Structure and mechanics of active colloids

11 pages Acknowledgments MCM thanks Xingbo Yang and Lisa Manning for their contribution to some aspects of the work reviewed here and for fruitful discussions. MCM was supported by NSF-DMR-305184. MCM and AP acknowledge support by the NSF IGERT program through award NSF-DGE-1068780. MCM, AP and DY were additionally supported by the Soft Matter Program at Syracuse University. AP acknowledges use of the Syracuse University HTC Campus Grid which is supported by NSF award ACI-1341006. YF was supported by NSF grant DMR-1149266 and the Brandeis Center for Bioinspired Soft Materials, an NSF MRSEC, DMR-1420382.

SCAPHOID AND LUNATE CARPAL MECHANICS OVER THE SPECTRUM OF HEALTHY FUNCTION

When ligaments within the wrist are damaged, the resulting loss in range of motion and grip strength can lead to reduced earning potential and restricted ability to perform important activities of daily living. Left untreated, ligament injuries ultimately lead to arthritis and chronic pain. Surgical repair can mitigate these issues but current procedures are often non-anatomic and unable to completely restore the wrist’s complex network of ligaments. An inability to quantitatively assess wrist function clinically, both before and after surgery, limits the ability to assess the response to clinical intervention. Previous work has shown that bones within the wrist move in a similar pattern across people, but these patterns remain challenging to predict and model. In an effort to quantify and further develop the understanding of normal carpal mechanics, we performed two studies using 3D in vivo carpal bone motion analysis techniques. For the first study, we measured wrist laxity and performed CT scans of the wrist to evaluate 3D carpal bone positions. We found that through mid-range radial-ulnar deviation range of motion the scaphoid and lunate primarily flexed and extended; however, there was a significant relationship between wrist laxity and row-column behaviour. We also found that there was a significant relationship between scaphoid flexion and active radial deviation range of motion. For the second study, an analysis was performed on a publicly available database. We evaluated scapholunate relative motion over a full range of wrist positions, and found that there was a significant amount of variation in the location and orientation of the rotation axis between the two bones. Together the findings from the two studies illustrate the complexity and subject specificity of normal carpal mechanics, and should provide insights that can guide the development of anatomical wrist ligament repair surgeries that restore normal function.

A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by Quantum mechanics/Molecular mechanics studies

The Ran GTPase protein is a guanine nucleotide-binding protein (GNBP) with an acknowledged profile in cancer onset, progression and metastases. The complex mechanism adopted by GNBPs in exchanging GDP for GTP is an intriguing process and crucial for Ran viability. The successful completion of the process is a fundamental aspect of propagating downstream signalling events. QM/MM molecular dynamics simulations were employed in this study to provide a deeper mechanistic understanding of the initiation of nucleotide exchange in Ran. Results indicate significant disruption of the metal-binding site upon interaction with RCC1 (the Ran guanine nucleotide exchange factor), overall culminating in the prominent shift of the divalent magnesium ion. The observed ion drifting is reasoned to occur as a consequence of the complex formation between Ran and RCC1 and is postulated to be a critical factor in the exchange process adopted by Ran. This is the first report to observe and detail such intricate dynamics for a protein in Ras superfamily.

Mapping Learning and Game Mechanics for Serious Games Analysis in Engineering Education

In a world where students are increasing digitally tethered to powerful, ‘always on’ mobile devices, new models of engagement and approaches to teaching and learning are required from educators. Serious Games (SG) have proved to have instructional potential but there is still a lack of methodologies and tools not only for their design but also to support game analysis and assessment. This paper explores the use of SG to increase student engagement and retention. The development phase of the Circuit Warz game is presented to demonstrate how electronic engineering education can be radically reimagined to create immersive, highly engaging learning experiences that are problem-centered and pedagogically sound. The Learning Mechanics–Game Mechanics (LM-GM) framework for SG game analysis is introduced and its practical use in an educational game design scenario is shown as a case study.

Coupled diusion and mechanics in battery electrodes

Thesis (Ph.D.)--University of Washington, 2016-08

A finite-volume computational mechanics framework for multi-physics coupled fluid-stress problems

Abstract not available

Computational solid mechanics using a vertex-based finite volume method

A number of research groups are now developing and using finite volume (FV) methods for computational solid mechanics (CSM). These methods are proving to be equivalent and in some cases superior to their finite element (FE) counterparts. In this paper we will describe a vertex-based FV method with arbitrarily structured meshes, for modelling the elasto-plastic deformation of solid materials undergoing small strains in complex geometries. Comparisons with rational FE methods will be given.

A generic strategy for dynamic load balancing of distributed memory parallel computational mechanics using unstructured meshes

A large class of computational problems are characterised by frequent synchronisation, and computational requirements which change as a function of time. When such a problem is solved on a message passing multiprocessor machine [5], the combination of these characteristics leads to system performance which deteriorate in time. As the communication performance of parallel hardware steadily improves so load balance becomes a dominant factor in obtaining high parallel efficiency. Performance can be improved with periodic redistribution of computational load; however, redistribution can sometimes be very costly. We study the issue of deciding when to invoke a global load re-balancing mechanism. Such a decision policy must actively weigh the costs of remapping against the performance benefits, and should be general enough to apply automatically to a wide range of computations. This paper discusses a generic strategy for Dynamic Load Balancing (DLB) in unstructured mesh computational mechanics applications. The strategy is intended to handle varying levels of load changes throughout the run. The major issues involved in a generic dynamic load balancing scheme will be investigated together with techniques to automate the implementation of a dynamic load balancing mechanism within the Computer Aided Parallelisation Tools (CAPTools) environment, which is a semi-automatic tool for parallelisation of mesh based FORTRAN codes.

Modelling continuum mechanics phenomena using three dimensional unstructured meshes on massively parallel processors

The difficulties encountered in implementing large scale CM codes on multiprocessor systems are now fairly well understood. Despite the claims of shared memory architecture manufacturers to provide effective parallelizing compilers, these have not proved to be adequate for large or complex programs. Significant programmer effort is usually required to achieve reasonable parallel efficiencies on significant numbers of processors. The paradigm of Single Program Multi Data (SPMD) domain decomposition with message passing, where each processor runs the same code on a subdomain of the problem, communicating through exchange of messages, has for some time been demonstrated to provide the required level of efficiency, scalability, and portability across both shared and distributed memory systems, without the need to re-author the code into a new language or even to support differing message passing implementations. Extension of the methods into three dimensions has been enabled through the engineering of PHYSICA, a framework for supporting 3D, unstructured mesh and continuum mechanics modeling. In PHYSICA, six inspectors are used. Part of the challenge for automation of parallelization is being able to prove the equivalence of inspectors so that they can be merged into as few as possible.

Software tools for automating the parallelisation of FORTRAN computational mechanics codes

It is now clear that the concept of a HPC compiler which automatically produces highly efficient parallel implementations is a pipe-dream. Another route is to recognise from the outset that user information is required and to develop tools that embed user interaction in the transformation of code from scalar to parallel form, and then use conventional compilers with a set of communication calls. This represents the key idea underlying the development of the CAPTools software environment. The initial version of CAPTools is focused upon single block structured mesh computational mechanics codes. The capability for unstructured mesh codes is under test now and block structured meshes will be included next. The parallelisation process can be completed rapidly for modest codes and the parallel performance approaches that which is delivered by hand parallelisations.

Dynamic load balancing of distributed memory parallel computational mechanics using unstructured meshes for multi-physical modelling

As the complexity of parallel applications increase, the performance limitations resulting from computational load imbalance become dominant. Mapping the problem space to the processors in a parallel machine in a manner that balances the workload of each processors will typically reduce the run-time. In many cases the computation time required for a given calculation cannot be predetermined even at run-time and so static partition of the problem returns poor performance. For problems in which the computational load across the discretisation is dynamic and inhomogeneous, for example multi-physics problems involving fluid and solid mechanics with phase changes, the workload for a static subdomain will change over the course of a computation and cannot be estimated beforehand. For such applications the mapping of loads to process is required to change dynamically, at run-time in order to maintain reasonable efficiency. The issue of dynamic load balancing are examined in the context of PHYSICA, a three dimensional unstructured mesh multi-physics continuum mechanics computational modelling code.

Automatic implementation of dynamic load balancing strategies for structured computational mechanics codes

This paper presents a new dynamic load balancing technique for structured mesh computational mechanics codes in which the processor partition range limits of just one of the partitioned dimensions uses non-coincidental limits, as opposed to using coincidental limits in all of the partitioned dimensions. The partition range limits are 'staggered', allowing greater flexibility in obtaining a balanced load distribution in comparison to when the limits are changed 'globally'. as the load increase/decrease on one processor no longer restricts the load decrease/increase on a neighbouring processor. The automatic implementation of this 'staggered' load balancing strategy within an existing parallel code is presented in this paper, along with some preliminary results.