Rob Phillips

Quasicontinuum analysis of defects in solids

We develop a method which permits the analysis of problems requiring the simultaneous resolution of continuum and atomistic length scales-and associated deformation processes-in a unified manner. A finite element methodology furnishes a continuum statement of the problem of interest and provides the requisite multiple-scale analysis capability by adaptively refining the mesh near lattice defects and other highly energetic regions. The method differs from conventional finite element analyses in that interatomic interactions are incorporated into the model through a crystal calculation based on the local state of deformation. This procedure endows the model with crucial properties, such as slip invariance, which enable the emergence of dislocations and other lattice defects. We assess the accuracy of the theory in the atomistic limit by way of three examples: a stacking fault on the (111) plane, and edge dislocations residing on (111) and (100) planes of an aluminium single crystal. The method correctly predicts the splitting of the (111) edge dislocation into Shockley partials. The computed separation of these partials is consistent with results obtained by direct atomistic simulations. The method predicts no splitting of the Al Lomer dislocation, in keeping with observation and the results of direct atomistic simulation. In both cases, the core structures are found to be in good agreement with direct lattice statics calculations, which attests to the accuracy of the method at the atomistic scale.

Emerging roles for lipids in shaping membrane-protein function

Studies of membrane proteins have revealed a direct link between the lipid environment and the structure and function of some of these proteins. Although some of these effects involve specific chemical interactions between lipids and protein residues, many can be understood in terms of protein-induced perturbations to the membrane shape. The free-energy cost of such perturbations can be estimated quantitatively, and measurements of channel gating in model systems of membrane proteins with their lipid partners are now confirming predictions of simple models.

An adaptive finite element approach to atomic-scale mechanics—the quasicontinuum method

Mixed atomistic and continuum methods offer the possibility of carrying out simulations of material properties at both larger length scales and longer times than direct atomistic calculations. The quasicontinuum method links atomistic and continuum models through the device of the finite element method which permits a reduction of the full set of atomistic degrees of freedom. The present paper gives a full description of the quasicontinuum method, with special reference to the ways in which the method may be used to model crystals with more than a single grain. The formulation is validated in terms of a series of calculations on grain boundary structure and energetics. The method is then illustrated in terms of the motion of a stepped twin boundary where a critical stress for the boundary motion is calculated and nanoindentation into a solid containing a subsurface grain boundary to study the interaction of dislocations with grain boundaries.

Quasicontinuum Models of Interfacial Structure and Deformation

Microscopic models of the interaction between grain boundaries (GBs) and both dislocations and cracks are of importance in understanding the role of microstructure in altering the mechanical properties of a material. A recently developed mixed atomistic and continuum method is reformulated to allow for the examination of the interactions between GBs, dislocations, and cracks. These calculations elucidate plausible microscopic mechanisms for these defect interactions and allow for the quantitative evaluation of critical parameters such as the force needed to induce GB migration.

Nanoindentation and incipient plasticity

This paper presents a large-scale atomic resolution simulation of nanoindentation into a thin aluminum film using the recently introduced quasicontinuum method. The purpose of the simulation was to study the initial stages of plastic deformation under the action of an indenter. Two different crystallographic orientations of the film and two different indenter geometries (a rectangular prism and a cylinder) were studied. We obtained both macroscopic load versus indentation depth curves, as well as microscopic quantities, such as the Peierls stress and density of geometrically necessary dislocations beneath the indenter. In addition, we obtain detailed information regarding the atomistic mechanisms responsible for the macroscopic curves. A strong dependence on geometry and orientation is observed. Two different microscopic mechanisms are observed to accommodate the applied loading: (i) nucleation and subsequent propagation into the bulk of edge dislocation dipoles and (ii) deformation twinning.

Forces during Bacteriophage DNA Packaging and Ejection

The conjunction of insights from structural biology, solution biochemistry, genetics, and single-molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this article we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure.

Mechanics of DNA packaging in viruses

A new generation of single-molecule experiments has opened up the possibility of reexamining many of the fundamental processes of biochemistry and molecular biology from a unique and quantitative perspective. One technique producing a host of intriguing results is the use of optical tweezers to measure the mechanical forces exerted by molecular motors during key processes such as the transcription of DNA or the packing of a viral genome into its capsid. The objective of the current article is to respond to such measurements on viruses and to use the theory of elasticity and a simple model of charge and hydration forces to derive the force required to pack DNA into a viral capsid as a function of the fraction of the viral genome that has been packed. The results are found to be in excellent accord with recent measurements and complement previous theoretical work. Because the packing of DNA in viral capsids occurs under circumstances of high internal pressure, we also compute how much pressure a capsid can sustain without rupture.

Quasicontinuum simulation of fracture at the atomic scale

We study the problem of atomic scale fracture using the recently developed quasicontinuum method in which there is a systematic thinning of the atomic-level degrees of freedom in regions where they are not needed. Fracture is considered in two distinct settings. First, a study is made of cracks in single crystals, and second, we consider a crack advancing towards a grain boundary (GB) in its path. In the investigation of single crystal fracture, we evaluate the competition between simple cleavage and crack-tip dislocation emission. In addition, we examine the ability of analytic models to correctly predict fracture behaviour, and find that the existing analytical treatments are too restrictive in their treatment of nonlinearity near the crack tip. In the study of GB-crack interactions, we have found a number of interesting deformation mechanisms which attend the advance of the crack. These include the migration of the GB, the emission of dislocations from the GB, and deflection of the crack front along the GB itself. In each case, these mechanisms are rationalized on the basis of continuum mechanics arguments.

Mechanosensitive channels: what can they do and how do they do it?

While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and perhaps also serving as a signal transducer for membrane tension or other functions. This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules.

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

Matching environmental phage with single, uncultured bacterial host cells reveals remarkable species specificity. Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments.