Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.

The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.

Nanocapillarity and Liquid Bridge-Mediated Force between Colloidal Nanoparticles.

In this work, we probe the concept of interface tension for ultrathin adsorbed liquid films on the nanoscale by studying the surface fluctuations of films down to the monolayer. Our results show that the spectrum of film height fluctuations of a liquid-vapor surface may be extended to ultrathin films provided we take into account the interactions of the substrate with the surface. Global fluctuations of the film height are described in terms of disjoining pressure, whereas surface deformations that are proportional to the interface area are accounted for by a film thickness-dependent surface tension. As a proof of concept, we model the capillary forces between colloidal nanoparticles held together by liquid bridges. Our results indicate that the classical equations for capillarity follow very precisely down to the nanoscale provided we account for the film height dependence of the surface tension.

On the critical Casimir interaction between anisotropic inclusions on a membrane.

Using a lattice model and a versatile thermodynamic integration scheme, we study the critical Casimir interactions between inclusions embedded in a two-dimensional critical binary mixtures. For single-domain inclusions we demonstrate that the interactions are very long range, and their magnitudes strongly depend on the affinity of the inclusions with the species in the binary mixtures, ranging from repulsive when two inclusions have opposing affinities to attractive when they have the same affinities. When one of the inclusions has no preference for either of the species, we find negligible critical Casimir interactions. For multiple-domain inclusions, mimicking the observations that membrane proteins often have several domains with varying affinities to the surrounding lipid species, the presence of domains with opposing affinities does not cancel the interactions altogether. Instead we can observe both attractive and repulsive interactions depending on their relative orientations. With increasing number of domains per inclusion, the range and magnitude of the effective interactions decrease in a similar fashion to those of electrostatic multipoles. Finally, clusters formed by multiple-domain inclusions can result in an effective affinity patterning due to the anisotropic character of the Casimir interactions between the building blocks.

Premelting-Induced Smoothening of the Ice-Vapor Interface.

We perform computer simulations of the quasiliquid layer of ice formed at the ice-vapor interface close to the ice Ih-liquid-vapor triple point of water. Our study shows that the two distinct surfaces bounding the film behave at small wavelengths as atomically rough and independent ice-water and water-vapor interfaces. For long wavelengths, however, the two surfaces couple, large scale parallel fluctuations are inhibited, and the ice-vapor interface becomes smooth. Our results could help explain the complex morphology of ice crystallites.

Interfacial free energy of the NaCl crystal-melt interface from capillary wave fluctuations.

In this work we study, by means of molecular dynamics simulations, the solid-liquid interface of NaCl under coexistence conditions. By analysing capillary waves, we obtain the stiffness for different orientations of the solid and calculate the interfacial free energy by expanding the dependency of the interfacial free energy with the solid orientation in terms of cubic harmonics. We obtain an average value for the solid-fluid interfacial free energy of 89 ± 6 mN m(-1) that is consistent with previous results based on the measure of nucleation free energy barriers [Valeriani et al., J. Chem. Phys. 122, 194501 (2005)]. We analyse the influence of the simulation setup on interfacial properties and find that facets prepared as an elongated rectangular stripe give the same results as those prepared as squares for all cases but the 111 face. For some crystal orientations, we observe at small wave-vectors a behaviour not consistent with capillary wave theory and show that this behavior does not depend on the simulation setup.

A study of the ice-water interface using the TIP4P/2005 water model.

In this work we study the ice-water interface under coexistence conditions by means of molecular simulations using the TIP4P/2005 water model. Following the methodology proposed by Hoyt and co-workers [J. J. Hoyt, M. Asta and A. Karma, Phys. Rev. Lett., 2001, 86, 5530] we measure the interfacial free energy of ice with liquid water by analysing the spectrum of capillary fluctuations of the interface. We get an orientationally averaged interfacial free energy of 27(2) mN m(-1), in good agreement with a recent estimate obtained from simulation data of the size of critical clusters [E. Sanz, C. Vega, J. R. Espinosa, R. Caballero-Bernal, J. L. F. Abascal and C. Valeriani, J. Am. Chem. Soc., 2013, 135, 15008]. We also estimate the interfacial free energy of different planes and obtain 27(2), 28(2) and 28(2) mN m(-1) for the basal, the primary prismatic and the secondary prismatic planes respectively. Finally, we inspect the structure of the interface and find that its thickness is approximately 4-5 molecular diameters. Moreover, we find that when the basal plane is exposed to the fluid the interface alternates regions of cubic ice with regions of hexagonal ice.

Computer simulation study of surface wave dynamics at the crystal-melt interface.

We study, by means of computer simulations, the crystal-melt interface of three different systems: hard-spheres, Lennard Jones, and the TIP4P/2005 water model. In particular, we focus on the dynamics of surface waves. We observe that the processes involved in the relaxation of surface waves are characterized by distinct time scales: a slow one related to the continuous recrystallization and melting, that is governed by capillary forces; and a fast one which we suggest to be due to a combination of processes that quickly cause small perturbations to the shape of the interface (e.g., Rayleigh waves, subdiffusion, or attachment/detachment of particles to/from the crystal). The relaxation of surface waves becomes dominated by the slow process as the wavelength increases. Moreover, we see that the slow relaxation is not influenced by the details of the microscopic dynamics. In a time scale characteristic for the diffusion of the liquid phase, the relaxation dynamics of the crystal-melt interface of water is around one order of magnitude slower than that of Lennard Jones or hard spheres, which we ascribe to the presence of orientational degrees of freedom in the water molecule. Finally, we estimate the rate of crystal growth from our analysis of the capillary wave dynamics and compare it with previous simulation studies and with experiments for the case of water.

Disjoining pressure and the film-height-dependent surface tension of thin liquid films: new insight from capillary wave fluctuations.

In this paper we review simulation and experimental studies of thermal capillary wave fluctuations as an ideal means for probing the underlying disjoining pressure and surface tensions, and more generally, fine details of the Interfacial Hamiltonian Model. We discuss recent simulation results that reveal a film-height-dependent surface tension not accounted for in the classical Interfacial Hamiltonian Model. We show how this observation may be explained bottom-up from sound principles of statistical thermodynamics and discuss some of its implications.

Capillary fluctuations and film-height-dependent surface tension of an adsorbed liquid film.

Our understanding of both structure and dynamics of adsorbed liquids heavily relies on the capillary wave Hamiltonian, but a thorough test of this model is still lacking. Here we study the capillary wave fluctuations of a liquid film with short-range forces adsorbed on a solid exhibiting van der Waals interactions. We show for the first time that the measured capillary wave spectrum right above the first order wetting transition provides an interface potential consistent with independent calculations from thermodynamic integration. However, the surface tension exhibits an oscillatory film thick dependence which reveals a hitherto unnoticed capillary wave broadening mechanism beyond mere interfacial displacements.

Semi-infinite boundary conditions for the simulation of interfaces: the Ar/CO2(s) model revisited.

We propose a method to account for the long tail corrections of dispersive forces in inhomogeneous systems. This method deals separately with the two interfaces that are usually present in a simulation setup, effectively establishing semi-infinite boundary conditions that are appropriate for the study of the interface between two infinite bulk phases. Using the wandering interface method, we calculate surface free energies of vapor-liquid, wall-liquid, and wall-vapor interfaces for a model of Lennard-Jones argon adsorbed on solid carbon dioxide. The results are employed as input to Young's equation, and the wetting temperature located. This estimate is compared with predictions from the method of effective interface potentials and good agreement is found. Our results show that truncating Ar-Ar interactions at two and a half molecular diameters results in a dramatic decrease of the wetting temperature of about 40%.