A review of High Performance Computing foundations for scientists

The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which otherwise would not be accessible, helps to improve experiments and provides new insights on systems which are analysed [3-6]. Knowing the fundamentals of computation can be very useful for scientists, for it can help them to improve the performance of their theoretical models and simulations. This review includes some technical essentials that can be useful to this end, and it is devised as a complement for researchers whose education is focused on scientific issues and not on technological respects. In this document we attempt to discuss the fundamentals of High Performance Computing (HPC) [7] in a way which is easy to understand without much previous background. We sketch the way standard computers and supercomputers work, as well as discuss distributed computing and discuss essential aspects to take into account when running scientific calculations in computers.Comment: 33 page

Parametric Polyhedra with at least kk Lattice Points: Their Semigroup Structure and the k-Frobenius Problem

Given an integral $d \times n$ matrix $A$, the well-studied affine semigroup \mbox{ Sg} (A)=\{ b : Ax=b, \ x \in {\mathbb Z}^n, x \geq 0\} can be stratified by the number of lattice points inside the parametric polyhedra $P_A(b)=\{x: Ax=b, x\geq0\}$. Such families of parametric polyhedra appear in many areas of combinatorics, convex geometry, algebra and number theory. The key themes of this paper are: (1) A structure theory that characterizes precisely the subset \mbox{ Sg}_{\geq k}(A) of all vectors b \in \mbox{ Sg}(A) such that $P_A(b) \cap {\mathbb Z}^n$ has at least $k$ solutions. We demonstrate that this set is finitely generated, it is a union of translated copies of a semigroup which can be computed explicitly via Hilbert bases computations. Related results can be derived for those right-hand-side vectors $b$ for which $P_A(b) \cap {\mathbb Z}^n$ has exactly $k$ solutions or fewer than $k$ solutions. (2) A computational complexity theory. We show that, when $n$, $k$ are fixed natural numbers, one can compute in polynomial time an encoding of \mbox{ Sg}_{\geq k}(A) as a multivariate generating function, using a short sum of rational functions. As a consequence, one can identify all right-hand-side vectors of bounded norm that have at least $k$ solutions. (3) Applications and computation for the $k$-Frobenius numbers. Using Generating functions we prove that for fixed $n,k$ the $k$-Frobenius number can be computed in polynomial time. This generalizes a well-known result for $k=1$ by R. Kannan. Using some adaptation of dynamic programming we show some practical computations of $k$-Frobenius numbers and their relatives

The 30/20 GHz flight experiment system, phase 2. Volume 2: Experiment system description

A detailed technical description of the 30/20 GHz flight experiment system is presented. The overall communication system is described with performance analyses, communication operations, and experiment plans. Hardware descriptions of the payload are given with the tradeoff studies that led to the final design. The spacecraft bus which carries the payload is discussed and its interface with the launch vehicle system is described. Finally, the hardwares and the operations of the terrestrial segment are presented

The use of oscillatory signals in the study of genetic networks

The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. It is found that there are important advantages in using oscillatory signals over step or impulse signals, and that the system may enter into a pure fluctuation resonance for a specific input frequency.Comment: 46 pages, 5 figures. Submitted to PNAS on May 27th 2004. The paper is under consideratio

A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line

The circadian clock regulates key cellular processes and its dysregulation is associated to several pathologies including cancer. Although the transcriptional regulation of gene expression by the clock machinery is well described, the role of the clock in the regulation of post-transcriptional processes, including splicing, remains poorly understood. In the present work, we investigated the putative interplay between the circadian clock and splicing in a cancer context. For this, we applied a computational pipeline to identify oscillating genes and alternatively spliced transcripts in time-course high-throughput data sets from normal cells and tissues, and cancer cell lines. We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z. Our data points to a connection between clock-controlled genes and splicing factors, which correlates with temporal alternative splicing in several genes in the HD-MY-Z cell line. These include the genes DPYD, SS18, VIPR1 and IRF4, involved in metabolism, cell cycle, apoptosis and proliferation. Our results highlight a role for the clock as a temporal regulator of alternative splicing, which may impact malignancy in this cellular model

Introduction to Logic Circuits & Logic Design with Verilog

The overall goal of this book is to fill a void that has appeared in the instruction of digital circuits over the past decade due to the rapid abstraction of system design. Up until the mid-1980s, digital circuits were designed using classical techniques. Classical techniques relied heavily on manual design practices for the synthesis, minimization, and interfacing of digital systems. Corresponding to this design style, academic textbooks were developed that taught classical digital design techniques. Around 1990, large-scale digital systems began being designed using hardware description languages (HDL) and automated synthesis tools. Broad-scale adoption of this modern design approach spread through the industry during this decade. Around 2000, hardware description languages and the modern digital design approach began to be taught in universities, mainly at the senior and graduate level. There were a variety of reasons that the modern digital design approach did not penetrate the lower levels of academia during this time. First, the design and simulation tools were difficult to use and overwhelmed freshman and sophomore students. Second, the ability to implement the designs in a laboratory setting was infeasible. The modern design tools at the time were targeted at custom integrated circuits, which are cost- and time-prohibitive to implement in a university setting. Between 2000 and 2005, rapid advances in programmable logic and design tools allowed the modern digital design approach to be implemented in a university setting, even in lower-level courses. This allowed students to learn the modern design approach based on HDLs and prototype their designs in real hardware, mainly fieldprogrammable gate arrays (FPGAs). This spurred an abundance of textbooks to be authored, teaching hardware description languages and higher levels of design abstraction. This trend has continued until today. While abstraction is a critical tool for engineering design, the rapid movement toward teaching only the modern digital design techniques has left a void for freshman- and sophomore-level courses in digital circuitry. Legacy textbooks that teach the classical design approach are outdated and do not contain sufficient coverage of HDLs to prepare the students for follow-on classes. Newer textbooks that teach the modern digital design approach move immediately into high-level behavioral modeling with minimal or no coverage of the underlying hardware used to implement the systems. As a result, students are not being provided the resources to understand the fundamental hardware theory that lies beneath the modern abstraction such as interfacing, gate-level implementation, and technology optimization. Students moving too rapidly into high levels of abstraction have little understanding of what is going on when they click the “compile and synthesize” button of their design tool. This leads to graduates who can model a breadth of different systems in an HDL but have no depth into how the system is implemented in hardware. This becomes problematic when an issue arises in a real design and there is no foundational knowledge for the students to fall back on in order to debug the problem

Introduction to Logic Circuits & Logic Design with VHDL

The overall goal of this book is to fill a void that has appeared in the instruction of digital circuits over the past decade due to the rapid abstraction of system design. Up until the mid-1980s, digital circuits were designed using classical techniques. Classical techniques relied heavily on manual design practices for the synthesis, minimization, and interfacing of digital systems. Corresponding to this design style, academic textbooks were developed that taught classical digital design techniques. Around 1990, large-scale digital systems began being designed using hardware description languages (HDL) and automated synthesis tools. Broad-scale adoption of this modern design approach spread through the industry during this decade. Around 2000, hardware description languages and the modern digital design approach began to be taught in universities, mainly at the senior and graduate level. There were a variety of reasons that the modern digital design approach did not penetrate the lower levels of academia during this time. First, the design and simulation tools were difficult to use and overwhelmed freshman and sophomore students. Second, the ability to implement the designs in a laboratory setting was infeasible. The modern design tools at the time were targeted at custom integrated circuits, which are cost- and time-prohibitive to implement in a university setting. Between 2000 and 2005, rapid advances in programmable logic and design tools allowed the modern digital design approach to be implemented in a university setting, even in lower-level courses. This allowed students to learn the modern design approach based on HDLs and prototype their designs in real hardware, mainly field programmable gate arrays (FPGAs). This spurred an abundance of textbooks to be authored teaching hardware description languages and higher levels of design abstraction. This trend has continued until today. While abstraction is a critical tool for engineering design, the rapid movement toward teaching only the modern digital design techniques has left a void for freshman- and sophomore-level courses in digital circuitry. Legacy textbooks that teach the classical design approach are outdated and do not contain sufficient coverage of HDLs to prepare the students for follow-on classes. Newer textbooks that teach the modern digital design approach move immediately into high-level behavioral modeling with minimal or no coverage of the underlying hardware used to implement the systems. As a result, students are not being provided the resources to understand the fundamental hardware theory that lies beneath the modern abstraction such as interfacing, gate-level implementation, and technology optimization. Students moving too rapidly into high levels of abstraction have little understanding of what is going on when they click the “compile and synthesize” button of their design tool. This leads to graduates who can model a breadth of different systems in an HDL but have no depth into how the system is implemented in hardware. This becomes problematic when an issue arises in a real design and there is no foundational knowledge for the students to fall back on in order to debug the problem