A thread calculus with molecular dynamics

We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist of structured data objects and computations take place by means of actions which may change the structure of the data objects. The features introduced include restriction of the scope of names used in threads to refer to data objects. Because that feature makes it troublesome to provide a model based on structural operational semantics and bisimulation, we construct a projective limit model for the theory.Comment: 47 pages; examples and results added, phrasing improved, references replace

Programming an interpreter using molecular dynamics

PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.Comment: 27 page

Real-time optical micro-manipulation using optimized holograms generated on the GPU

Holographic optical tweezers allow the three dimensional, dynamic, multipoint manipulation of micron sized dielectric objects. Exploiting the massive parallel architecture of modern GPUs we can generate highly optimized holograms at video frame rate allowing the interactive micro-manipulation of 3D structures.Comment: 13 pages, 8 figure

Data linkage algebra, data linkage dynamics, and priority rewriting

We introduce an algebra of data linkages. Data linkages are intended for modelling the states of computations in which dynamic data structures are involved. We present a simple model of computation in which states of computations are modelled as data linkages and state changes take place by means of certain actions. We describe the state changes and replies that result from performing those actions by means of a term rewriting system with rule priorities. The model in question is an upgrade of molecular dynamics. The upgrading is mainly concerned with the features to deal with values and the features to reclaim garbage.Comment: 48 pages, typos corrected, phrasing improved, definition of services replaced; presentation improved; presentation improved and appendix adde

NEXUS/Physics: An interdisciplinary repurposing of physics for biologists

In response to increasing calls for the reform of the undergraduate science curriculum for life science majors and pre-medical students (Bio2010, Scientific Foundations for Future Physicians, Vision & Change), an interdisciplinary team has created NEXUS/Physics: a repurposing of an introductory physics curriculum for the life sciences. The curriculum interacts strongly and supportively with introductory biology and chemistry courses taken by life sciences students, with the goal of helping students build general, multi-discipline scientific competencies. In order to do this, our two-semester NEXUS/Physics course sequence is positioned as a second year course so students will have had some exposure to basic concepts in biology and chemistry. NEXUS/Physics stresses interdisciplinary examples and the content differs markedly from traditional introductory physics to facilitate this. It extends the discussion of energy to include interatomic potentials and chemical reactions, the discussion of thermodynamics to include enthalpy and Gibbs free energy, and includes a serious discussion of random vs. coherent motion including diffusion. The development of instructional materials is coordinated with careful education research. Both the new content and the results of the research are described in a series of papers for which this paper serves as an overview and context.Comment: 12 page