Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?

We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from molecular dynamics simulations in explicit solvent as a function of particle separation. In agreement with our recent work on nanospheres [J. Phys. Chem. B 116, 378 (2012)] regions of high friction are found to be engendered by large and slow solvent fluctuations. These slow fluctuations can be due to either drying or confinement. The mean first passage times for assembly are computed by means of molecular dynamics simulations in explicit solvent and by Brownian dynamics simulations along the reaction path. Brownian dynamics makes use of the potential of mean force and hydrodynamic profile that we determined. Surprisingly, we find reasonable agreement between full scale molecular dynamics and Brownian dynamics, despite the role of slow solvent relaxation in the assembly process. We found that molecular scale hydrodynamic interactions are essential in describing the kinetics of assembly.Comment: 6 figures, 13 page

The role of water and steric constraints in the kinetics of cavity-ligand unbinding

A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but extremely difficult task due to the long timescales involved. This gets further complicated by the presence of biophysical factors such as steric and solvation effects. In this work, we perform molecular dynamics (MD) simulations of the unbinding of a popular prototypical hydrophobic cavity-ligand system using a metadynamics based approach that allows direct assessment of kinetic pathways and parameters. When constrained to move in an axial manner, we find the unbinding time to be on the order of 4000 sec. In accordance with previous studies, we find that the ligand must pass through a region of sharp dewetting transition manifested by sudden and high fluctuations in solvent density in the cavity. When we remove the steric constraints on ligand, the unbinding happens predominantly by an alternate pathway, where the unbinding becomes 20 times faster, and the sharp dewetting transition instead becomes continuous. We validate the unbinding timescales from metadynamics through a Poisson analysis, and by comparison through detailed balance to binding timescale estimates from unbiased MD. This work demonstrates that enhanced sampling can be used to perform explicit solvent molecular dynamics studies at timescales previously unattainable, obtaining direct and reliable pictures of the underlying physio-chemical factors including free energies and rate constants.Comment: 7 pages, 4 figures, supplementary PDF file, submitte

Momentum distribution, vibrational dynamics and the potential of mean force in ice

By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasi-harmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasi-harmonic context, anharmonicity in the ground state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies

Blind protein structure prediction using accelerated free-energy simulations.

We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition

Displaced path integral formulation for the momentum distribution of quantum particles

The proton momentum distribution, accessible by deep inelastic neutron scattering, is a very sensitive probe of the potential of mean force experienced by the protons in hydrogen-bonded systems. In this work we introduce a novel estimator for the end to end distribution of the Feynman paths, i.e. the Fourier transform of the momentum distribution. In this formulation, free particle and environmental contributions factorize. Moreover, the environmental contribution has a natural analogy to a free energy surface in statistical mechanics, facilitating the interpretation of experiments. The new formulation is not only conceptually but also computationally advantageous. We illustrate the method with applications to an empirical water model, ab-initio ice, and one dimensional model systems

Problems Affecting Labor

Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by ℙ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G A (a 3-α helix fold) and G B (an α/β fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G A domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G Bs, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed

Differential effects on membrane permeability and viability of human keratinocyte cells undergoing very low intensity megasonic fields

Among different therapeutic applications of Ultrasound (US), transient membrane sonoporation (SP) - a temporary, non-lethal porosity, mechanically induced in cell membranes through US exposure - represents a compelling opportunity towards an efficient and safe drug delivery. Nevertheless, progresses in this field have been limited by an insufficient understanding of the potential cytotoxic effects of US related to the failure of the cellular repair and to the possible activation of inflammatory pathway. In this framework we studied the in vitro effects of very low-intensity US on a human keratinocyte cell line, which represents an ideal model system of skin protective barrier cells which are the first to be involved during medical US treatments. Bioeffects linked to US application at 1 MHz varying the exposure parameters were investigated by fluorescence microscopy and fluorescence activated cell sorting. Our results indicate that keratinocytes undergoing low US doses can uptake drug model molecules with size and efficiency which depend on exposure parameters. According to sub-cavitation SP models, we have identified the range of doses triggering transient membrane SP, actually with negligible biological damage. By increasing US doses we observed a reduced cells viability and an inflammatory gene overexpression enlightening novel healthy relevant strategies

Tunneling and delocalization in hydrogen bonded systems: a study in position and momentum space

Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.Comment: 14 pages, 13 figure

El líder étnico, liderar y liderazgo. Los Yahatti, Lepin, Juan Manuel Cachul y Juan Catriel: hombres políticos en la frontera bonaerense

Desde que se asume que los encuentros entre hispanocriollos e indígenas no fueron sólo bélicos, que hubo convivencias cotidianas, intercambios y contactos armónicos, se abre la posibilidad de pensar y analizar este contacto –violento o armónico– como el contexto relacional que exteriorizó y demandó líderes o interlocutores en cada sociedad. La región de la actual provincia de Buenos Aires conocida como “frontera bonaerense”, durante mediados del siglo XVIII y la primera mitad del XIX, será el marco espacio-temporal que permitirá situar el análisis de cuatro hombres políticos: los Yahatti, Lepin, Juan Manuel Cachul y Juan Catriel. Este análisis busca aportar elementos nominadores y significativos sobre el liderazgo étnico. En consecuencia, buscamos territorializar e historizar el liderazgo étnico de estos hombres, para poder determinar si es factible hablar de transformaciones en el liderazgo y cambios de los líderes en la relación con sus seguidores a partir del acuerdo de paces establecido con las autoridades estatales. Es decir, buscamos establecer fisonomías que nos permitan construir una enunciación descriptiva y analítica sobre dichos líderes y sus estrategias de construcción y sostenimiento de autoridad.Since it is assumed that contact between Hispanic-Creole and indigenous people was not only violent, and that it included daily life coexistence, exchanges and harmonic contact, it is possible to think and analyze these aspects as the relational context that exteriorized and required new leaders or mediators from each society. The region of present Buenos Aires province known as “frontera bonaerense”, from mid-eighteenth century to the first half of the nineteenth century, will be the space-time frame to analyze four political men: the Yahatti, Lepin, Juan Manuel Cachul and Juan Catriel. This research tries to support nominative and significant elements about ethnic leadership. Therefore, we look forward to territorialize and historicize the ethnic leadership of these men in order to determinate to which extent is viable to speak about its transformations towards their followers by means of treating peace with state authorities. Taking everything into account, we try to set characters which allow us to build a descriptive and analytical enunciation about those leaders and their authority strategies