Optical Mineralogy in a Modern Earth Sciences Curriculum

Provides pedagogical insight concerning the skill of studying minerals The resource being annotated is: http://www.dlese.org/dds/catalog_SERC-NAGT-000-000-000-651.htm

Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.

ForceGen is a template-free, non-stochastic approach for 2D to 3D structure generation and conformational elaboration for small molecules, including both non-macrocycles and macrocycles. For conformational search of non-macrocycles, ForceGen is both faster and more accurate than the best of all tested methods on a very large, independently curated benchmark of 2859 PDB ligands. In this study, the primary results are on macrocycles, including results for 431 unique examples from four separate benchmarks. These include complex peptide and peptide-like cases that can form networks of internal hydrogen bonds. By making use of new physical movements ("flips" of near-linear sub-cycles and explicit formation of hydrogen bonds), ForceGen exhibited statistically significantly better performance for overall RMS deviation from experimental coordinates than all other approaches. The algorithmic approach offers natural parallelization across multiple computing-cores. On a modest multi-core workstation, for all but the most complex macrocycles, median wall-clock times were generally under a minute in fast search mode and under 2 min using thorough search. On the most complex cases (roughly cyclic decapeptides and larger) explicit exploration of likely hydrogen bonding networks yielded marked improvements, but with calculation times increasing to several minutes and in some cases to roughly an hour for fast search. In complex cases, utilization of NMR data to constrain conformational search produces accurate conformational ensembles representative of solution state macrocycle behavior. On macrocycles of typical complexity (up to 21 rotatable macrocyclic and exocyclic bonds), design-focused macrocycle optimization can be practically supported by computational chemistry at interactive time-scales, with conformational ensemble accuracy equaling what is seen with non-macrocyclic ligands. For more complex macrocycles, inclusion of sparse biophysical data is a helpful adjunct to computation

Fast, Scalable, and Interactive Software for Landau-de Gennes Numerical Modeling of Nematic Topological Defects

Numerical modeling of nematic liquid crystals using the tensorial Landau-de Gennes (LdG) theory provides detailed insights into the structure and energetics of the enormous variety of possible topological defect configurations that may arise when the liquid crystal is in contact with colloidal inclusions or structured boundaries. However, these methods can be computationally expensive, making it challenging to predict (meta)stable configurations involving several colloidal particles, and they are often restricted to system sizes well below the experimental scale. Here we present an open-source software package that exploits the embarrassingly parallel structure of the lattice discretization of the LdG approach. Our implementation, combining CUDA/C++ and OpenMPI, allows users to accelerate simulations using both CPU and GPU resources in either single- or multiple-core configurations. We make use of an efficient minimization algorithm, the Fast Inertial Relaxation Engine (FIRE) method, that is well-suited to large-scale parallelization, requiring little additional memory or computational cost while offering performance competitive with other commonly used methods. In multi-core operation we are able to scale simulations up to supra-micron length scales of experimental relevance, and in single-core operation the simulation package includes a user-friendly GUI environment for rapid prototyping of interfacial features and the multifarious defect states they can promote. To demonstrate this software package, we examine in detail the competition between curvilinear disclinations and point-like hedgehog defects as size scale, material properties, and geometric features are varied. We also study the effects of an interface patterned with an array of topological point-defects.Comment: 16 pages, 6 figures, 1 youtube link. The full catastroph

What is Autonomy?

A system is autonomous if it uses its own information to modify itself and its environment to enhance its survival, responding to both environmental and internal stimuli to modify its basic functions to increase its viability. Autonomy is the foundation of functionality, intentionality and meaning. Autonomous systems accommodate the unexpected through self-organizing processes, together with some constraints that maintain autonomy. Early versions of autonomy, such as autopoiesis and closure to efficient cause, made autonomous systems dynamically closed to information. This contrasts with recent work on open systems and information dynamics. On our account, autonomy is a matter of degree depending on the relative organization of the system and system environment interactions. A choice between third person openness and first person closure is not required

Computing and teaching microsymposia at ECM [European Crystallographic Meeting 20, Krakow, August 2001]

Microsymposia on the contemporary topic of Computing and Teaching Some key issues regarding different models for delivery of the curriculum, the pace of introducing the new technologies, the role of government in delivering mass education and the pressures on institutions in responding to the novel methods of education were raised during the talks

Non-catalytic bromination of benzene: a combined computational and experimental study

The non-catalytic bromination of benzene is shown experimentally to require high 5-14M concentrations of bromine in order to proceed at ambient temperatures to form predominantly bromobenzene, along with detectable (The non-catalytic bromination of benzene is shown experimentally to require high 5-14M concentrations of bromine in order to proceed at ambient temperatures to form predominantly bromobenzene, along with detectable (The non-catalytic bromination of benzene is shown experimentally to require high 5-14M concentrations of bromine in order to proceed at ambient temperatures to form predominantly bromobenzene, along with detectable

Multi-scale simulation of the nano-metric cutting process

Molecular dynamics (MD) simulation and the finite element (FE) method are two popular numerical techniques for the simulation of machining processes. The two methods have their own strengths and limitations. MD simulation can cover the phenomena occurring at nano-metric scale but is limited by the computational cost and capacity, whilst the FE method is suitable for modelling meso- to macro-scale machining and for simulating macro-parameters, such as the temperature in a cutting zone, the stress/strain distribution and cutting forces, etc. With the successful application of multi-scale simulations in many research fields, the application of simulation to the machining processes is emerging, particularly in relation to machined surface generation and integrity formation, i.e. the machined surface roughness, residual stress, micro-hardness, microstructure and fatigue. Based on the quasi-continuum (QC) method, the multi-scale simulation of nano-metric cutting has been proposed. Cutting simulations are performed on single-crystal aluminium to investigate the chip formation, generation and propagation of the material dislocation during the cutting process. In addition, the effect of the tool rake angle on the cutting force and internal stress under the workpiece surface is investigated: The cutting force and internal stress in the workpiece material decrease with the increase of the rake angle. Finally, to ease multi-scale modelling and its simulation steps and to increase their speed, a computationally efficient MATLAB-based programme has been developed, which facilitates the geometrical modelling of cutting, the simulation conditions, the implementation of simulation and the analysis of results within a unified integrated virtual-simulation environment