The self-assembly and evolution of homomeric protein complexes

We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of such complexes naturally takes the system into a region of interaction space where (i) the evolutionarily newer interactions are weaker, (ii) subcomplexes involving the stronger interactions are observed to be thermodynamically stable on destabilization of the protein-protein interactions and (iii) the self-assembly dynamics are hierarchical with these same subcomplexes acting as kinetic intermediates.Comment: 4 pages, 4 figure

Axial form factor of the nucleon in the perturbative chiral quark model

We apply the perturbative chiral quark model (PCQM) at one loop to analyze the axial form factor of the nucleon. This chiral quark model is based on an effective Lagrangian, where baryons are described by relativistic valence quarks and a perturbative cloud of Goldstone bosons as dictated by chiral symmetry. We apply the formalism to obtain analytical expressions for the axial form factor of the nucleon, which is given in terms of fundamental parameters of low-energy pion-nucleon physics (weak pion decay constant, strong pion-nucleon form factor) and of only one model parameter (radius of the nucleonic three-quark core).Comment: 23 pages, 5 figures, accepted for publication in J. Phys.

The neutron electric dipole form factor in the perturbative chiral quark model

We calculate the electric dipole form factor of the neutron in a perturbative chiral quark model, parameterizing CP-violation of generic origin by means of effective electric dipole moments of the constituent quarks and their CP-violating couplings to the chiral fields. We discuss the relation of these effective parameters to more fundamental ones such as the intrinsic electric and chromoelectric dipole moments of quarks and the Weinberg parameter. From the existing experimental upper limits on the neutron EDM we derive constraints on these CP-violating parameters.Comment: 20 pages, 3 figure

Phase separation of a multiple occupancy lattice gas

A binary lattice gas model that allows for multiple occupancy of lattice sites, inspired by recent coarse-grained descriptions of solutions of interacting polymers, is investigated by combining the steepest descent approximation with an exploration of the multidimensional energy landscape, and by Gibbs ensemble Monte Carlo simulations. The one-component version of the model, involving on site and nearest neighbour interactions, is shown to exhibit microphase separation into two sub-lattices with different mean occupation numbers. The symmetric two-component version of the multiple occupancy lattice gas is shown to exhibit a demixing transition into two phases above a critical mean occupation number.Comment: submitted to Journal of Physics

Directed Ising type dynamic preroughening transition in one dimensional interfaces

We present a realization of directed Ising (DI) type dynamic absorbing state phase transitions in the context of one-dimensional interfaces, such as the relaxation of a step on a vicinal surface. Under the restriction that particle deposition and evaporation can only take place near existing kinks, the interface relaxes into one of three steady states: rough, perfectly ordered flat (OF) without kinks, or disordered flat (DOF) with randomly placed kinks but in perfect up-down alternating order. A DI type dynamic preroughening transition takes place between the OF and DOF phases. At this critical point the asymptotic time evolution is controlled not only by the DI exponents but also by the initial condition. Information about the correlations in the initial state persists and changes the critical exponents.Comment: 12 pages, 10 figure

Genera of phytopathogenic fungi: GOPHY 3

This paper represents the third contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions, information about the pathology, distribution, hosts and disease symptoms for the treated genera, as well as primary and secondary DNA barcodes for the currently accepted species included in these. This third paper in the GOPHY series treats 21 genera of phytopathogenic fungi and their relatives including: Allophoma, Alternaria, Brunneosphaerella, Elsinoe, Exserohilum, Neosetophoma, Neostagonospora, Nothophoma, Parastagonospora, Phaeosphaeriopsis, Pleiocarpon, Pyrenophora, Ramichloridium, Seifertia, Seiridium, Septoriella, Setophoma, Stagonosporopsis, Stemphylium, Tubakia and Zasmidium. This study includes three new genera, 42 new species, 23 new combinations, four new names, and three typifications of older names

Atomic Tunneling from a STM/AFM tip: Dissipative Quantum Effects from Phonons

We study the effects of phonons on the tunneling of an atom between two surfaces. In contrast to an atom tunneling in the bulk, the phonons couple very strongly, and qualitatively change the tunneling behavior. This is the first example of {\it ohmic} coupling from phonons for a two-state system. We propose an experiment in which an atom tunnels from the tip of an STM, and show how its behavior would be similar to the Macroscopic Quantum Coherence behavior predicted for SQUIDS. The ability to tune and calculate many parameters would lead to detailed tests of the standard theories. (For a general intro to this work on the on the World-Wide-Web: http://www.lassp.cornell.edu. Click on ``Entertaining Science Done Here'' and ``Quantum Tunneling of Atoms'')Comment: 12 pages, ReVTex3.0, two figures (postscript). This is a (substantially) revised version of cond-mat/9406043. More info (+ postscript text) at : http://www.lassp.cornell.edu/ardlouis/publications.htm

DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat

Thermographic imaging in sports and exercise medicine: A Delphi study and consensus statement on the measurement of human skin temperature

This is an accepted manuscript of an article published by Elsevier in Journal of Thermal Biology on 18/07/2017, available online: https://doi.org/10.1016/j.jtherbio.2017.07.006 The accepted version of the publication may differ from the final published version.© 2017 Elsevier Ltd The importance of using infrared thermography (IRT) to assess skin temperature (tsk) is increasing in clinical settings. Recently, its use has been increasing in sports and exercise medicine; however, no consensus guideline exists to address the methods for collecting data in such situations. The aim of this study was to develop a checklist for the collection of tsk using IRT in sports and exercise medicine. We carried out a Delphi study to set a checklist based on consensus agreement from leading experts in the field. Panelists (n  =  24) representing the areas of sport science (n = 8; 33%), physiology (n = 7; 29%), physiotherapy (n = 3; 13%) and medicine (n = 6; 25%), from 13 different countries completed the Delphi process. An initial list of 16 points was proposed which was rated and commented on by panelists in three rounds of anonymous surveys following a standard Delphi procedure. The panel reached consensus on 15 items which encompassed the participants’ demographic information, camera/room or environment setup and recording/analysis of tsk using IRT. The results of the Delphi produced the checklist entitled “Thermographic Imaging in Sports and Exercise Medicine (TISEM)” which is a proposal to standardize the collection and analysis of tsk data using IRT. It is intended that the TISEM can also be applied to evaluate bias in thermographic studies and to guide practitioners in the use of this technique.Published versio