Theoretical description of coherent doublon creation via lattice modulation spectroscopy

Using a recently developed strong-coupling method, we present a comprehensive theory for doublon production processes in modulation spectroscopy of a three-dimensional system of ultracold fermionic atoms in an optical lattice with a trap. The theoretical predictions compare well to the experimental time traces of doublon production. For experimentally feasible conditions, we provide a quantitative prediction for the presence of a nonlinear ``two-photon'' excitation at strong modulation amplitudes.

Evaluating FuncSION: A software for automated synthesis of design solutions for stimulating ideation during mechanical conceptual design

The goal of the work reported in this paper is to use automated, combinatorial synthesis to generate alternative solutions to be used as stimuli by designers for ideation. FuncSION, a computational synthesis tool that can automatically synthesize solution concepts for mechanical devices by combining building blocks from a library, is used for this purpose. The objectives of FuncSION are to help generate a variety of functional requirements for a given problem and a variety of concepts to fulfill these functions. A distinctive feature of FuncSION is its focus on automated generation of spatial configurations, an aspect rarely addressed by other computational synthesis programs. This paper provides an overview of FuncSION in terms of representation of design problems, representation of building blocks, and rules with which building blocks are combined to generate concepts at three levels of abstraction: topological, spatial, and physical. The paper then provides a detailed account of evaluating FuncSION for its effectiveness in providing stimuli for enhanced ideation.

Using formal reasoning on a model of tasks for FreeRTOS

FreeRTOS is an open-source real-time microkernel that has a wide community of users. We present the formal specification of the behaviour of the task part of FreeRTOS that deals with the creation, management, and scheduling of tasks using priority-based preemption. Our model is written in the Z notation, and we verify its consistency using the Z/Eves theorem prover. This includes a precise statement of the preconditions for all API commands. This task model forms the basis for three dimensions of further work: (a) the modelling of the rest of the behaviour of queues, time, mutex, and interrupts in FreeRTOS; (b) refinement of the models to code to produce a verified implementation; and (c) extension of the behaviour of FreeRTOS to multi-core architectures. We propose all three dimensions as benchmark challenge problems for Hoare's Verified Software Initiative.

Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005-1013. (c) 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Strength of Offshore Pipelines in Different Operation States and Analyzing Software

在近海管线的铺设、安装、使用过程中有多种作业状态：在位、悬跨、挖沟、提吊、铺管等。各种状态下管线的受力特点不同,加上管线结构、海况和海底土壤等因素又都很复杂,所以近海管线的强度分析难度大、内容多。分别采用解析方法、数值方法（有限元法、打靶法）和二者结合来解决理论上的（如几何非线性、动边界等）、实用性方面的难点。在理论分析的基础上,编制了符合产业部门工程师使用要求的近海管线强度分析软件。介绍了该软件进行力学分析时采用的理论以及软件界面。

Comparison Of Shear Banding In Bmgs Due To Thermal-Softening And Free Volume Creation

This paper reports a comparative study of shear banding in BMGs resulting from thermal softening and free volume creation. Firstly, the effects of thermal softening and free volume creation on shear instability are discussed. It is known that thermal softening governs thermal shear banding, hence it is essentially energy related. However, compound free volume creation is the key factor to the other instability, though void-induced softening seems to be the counterpart of thermal softening. So, the driving force for shear instability owing to free volume creation is very different from the thermally assisted one. In particular, long wave perturbations are always unstable owing to compound free volume creation. Therefore, the shear instability resulting from coupled compound free volume creation and thermal softening may start more like that due to free volume creation. Also, the compound free volume creation implies a specific and intrinsic characteristic growth time of shear instability. Finally, the mature shear band width is governed by the corresponding diffusions (thermal or void diffusion) within the band. As a rough guide, the dimensionless numbers: Thermal softening related number B, Deborah number (denoting the relation of instability growth rate owing to compound free volume and loading time) and Lewis number (denoting the competition of different diffusions) show us their relative importance of thermal softening and free volume creation in shear banding. All these results are of particular significance in understanding the mechanism of shear banding in bulk metallic glasses (BMGs).