Nanoindentation of virus capsids in a molecular model

A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that consitute the capsids and is described in terms of the C-alpha atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments, showing an elastic region followed by an irreversible drop in force. The mechanical response of CPMV has not been studied, but the molecular model predicts an order of magnitude higher stiffness and a much shorter elastic region than for CCMV. These large changes result from small structural changes that increase the number of bonds by only 30% and would be difficult to capture in continuum models. Direct comparison of local deformations in continuum and molecular models of CCMV shows that the molecular model undergoes a gradual symmetry breaking rotation and accommodates more strain near the walls than the continuum model. The irreversible drop in force at small separations is associated with rupturing nearly all of the bonds between capsid proteins in the molecular model while a buckling transition is observed in continuum models.Comment: 18 figure

Green's Relations in Finite Transformation Semigroups

We consider the complexity of Green's relations when the semigroup is given by transformations on a finite set. Green's relations can be defined by reachability in the (right/left/two-sided) Cayley graph. The equivalence classes then correspond to the strongly connected components. It is not difficult to show that, in the worst case, the number of equivalence classes is in the same order of magnitude as the number of elements. Another important parameter is the maximal length of a chain of components. Our main contribution is an exponential lower bound for this parameter. There is a simple construction for an arbitrary set of generators. However, the proof for constant alphabet is rather involved. Our results also apply to automata and their syntactic semigroups.Comment: Full version of a paper submitted to CSR 2017 on 2016-12-1

Melting-freezing cycles in a relatively sheared pair of crystalline monolayers

The nonequilibrium dynamical behaviour that arises when two ordered two-dimensional monolayers of particles are sheared over each other is studied in Brownian dynamics simulations. A curious sequence of nonequilibrium states is observed as the driving rate is increased, the most striking of which is a sliding state with irregular alternation between disordered and ordered states. We comment on possible mechanisms underlying these cycles, and experiments that could observe them.Comment: 7 pages, 8 figures, minor changes in text and figures, references adde

Superlubricity - a new perspective on an established paradigm

Superlubricity is a frictionless tribological state sometimes occurring in nanoscale material junctions. It is often associated with incommensurate surface lattice structures appearing at the interface. Here, by using the recently introduced registry index concept which quantifies the registry mismatch in layered materials, we prove the existence of a direct relation between interlayer commensurability and wearless friction in layered materials. We show that our simple and intuitive model is able to capture, down to fine details, the experimentally measured frictional behavior of a hexagonal graphene flake sliding on-top of the surface of graphite. We further predict that superlubricity is expected to occur in hexagonal boron nitride as well with tribological characteristics very similar to those observed for the graphitic system. The success of our method in predicting experimental results along with its exceptional computational efficiency opens the way for modeling large-scale material interfaces way beyond the reach of standard simulation techniques.Comment: 18 pages, 7 figure

Complex Periodic Orbits and Tunnelling in Chaotic Potentials

We derive a trace formula for the splitting-weighted density of states suitable for chaotic potentials with isolated symmetric wells. This formula is based on complex orbits which tunnel through classically forbidden barriers. The theory is applicable whenever the tunnelling is dominated by isolated orbits, a situation which applies to chaotic systems but also to certain near-integrable ones. It is used to analyse a specific two-dimensional potential with chaotic dynamics. Mean behaviour of the splittings is predicted by an orbit with imaginary action. Oscillations around this mean are obtained from a collection of related orbits whose actions have nonzero real part

Jamming under tension in polymer crazes

Molecular dynamics simulations are used to study a unique expanded jammed state. Tension transforms many glassy polymers from a dense glass to a network of fibrils and voids called a craze. Entanglements between polymers and interchain friction jam the system after a fixed increase in volume. As in dense jammed systems, the distribution of forces is exponential, but they are tensile rather than compressive. The broad distribution of forces has important implications for fibril breakdown and the ultimate strength of crazes.Comment: 4 pages, 4 figure

Impact Ionization in ZnS

The impact ionization rate and its orientation dependence in k space is calculated for ZnS. The numerical results indicate a strong correlation to the band structure. The use of a q-dependent screening function for the Coulomb interaction between conduction and valence electrons is found to be essential. A simple fit formula is presented for easy calculation of the energy dependent transition rate.Comment: 9 pages LaTeX file, 3 EPS-figures (use psfig.sty), accepted for publication in PRB as brief Report (LaTeX source replaces raw-postscript file

Enhanced Learnability of Flight Techniques Through the Introduction of Targeted Observation Flights with Ab-Initio through Advanced Flight Training Candidates

Flight training paradigms exist to provide a framework for instructors to relay both technical and applied knowledge to students in the most efficient way possible. Traditional methods imply the use of pre/post flight briefings coincident with flight in either an actual or simulated environments. The demonstration of maneuvers may be accomplished by the instructor followed by the student or solely by the student. In this phase, aeronautical knowledge, procedural knowledge, and performance metrics are usually assessed. With regard to enhanced learnability, the study of effectiveness becomes critical to the application of new methods that could significantly lower the amount of flight time required to meet objectives or performance criteria for a given lesson. As industry continues to evolve with the use of automation, efficient pathways from initial to advanced flight training must be assessed in order to ensure students are receiving the most out of each activity. The direct observation of flights as an in-flight observer may improve performance and enhance the learnability of certain aspects of flight training, therefore reducing the number of flight hours necessary to achieve flight training landmarks. An experiential assessment of this technique will provide insight into the use of observation flights and how they may be correlated to improvement in student retention and performance

Contact of Single Asperities with Varying Adhesion: Comparing Continuum Mechanics to Atomistic Simulations

Atomistic simulations are used to test the equations of continuum contact mechanics in nanometer scale contacts. Nominally spherical tips, made by bending crystals or cutting crystalline or amorphous solids, are pressed into a flat, elastic substrate. The normal displacement, contact radius, stress distribution, friction and lateral stiffness are examined as a function of load and adhesion. The atomic scale roughness present on any tip made of discrete atoms is shown to have profound effects on the results. Contact areas, local stresses, and the work of adhesion change by factors of two to four, and the friction and lateral stiffness vary by orders of magnitude. The microscopic factors responsible for these changes are discussed. The results are also used to test methods for analyzing experimental data with continuum theory to determine information, such as contact area, that can not be measured directly in nanometer scale contacts. Even when the data appear to be fit by continuum theory, extracted quantities can differ substantially from their true values