Subheap-Augmented Garbage Collection

Automated memory management avoids the tedium and danger of manual techniques. However, as no programmer input is required, no widely available interface exists to permit principled control over sometimes unacceptable performance costs. This dissertation explores the idea that performance-oriented languages should give programmers greater control over where and when the garbage collector (GC) expends effort. We describe an interface and implementation to expose heap partitioning and collection decisions without compromising type safety. We show that our interface allows the programmer to encode a form of reference counting using Hayes\u27 notion of key objects. Preliminary experimental data suggests that our proposed mechanism can avoid high overheads suffered by tracing collectors in some scenarios, especially with tight heaps. However, for other applications, the costs of applying subheaps---in human effort and runtime overheads---remain daunting

Fluctuating Currents in Stochastic Thermodynamics II. Energy Conversion and Nonequilibrium Response in Kinesin Models

Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational states of these biological macromolecules. A recently developed theoretical framework [Wachtel, Vollmer, Altaner: "Fluctuating Currents in Stochastic Thermodynamics I. Gauge Invariance of Asymptotic Statistics"] provides a simple algorithm for the determination of macroscopic currents and correlation integrals of arbitrary fluctuating currents. Here, we use it to discuss energy conversion and nonequilibrium response in different models for the molecular motor kinesin. Methodologically, our results demonstrate the effectiveness of the algorithm in dealing with parameter-dependent stochastic models. For the concrete biophysical problem our results reveal two interesting features in experimentally accessible parameter regions: The validity of a non-equilibrium Green--Kubo relation at mechanical stalling as well as negative differential mobility for superstalling forces.Comment: PACS numbers: 05.70.Ln, 05.40.-a, 87.10.Mn, 87.16.Nn. An accompanying publication "Fluctuating Currents in Stochastic Thermodynamics I. Gauge Invariance of Asymptotic Statistics" is available at http://arxiv.org/abs/1407.206

Modeling the Self-Assembly of Ordered Nanoporous Materials

Porous materials are of great importance in many fields due to their wide applications. An ongoing theme in this area is the tailoring of materials for specific applications. With a better understanding of the formation mechanisms, tailoring and controlling the pore structure may be achieved. The objective of this research is acquiring further understanding of the fundamental physics that govern the formation of these materials using molecular simulations. We are aiming to unravel the assembly process of silica porous materials using a semi-rigid silica tetrahedral model. This model together with reaction ensemble Monte Carlo simulations allows us to study the formation of silica nanoparticles, the initial stages of microporous material formation. A two-step formation mechanism was found to be crucial for generating the nanoparticles. A replica-exchange reaction ensemble Monte Carlo sampling together with the silica tetrahedral model is developed and applied to cross the energy barrier between amorphous silica to crystalline silica materials for searching for the ground state structure of this model. The technique involves simulating several system copies with different equilibrium constants controlling silica condensation/hydrolysis reactions, which are essential for building higher-order network structures and eventually crystals, was preformed. Different silica polymorphs including all-silica zeolite frameworks were obtained. This model shows a great potential to study the crystallization of microporous materials. We also study the formation of mesoporous materials using molecular dynamics simulations. We investigate the interplay of silica molecules and surfactants, and different mesophases such as micellar rods, hexagonal, bicontinuous and lamellar phases were obtained. Multiple charges on silicate oligomers were found to play an important role in the formation of hexagonal phases. To study the later stages of MCM-41 formation, a hybrid molecular dynamics and Monte Carlo approach is proposed. The cooperation between the physical interaction and chemical reaction can be taken into account simultaneously. Preliminary study shows that the ratio of silicate to surfactant higher than 4 is essential to the growth of MCM-41. With a further enhancement on the model, this hybrid approach will be a powerful tool to simulate the formation of MCM-41 in a large system and at a long time scale

Numerics of High Performance Computers and Benchmark Evaluation of Distributed Memory Computers

The internal representation of numerical data, their speed of manipulation to generate the desired result through efficient utilisation of central processing unit, memory, and communication links are essential steps of all high performance scientific computations. Machine parameters, in particular, reveal accuracy and error bounds of computation, required for performance tuning of codes. This paper reports diagnosis of machine parameters, measurement of computing power of several workstations, serial and parallel computers, and a component-wise test procedure for distributed memory computers. Hierarchical memory structure is illustrated by block copying and unrolling techniques. Locality of reference for cache reuse of data is amply demonstrated by fast Fourier transform codes. Cache and register-blocking technique results in their optimum utilisation with consequent gain in throughput during vector-matrix operations. Implementation of these memory management techniques reduces cache inefficiency loss, which is known to be proportional to the number of processors. Of the two Linux clusters-ANUP16, HPC22 and HPC64, it has been found from the measurement of intrinsic parameters and from application benchmark of multi-block Euler code test run that ANUP16 is suitable for problems that exhibit fine-grained parallelism. The delivered performance of ANUP16 is of immense utility for developing high-end PC clusters like HPC64 and customised parallel computers with added advantage of speed and high degree of parallelism

Proceedings of the 2011 New York Workshop on Computer, Earth and Space Science

The purpose of the New York Workshop on Computer, Earth and Space Sciences is to bring together the New York area's finest Astronomers, Statisticians, Computer Scientists, Space and Earth Scientists to explore potential synergies between their respective fields. The 2011 edition (CESS2011) was a great success, and we would like to thank all of the presenters and participants for attending. This year was also special as it included authors from the upcoming book titled "Advances in Machine Learning and Data Mining for Astronomy". Over two days, the latest advanced techniques used to analyze the vast amounts of information now available for the understanding of our universe and our planet were presented. These proceedings attempt to provide a small window into what the current state of research is in this vast interdisciplinary field and we'd like to thank the speakers who spent the time to contribute to this volume.Comment: Author lists modified. 82 pages. Workshop Proceedings from CESS 2011 in New York City, Goddard Institute for Space Studie