusive corrections and recrossing rates are also considered and evaluated. It is shown that the selectivity found in usual K+, gramicidin, Na+, cyclic nucleotide gated, and end plate channels can be explained also in the absence of any charged or polar group. If these groups are present, they significantly change the permeability ratio only if the ion at the selectivity filter is in van der Waals contact with them, otherwise these groups simply affect the channel conductance, lowering the free energy barrier of the same amount for the two ions, thus explaining why single channel conductance, as it is experimentally observed, can be very different in channels sharing the same selectivity sequence. The proposed theory also provides an estimate of channel minimum radius for K+, gramicidin, Na+, and cyclic nucleotide gated channels.

Predicting crystal structures: the Parrinello-Rahman method revisited.

By suitably adapting a recent approach [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12 562 (2002)]] we develop a powerful molecular dynamics method for the study of pressure-induced structural transformations. We use the edges of the simulation cell as collective variables and define a metadynamics that drives the system away from the local minimum towards a new crystal structure. In contrast to the Parrinello-Rahman method, our approach shows no hysteresis, and crystal structure transformations can occur at the equilibrium pressure. We illustrate the power of the method by studying the pressure-induced diamond to simple hexagonal phase transition in a model of silicon.

Deciphering the folding kinetics of transmembrane helical proteins.

Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key problem in structural biology. Here, we introduce a general model and use computer simulations to study the equilibrium properties and the folding kinetics of a C(alpha)-based two-helix bundle fragment (comprised of 66 aa) of bacteriorhodopsin. Various intermediates are identified and their free energy are calculated together with the free energy barrier between them. In 40% of folding trajectories, the folding rate is considerably increased by the presence of nonobligatory intermediates acting as traps. In all cases, a substantial portion of the helices is rapidly formed. This initial stage is followed by a long period of consolidation of the helices accompanied by their correct packing within the membrane. Our results provide the framework for understanding the variety of folding pathways of helical transmembrane proteins.

Physics of iron at Earth's core conditions

The bulk properties of iron at the pressure and temperature conditions of Earth's core were determined by a method that combines first-principles and classical molecular dynamic simulations. The theory indicates that (i) the iron melting temperature at inner-core boundary (ICB) pressure (330 gigapascals) is 5400 (+/-400) kelvin; (ii) liquid iron at ICB conditions is about 6% denser than Earth's outer core; and (iii) the shear modulus of solid iron close to its melting line is 140 gigapascals, consistent with the seismic value for the inner core. These results reconcile melting temperature estimates based on sound velocity shock wave data with those based on diamond anvil cell experiments.