WorldWideScience

Sample records for biophysics lab simulation

  1. Biophysics

    CERN Document Server

    Glaser, Roland

    1999-01-01

    The message of this book is that biophysics is the science of physical principles underlying the "phenomenon life" on all levels of organization. Rather than teaching "physics for biologists" or "physical methods applied to biology", it regards its subject as a defined discipline with its own network of ideas and approaches. The book starts by explaining molecular structures of biological systems, various kinds of atomic, molecular and ionic interactions, movements, energy transfer, self organization of supramolecular structures and dynamic properties of biological membranes. It then goes on to introduce the biological organism as a non-equilibrium system, before treating thermodynamic concepts of osmotic and electrolyte equilibria as well as currents and potential profiles. It continues with topics of environmental biophysics and such medical aspects as the influence of electromagnetic fields or radiation on living systems and the biophysics of hearing and noice protection. The book concludes with a discussi...

  2. Mathematical biophysics

    CERN Document Server

    Rubin, Andrew

    2014-01-01

    This book presents concise descriptions and analysis of the classical and modern models used in mathematical biophysics. The authors ask the question "what new information can be provided by the models that cannot be obtained directly from experimental data?" Actively developing fields such as regulatory mechanisms in cells and subcellular systems and electron transport and energy transport in membranes are addressed together with more classical topics such as metabolic processes, nerve conduction and heart activity, chemical kinetics, population dynamics, and photosynthesis. The main approach is to describe biological processes using different mathematical approaches necessary to reveal characteristic features and properties of simulated systems. With the emergence of powerful mathematics software packages such as MAPLE, Mathematica, Mathcad, and MatLab, these methodologies are now accessible to a wide audience. Provides succinct but authoritative coverage of a broad array of biophysical topics and models Wr...

  3. Flow lab.: flow visualization and simulation

    Energy Technology Data Exchange (ETDEWEB)

    Park, Chung Kyun; Cho, Won Jin; Hahn, Pil Soo [Korea Atomic Energy Research Institute, Taejeon (Korea, Republic of)

    2005-11-15

    The experimental setups for flow visualization and processes identification in laboratory scale (so called Flow Lab.) has developed to get ideas and answer fundamental questions of flow and migration in geologic media. The setup was made of a granite block of 50x50cm scale and a transparent acrylate plate. The tracers used in this experiments were tritiated water, anions, and sorbing cations as well as an organic dye, eosine, to visualize migration paths. The migration plumes were taken with a digital camera as a function of time and stored as digital images. A migration model was also developed to describe and identify the transport processes. Computer simulation was carried out not only for the hydraulic behavior such as distributions of pressure and flow vectors in the fracture but also for the migration plume and the elution curves.

  4. A comparative study on real lab and simulation lab in communication engineering from students' perspectives

    Science.gov (United States)

    Balakrishnan, B.; Woods, P. C.

    2013-05-01

    Over the years, rapid development in computer technology has engendered simulation-based laboratory (lab) in addition to the traditional hands-on (physical) lab. Many higher education institutions adopt simulation lab, replacing some existing physical lab experiments. The creation of new systems for conducting engineering lab activities has raised concerns among educators on the merits and shortcomings of both physical and simulation labs; at the same time, many arguments have been raised on the differences of both labs. Investigating the effectiveness of both labs is complicated, as there are multiple factors that should be considered. In view of this challenge, a study on students' perspectives on their experience related to key aspects on engineering laboratory exercise was conducted. In this study, the Visual Auditory Read and Kinetic model was utilised to measure the students' cognitive styles. The investigation was done through a survey among participants from Multimedia University, Malaysia. The findings revealed that there are significant differences for most of the aspects in physical and simulation labs.

  5. Skill-Building Simulations in Cardiology: The HeartLab and EkgLab Experience

    OpenAIRE

    Bergeron, Bryan P.; Greenes, Robert A

    1987-01-01

    HeartLab and EkgLab are two simulation-based programs designed to teach medical students the essentials of the auscultatory cardiac exam and of electrocardiogram interpretation, respectively. The issues considered throughout the development of these projects, namely implementation language selection, program architecture, simulation design, patient models, and the approach to validation, are applicable to the design of any simulation-based system.

  6. Chapter 3 – VPPD-Lab: The Chemical Product Simulator

    DEFF Research Database (Denmark)

    Kalakul, Sawitree; Cignitti, Stefano; Zhang, L.;

    2017-01-01

    for computer-aided chemical product design and evaluation, implemented in the software called VPPD-Lab, is presented. In the same way a typical process simulator works, the VPPD-Lab allows users to: (1) analyze chemical-based products by performing virtual experiments (product property and performance...... as property calculations and property model consistency tests) for specific product property prediction, design, and/or analysis tasks. The application of VPPD-Lab is highlighted through case studies involving solvent mixture stability check, lubricant blend design, jet fuel blend design, and insect repellent...

  7. VPPD Lab - The Chemical Product Simulator

    DEFF Research Database (Denmark)

    Kalakul, Sawitree; Hussain, Rehan; Elbashir, Nimir;

    2015-01-01

    of product performance models and product-chemical property models are used to evaluate different classes of product. The product classes are single molecular structure chemicals (lipids, solvents, aroma, etc.), blended products (gasoline, jet-fuels, lubricants, etc.), and emulsified product (hand wash......In this paper, the development of a systematic model-based framework for product design, implemented in the new product design software called VPPD-Lab is presented. This framework employs its in-house knowledge-based system to design and evaluate chemical products. The built-in libraries...

  8. Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

    Science.gov (United States)

    Peng, Zhangli; Chen, Yeng-Long; Lu, Huijie; Pan, Zehao; Chang, Hsueh-Chia

    2015-12-01

    Computational modeling has become increasingly important in biophysics, but the great challenge in numerical simulations due to the multiscale feature of biological systems limits the capability of modeling in making discoveries in biology. Innovative multiscale modeling approaches are desired to bridge different scales from nucleic acids and proteins to cells and tissues. Although all-atom molecular dynamics has been successfully applied in many microscale biological processes such as protein folding, it is still prohibitively expensive for studying macroscale problems such as biophysics of cells and tissues. On the other hand, continuum-based modeling has become a mature procedure for analysis and design in many engineering fields, but new insights for biological systems in the microscale are limited when molecular details are missing in continuum-based modeling. In this context, mesoscale modeling approaches such as Langevin dynamics, lattice Boltzmann method, and dissipative particle dynamics have become popular by simultaneously incorporating molecular interactions and long-range hydrodynamic interactions, providing insights to properties on longer time and length scales than molecular dynamics. In this review, we summarized several mesoscale simulation approaches for studying two model systems in biophysics: red blood cells (RBCs) and deoxyribonucleic acids (DNAs). The RBC is a model system for cell mechanics and biological membranes, while the DNA represents a model system for biopolymers. We introduced the motivations of studying these problems and presented the key features of different mesoscale methods. Furthermore, we described the latest progresses in these methods and highlighted the major findings for modeling RBCs and DNAs. Finally, we also discussed the challenges and potential issues of different approaches.

  9. Simulation of Tillage Systems Impact on Soil Biophysical Properties Using the SALUS Model

    Directory of Open Access Journals (Sweden)

    Luigi Sartori

    2011-02-01

    Full Text Available A sustainable land management has been defined as the management system that allows for production, while minimizing risk, maintaining quality of soil and water. Tillage systems can significantly decrease soil carbon storage and influence the soil environment of a crop. Crop growth models can be useful tools in evaluating the impact of different tillage systems on soil biophysical properties and on the growth and final yield of the crops. The objectives of this paper were i to illustrate the SALUS model and its tillage component; ii to evaluate the effects of different tillage systems on water infiltration and time to ponding, iii to simulate the effect of tillage systems on some soil biophysical properties. The SALUS (System Approach to Land Use Sustainability model is designed to simulate continuous crop, soil, water and nutrient conditions under different tillage and crop residues management strategies for multiple years. Predictions of changes in surface residue, bulk density, runoff, drainage and evaporation were consistent with expected behaviours of these parameters as described in the literature. The experiment to estimate the time to ponding curve under different tillage system confirmed the theory and showed the beneficial effects of the residue on soil surface with respect to water infiltration. It also showed that the no-tillage system is a more appropriate system to adopt in areas characterized by high intensity rainfall.

  10. Simulators, Remote Labs and Robotic Telescopes

    Science.gov (United States)

    Folhas, Alvaro

    2015-04-01

    There is an increasing gap between students of the twenty-first century and the teaching methodology still stuck in the past century. The myriad stimuli that involve our students, immediate consumption of information, and the availability of resources, should cast the teacher in search methodologies that encourage the student to learn. The simulators, virtual laboratories and remote controlled robotic equipment are examples of high didactic potential resources, created by scientific organizations and universities, to be used in education, providing a direct interaction with science and motivating our students to a future career in science. It is up to us to take advantage of that work, and those resources, to light the sparkle in the eyes of our students. In Astronomy Club I've developed with high school students some practical projects in science, using, over the web, the robotic telescopes through which the students are studying and photographing deep sky objects; or the European network of radio telescope, measuring the speed of the arms of our galaxy in our galactic dance, their temperatures showing where it is more likely to form new stars. Students use these tools, engaging in their own knowledge construction, and forego their Friday afternoons without a hurry to go home for the weekend. That's the spirit we want for the school.

  11. Using LabVIEW: Simulation Exciter of Devices Jamming

    OpenAIRE

    Elan Djaelani; Nina Siti Aminah; Ridodi Anantaprama

    2012-01-01

    It has been made exciter of devices jamming, by using component voltage controled oscilator (vco). It has been done measurements: signal noise,signal sawtooth and level DC voltage at those signals. Being wanted those devices jamming could be raised it’s performance. With helping software LabVIEW being made exciter. Result Simulation are graphic and table relation between input exciter and it’s output. Input exciter are: signal sawtooth, signal noise and level DC voltage that could be changing...

  12. Computer Simulation and Data Analysis in Molecular Biology and Biophysics An Introduction Using R

    CERN Document Server

    Bloomfield, Victor

    2009-01-01

    This book provides an introduction, suitable for advanced undergraduates and beginning graduate students, to two important aspects of molecular biology and biophysics: computer simulation and data analysis. It introduces tools to enable readers to learn and use fundamental methods for constructing quantitative models of biological mechanisms, both deterministic and with some elements of randomness, including complex reaction equilibria and kinetics, population models, and regulation of metabolism and development; to understand how concepts of probability can help in explaining important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data from spectroscopic, genomic, and proteomic sources. These quantitative tools are implemented using the free, open source software program R. R provides an excellent environment for general numerical and statistical computing and graphics, with capabilities similar to Matlab®. Since R is increasingly used in bioinformat...

  13. Using LabVIEW: Simulation Exciter of Devices Jamming

    Directory of Open Access Journals (Sweden)

    Elan Djaelani

    2012-10-01

    Full Text Available It has been made exciter of devices jamming, by using component voltage controled oscilator (vco. It has been done measurements: signal noise,signal sawtooth and level DC voltage at those signals. Being wanted those devices jamming could be raised it’s performance. With helping software LabVIEW being made exciter. Result Simulation are graphic and table relation between input exciter and it’s output. Input exciter are: signal sawtooth, signal noise and level DC voltage that could be changing it’s amplitude. Output exciter are frequency RF, sweeping from frequency f1 to f2 with frequency medium f0. Result simulation could be used for development device jamming.

  14. Publicly Releasing a Large Simulation Dataset with NDS Labs

    Science.gov (United States)

    Goldbaum, Nathan

    2016-03-01

    Optimally, all publicly funded research should be accompanied by the tools, code, and data necessary to fully reproduce the analysis performed in journal articles describing the research. This ideal can be difficult to attain, particularly when dealing with large (>10 TB) simulation datasets. In this lightning talk, we describe the process of publicly releasing a large simulation dataset to accompany the submission of a journal article. The simulation was performed using Enzo, an open source, community-developed N-body/hydrodynamics code and was analyzed using a wide range of community- developed tools in the scientific Python ecosystem. Although the simulation was performed and analyzed using an ecosystem of sustainably developed tools, we enable sustainable science using our data by making it publicly available. Combining the data release with the NDS Labs infrastructure allows a substantial amount of added value, including web-based access to analysis and visualization using the yt analysis package through an IPython notebook interface. In addition, we are able to accompany the paper submission to the arXiv preprint server with links to the raw simulation data as well as interactive real-time data visualizations that readers can explore on their own or share with colleagues during journal club discussions. It is our hope that the value added by these services will substantially increase the impact and readership of the paper.

  15. A biophysical model of brain deformation to simulate and analyze longitudinal MRIs of patients with Alzheimer's disease

    OpenAIRE

    Khanal, Bishesh; Lorenzi, Marco; Ayache, Nicholas; Pennec, Xavier

    2016-01-01

    We propose a framework for developing a comprehensive biophysical model that could predict and simulate realistic longitudinal MRIs of patients with Alzheimer's Disease (AD). The framework includes three major building blocks: i) Atrophy generation ii) Brain deformation iii) Realistic MRI generation. Within this framework, this paper focuses on a detailed implementation of the brain deformation block with a carefully designed biomechanics-based tissue loss model. For a given baseline brain MR...

  16. Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation

    Science.gov (United States)

    Freeman, Gordon Samuel

    DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems. In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood. The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence

  17. The Virtual Genetics Lab II: Improvements to a Freely Available Software Simulation of Genetics

    Science.gov (United States)

    White, Brian T.

    2012-01-01

    The Virtual Genetics Lab II (VGLII) is an improved version of the highly successful genetics simulation software, the Virtual Genetics Lab (VGL). The software allows students to use the techniques of genetic analysis to design crosses and interpret data to solve realistic genetics problems involving a hypothetical diploid insect. This is a brief…

  18. Biophysics demystified

    CERN Document Server

    Goldfarb, Daniel

    2011-01-01

    Written in a step-by-step format, this practical guide begins with an introduction to the science of biophysics, covering biophysical techniques and applications. Next, you'll learn the principles of physics, biology, and chemistry required to understand biophysics, including free energy, entropy, and statistical mechanics. Biomolecules and the forces that influence their structure and conformation are also covered, as are protein, nucleic acid, and membrane biophysics. Detailed examples and concise explanations make it easy to understand the material, and end-of-chapter quizzes and a final exam help reinforce key concepts.

  19. Clinical biophysics

    Energy Technology Data Exchange (ETDEWEB)

    Anbar, M.; Spangler, R.A.; Scott, P.

    1985-01-01

    Chapters are included on clinical decision making, principles of biomedical engineering, computers and their medical uses, clinical radiobiology, diagnostic x-ray radiology, clinical applications of ultrasonics, nuclear medicine, NMR imaging, diagnostic imaging, bioelectric techniques in diagnosis and therapy, biophysical aspects of the clinical laboratory, and biophysical aspects of modern surgery.

  20. Encyclopedia of biophysics

    CERN Document Server

    2013-01-01

    The Encyclopedia of Biophysics is envisioned both as an easily accessible source of information and as an introductory guide to the scientific literature. It includes entries describing both Techniques and Systems.  In the Techniques entries, each of the wide range of methods which fall under the heading of Biophysics are explained in detail, together with the value and the limitations of the information each provides. Techniques covered range from diffraction (X-ray, electron and neutron) through a wide range of spectroscopic methods (X-ray, optical, EPR, NMR) to imaging (from electron microscopy to live cell imaging and MRI), as well as computational and simulation approaches. In the Systems entries, biophysical approaches to specific biological systems or problems – from protein and nucleic acid structure to membranes, ion channels and receptors – are described. These sections, which place emphasis on the integration of the different techniques, therefore provide an inroad into Biophysics from a biolo...

  1. Design and Simulation of Lab-on-a-Chip Devices

    DEFF Research Database (Denmark)

    Dimaki, Maria; Okkels, Fridolin

    2015-01-01

    Microfluidic channels are an essential part of any lab-on-a-chip system. They usually perform various functions, such as transporting liquids from A to B or mixing or separating liquids. As production costs for such systems are not insignificant, it is essential that the systems are designed...

  2. Simulations, Games, and Virtual Labs for Science Education: a Compendium and Some Examples

    Science.gov (United States)

    Russell, R. M.

    2011-12-01

    We have assembled a list of computer-based simulations, games, and virtual labs for science education. This list, with links to the sources of these resources, is available online. The entries span a broad range of science, math, and engineering topics. They also span a range of target student ages, from elementary school to university students. We will provide a brief overview of this web site and the resources found on it. We will also briefly demonstrate some of our own educational simulations, including the "Very, Very Simple Climate Model", and report on formative evaluations of these resources. Computer-based simulations and virtual labs are valuable resources for science educators in various settings, allowing learners to experiment and explore "what if" scenarios. Educational computer games can motivate learners in both formal and informal settings, encouraging them to spend much more time exploring a topic than they might otherwise be inclined to do. Part of this presentation is effectively a "literature review" of numerous sources of simulations, games, and virtual labs. Although we have encountered several nice collections of such resources, those collections seem to be restricted in scope. They either represent materials developed by a specific group or agency (e.g. NOAA's games web site) or are restricted to a specific discipline (e.g. geology simulations and virtual labs). This presentation directs viewers to games, simulations, and virtual labs from many different sources and spanning a broad range of STEM disciplines.

  3. Games, Simulations and Virtual Labs for Science Education: a Compendium and Some Examples

    Science.gov (United States)

    Russell, R. M.

    2012-12-01

    We have assembled a list of computer-based simulations, games, and virtual labs for science education. This list, with links to the sources of these resources, is available online. The entries span a broad range of science, math, and engineering topics. They also span a range of target student ages, from elementary school to university students. We will provide a brief overview of this web site and the resources found on it. We will also briefly demonstrate some of our own educational simulations and games. Computer-based simulations and virtual labs are valuable resources for science educators in various settings, allowing learners to experiment and explore "what if" scenarios. Educational computer games can motivate learners in both formal and informal settings, encouraging them to spend much more time exploring a topic than they might otherwise be inclined to do. Part of this presentation is effectively a "literature review" of numerous sources of simulations, games, and virtual labs. Although we have encountered several nice collections of such resources, those collections seem to be restricted in scope. They either represent materials developed by a specific group or agency (e.g. NOAA's games web site) or are restricted to a specific discipline (e.g. geology simulations and virtual labs). This presentation directs viewers to games, simulations, and virtual labs from many different sources and spanning a broad range of STEM disciplines.

  4. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies

    Science.gov (United States)

    Soler, Miguel A.; de Marco, Ario; Fortuna, Sara

    2016-01-01

    Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules. PMID:27721441

  5. A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

    Science.gov (United States)

    Jo, Sunhwan; Jiang, Wei

    2015-12-01

    Replica Exchange with Solute Tempering (REST2) is a powerful sampling enhancement algorithm of molecular dynamics (MD) in that it needs significantly smaller number of replicas but achieves higher sampling efficiency relative to standard temperature exchange algorithm. In this paper, we extend the applicability of REST2 for quantitative biophysical simulations through a robust and generic implementation in greatly scalable MD software NAMD. The rescaling procedure of force field parameters controlling REST2 "hot region" is implemented into NAMD at the source code level. A user can conveniently select hot region through VMD and write the selection information into a PDB file. The rescaling keyword/parameter is written in NAMD Tcl script interface that enables an on-the-fly simulation parameter change. Our implementation of REST2 is within communication-enabled Tcl script built on top of Charm++, thus communication overhead of an exchange attempt is vanishingly small. Such a generic implementation facilitates seamless cooperation between REST2 and other modules of NAMD to provide enhanced sampling for complex biomolecular simulations. Three challenging applications including native REST2 simulation for peptide folding-unfolding transition, free energy perturbation/REST2 for absolute binding affinity of protein-ligand complex and umbrella sampling/REST2 Hamiltonian exchange for free energy landscape calculation were carried out on IBM Blue Gene/Q supercomputer to demonstrate efficacy of REST2 based on the present implementation.

  6. Bus.py: A GridLAB-D Communication Interface for Smart Distribution Grid Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Timothy M.; Palmintier, Bryan; Suryanarayanan, Siddharth; Maciejewski, Anthony A.; Siegel, Howard Jay

    2015-07-03

    As more Smart Grid technologies (e.g., distributed photovoltaic, spatially distributed electric vehicle charging) are integrated into distribution grids, static distribution simulations are no longer sufficient for performing modeling and analysis. GridLAB-D is an agent-based distribution system simulation environment that allows fine-grained end-user models, including geospatial and network topology detail. A problem exists in that, without outside intervention, once the GridLAB-D simulation begins execution, it will run to completion without allowing the real-time interaction of Smart Grid controls, such as home energy management systems and aggregator control. We address this lack of runtime interaction by designing a flexible communication interface, Bus.py (pronounced bus-dot-pie), that uses Python to pass messages between one or more GridLAB-D instances and a Smart Grid simulator. This work describes the design and implementation of Bus.py, discusses its usefulness in terms of some Smart Grid scenarios, and provides an example of an aggregator-based residential demand response system interacting with GridLAB-D through Bus.py. The small scale example demonstrates the validity of the interface and shows that an aggregator using said interface is able to control residential loads in GridLAB-D during runtime to cause a reduction in the peak load on the distribution system in (a) peak reduction and (b) time-of-use pricing cases.

  7. Online simulation of classical inorganic analysis - interactive, self instructive simulations give more lab-time

    DEFF Research Database (Denmark)

    Josephsen, Jens

    2005-01-01

    and this has lead to the development of self-instructing, interactive PC-based learning resources closely related to an actual, running course in introductory inorganic chemistry [8]. Such a development is rather time consuming, but since the first experience was positive [8] it was considered worthwhile......Laboratory exercises, investigations, and experiments are invariably included in university chemistry teaching. The learning of empirical facts, chemical procedures and methods in chemistry depends heavily on the experience, which may be obtained from such teaching activities [1]. Experimental work...... (and in university programmes it often isn’t), but rather to give them experience with chemicals and methods, a computer-based laboratory simulation may function as a cheap and fast extension of student lab time. Virtual investigations seem to be a promising kind of tool [6,7,8] for several reasons...

  8. Development of an Android Application in the Form of a Simulation Lab as Learning Media for Senior High School Students

    Science.gov (United States)

    Astra, I Made; Nasbey, Hadi; Nugraha, Aditiya

    2015-01-01

    The aim of this research is to create learning media for senior high school students through an android application in the form of a simulation lab. The method employed in the study is research and development. A simulation lab which has been made subsequently validated by concept and media experts, further empirical testing by teachers and…

  9. GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Fuller, Jason C.; Djilali, Ned

    2014-06-23

    Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies, and the plethora of other resources and assets that are becoming part of modern electricity production, delivery, and consumption systems. As a result, the US Department of Energy’s Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D that uses an agent-based approach to simulating smart grids. This paper presents the numerical methods and approach to time-series simulation used by GridLAB-D and reviews applications in power system studies, market design, building control system design, and integration of wind power in a smart grid.

  10. GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

    Directory of Open Access Journals (Sweden)

    David P. Chassin

    2014-01-01

    Full Text Available Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies, and the plethora of other resources and assets that are becoming part of modern electricity production, delivery, and consumption systems. As a result, the US Department of Energy’s Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D that uses an agent-based approach to simulating smart grids. This paper presents the numerical methods and approach to time-series simulation used by GridLAB-D and reviews applications in power system studies, market design, building control system design, and integration of wind power in a smart grid.

  11. Modeling the Biophysical Effects in a Carbon Beam Delivery Line using Monte Carlo Simulation

    CERN Document Server

    Cho, Ilsung; Cho, Sungho; Kim, Eun Ho; Song, Yongkeun; Shin, Jae-ik; Jung, Won-Gyun

    2016-01-01

    Relative biological effectiveness (RBE) plays an important role in designing a uniform dose response for ion beam therapy. In this study the biological effectiveness of a carbon ion beam delivery system was investigated using Monte Carlo simulation. A carbon ion beam delivery line was designed for the Korea Heavy Ion Medical Accelerator (KHIMA) project. The GEANT4 simulation tool kit was used to simulate carbon beam transporting into media. An incident energy carbon ion beam in the range between 220 MeV/u and 290 MeV/u was chosen to generate secondary particles. The microdosimetric-kinetic (MK) model is applied to describe the RBE of 10% survival in human salivary gland (HSG) cells. The RBE weighted dose was estimated as a function of the penetrating depth of the water phantom along the incident beam direction. A biologically photon-equivalent Spread Out Bragg Peak (SOBP) was designed using the RBE weighted absorbed dose. Finally, the RBE of mixed beams was predicted as a function of the water phantom depth.

  12. Modeling the biophysical effects in a carbon beam delivery line by using Monte Carlo simulations

    Science.gov (United States)

    Cho, Ilsung; Yoo, SeungHoon; Cho, Sungho; Kim, Eun Ho; Song, Yongkeun; Shin, Jae-ik; Jung, Won-Gyun

    2016-09-01

    The Relative biological effectiveness (RBE) plays an important role in designing a uniform dose response for ion-beam therapy. In this study, the biological effectiveness of a carbon-ion beam delivery system was investigated using Monte Carlo simulations. A carbon-ion beam delivery line was designed for the Korea Heavy Ion Medical Accelerator (KHIMA) project. The GEANT4 simulation tool kit was used to simulate carbon-ion beam transport into media. An incident energy carbon-ion beam with energy in the range between 220 MeV/u and 290 MeV/u was chosen to generate secondary particles. The microdosimetric-kinetic (MK) model was applied to describe the RBE of 10% survival in human salivary-gland (HSG) cells. The RBE weighted dose was estimated as a function of the penetration depth in the water phantom along the incident beam's direction. A biologically photon-equivalent Spread Out Bragg Peak (SOBP) was designed using the RBE-weighted absorbed dose. Finally, the RBE of mixed beams was predicted as a function of the depth in the water phantom.

  13. Computer simulation of thermal-hydraulics of MNSR fuel-channel assembly using LabView

    International Nuclear Information System (INIS)

    A LabView simulator of thermal hydraulics has been developed to demonstrate the temperature profile of coolant flow in the reactor core during normal operation. The simulator could equally be used for any transient behaviour of the reactor. Heat generation, transfer and the associated temperature profile in the fuel-channel elements viz: the coolant, cladding and fuel were studied and the corresponding analytical temperature equations in the axial and radial directions for the coolant, outer surface of the cladding, fuel surface and fuel center were obtained for the simulation using LabView. Tables of values for the equations were constructed by MATLAB and excel software programs. Plots of the equations with LabView were verified and validated with the graphs drawn by the MATLAB. In this thesis, an analysis of the effects of the coolant inlet temperature of 24.5°C and exit temperature of 70.0° on the temperature distribution in fuel-channel elements of the reactor core of cylindrical geometry was carried out. Other parameters, including the total fuel channel power, mass flow rate and convective heat transfer coefficient were varied to study the effects on the temperature profile. The analytical temperature equations in the fuel channel elements of the reactor core were obtained. MATLAB and Excel software were used to construct data for the equations. The plots by MATLAB were used to benchmark the LabVIEW simulation. Excellent agreement was obtained between the MATLAB plots and the LabView simulation results with an error margin of 0.001. The analysis of the results by comparing gradients of inlet temperature, total reactor channel power and mass flow indicated that inlet temperature gradient is one of the key parameters in determining the temperature profile in the MNSR core. (au)

  14. GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

    OpenAIRE

    Chassin, David P.; Jason C. Fuller; Ned Djilali

    2014-01-01

    Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies and the plethora of other resources and assets that are becoming part of modern electricity production, delivery and consumption systems. As a result, the US Department of Energy's Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D(TM) that uses an agent-based approach to simula...

  15. Do Computer Simulations Allow a Better Understanding of Basic Electrical Circuits than Real Lab Experiments?

    CERN Document Server

    Schmekel, Bjoern S

    2010-01-01

    Several Authors have demonstrated that substituting computer simulations for real experiments conducted in a lab may help to improve students' understanding of the material. In the present work we try to understand the reasons for this intriguing finding and investigate possible prerequisites necessary to achieve this outcome. The study was conducted in an introductory college-level physics class in Germany. All simulations were performed using PSPICE.

  16. VIBA-LAB2: a virtual ion beam analysis laboratory software package incorporating elemental map simulations

    International Nuclear Information System (INIS)

    The software package VIBA-lab1, which incorporates PIXE and RBS energy spectra simulation has now been extended to include the simulation of elemental maps from 3D structures. VIBA-lab1 allows the user to define a wide variety of experimental parameters, e.g. energy and species of incident ions, excitation and detection geometry, etc. When the relevant experimental parameters as well as target composition are defined, the program can then simulate the corresponding PIXE and RBS spectra. VIBA-LAB2 has been written with applications in nuclear microscopy in mind. A set of drag-and-drop tools has been incorporated to allow the user to define a three-dimensional sample object of mixed elemental composition. PIXE energy spectra simulations are then carried out on pixel-by-pixel basis and the corresponding intensity distributions or elemental maps can be computed. Several simulated intensity distributions for some 3D objects are demonstrated, and simulations obtained from a simple IC are compared with experimental results

  17. Testing Astrophysics in the Lab: Simulations with the FLASH code

    Science.gov (United States)

    Dwarkadas, Vikram

    2003-10-01

    FLASH is a multi-physics, block-structured adaptive mesh refinement code for studying compressible, reactive flows in various astrophysical environments. We compare the results of two- and three-dimensional FLASH simulations to experimental data obtained at Los Alamos National Laboratory (LANL). The LANL experiment (Tomkins et al. 2003, PhFl, 15, 896) involves the lateral interaction between a planar Ma=1.2 shock wave with one or two cylinders of sulphur hexafluoride (SF6) gas. The development of primary and secondary flow instabilities after the passage of the shock, as observed in the experiments and numerical simulations, are reviewed and compared. We investigate the deposition of vorticity due to the impact of the shock wave on the cylinder, and the transition from laminar to turbulent flow. The interaction of shock waves with high-density clouds is a common phenomenon in astrophysics. Shock-cloud interactions are seen in the interstellar medium and within supernova remnants and wind-driven nebulae. On large scales, refraction of galactic radio jets flowing past density gradients provides conditions suitable for strong vorticity generation, jet bending, and eventual jet disruption. On smaller scales, interactions between shocks and clouds have been proposed as a means to trigger the collapse of giant molecular clouds, leading to the onset of star formation. By carefully comparing our numerical simulations with experimental data we will validate FLASH for shock-cloud interactions, albeit in the restricted regime of low-Mach number adiabatic planar shocks and for low density contrasts. Following similarity arguments, such comparisons build confidence that the numerical simulations adequately describe the hydrodynamical evolution of shock-cloud interactions on timescales inaccessible to direct observations.

  18. Strategic planning for skills and simulation labs in colleges of nursing.

    Science.gov (United States)

    Gantt, Laura T

    2010-01-01

    While simulation laboratories for clinical nursing education are predicted to grow, budget cuts may threaten these programs. One of the ways to develop a new lab, as well as to keep an existing one on track, is to develop and regularly update a strategic plan. The process of planning not only helps keep the lab faculty and staff apprised of the challenges to be faced, but it also helps to keep senior level management engaged by reason of the need for their input and approval of the plan. The strategic planning documents drafted by those who supervised the development of the new building and Concepts Integration Labs (CILs) helped guide and orient faculty and other personnel hired to implement the plan and fulfill the vision. As the CILs strategic plan was formalized, the draft plans, including the SWOT analysis, were reviewed to provide historical perspective, stimulate discussion, and to make sure old or potential mistakes were not repeated. PMID:21158251

  19. Strategic planning for skills and simulation labs in colleges of nursing.

    Science.gov (United States)

    Gantt, Laura T

    2010-01-01

    While simulation laboratories for clinical nursing education are predicted to grow, budget cuts may threaten these programs. One of the ways to develop a new lab, as well as to keep an existing one on track, is to develop and regularly update a strategic plan. The process of planning not only helps keep the lab faculty and staff apprised of the challenges to be faced, but it also helps to keep senior level management engaged by reason of the need for their input and approval of the plan. The strategic planning documents drafted by those who supervised the development of the new building and Concepts Integration Labs (CILs) helped guide and orient faculty and other personnel hired to implement the plan and fulfill the vision. As the CILs strategic plan was formalized, the draft plans, including the SWOT analysis, were reviewed to provide historical perspective, stimulate discussion, and to make sure old or potential mistakes were not repeated.

  20. TCA Evaluation. Lab Measurements, Modelling and System Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bales, Chris; Nordlander, Svante

    2005-12-15

    The study reported here is part of a large project for evaluation of the Thermo-Chemical Accumulator (TCA), a technology under development by the Swedish company ClimateWell AB. The studies concentrate on the use of the technology for comfort cooling. This report concentrates on measurements in the laboratory, modelling and system simulation. The TCA is a three-phase absorption heat pump that stores energy in the form of crystallised salt, in this case Lithium Chloride (LiCl) with water being the other substance. The process requires vacuum conditions as with standard absorption chillers using LiBr/water. Measurements were carried out in the laboratories at the Solar Energy Research Center SERC, at Hoegskolan Dalarna as well as at ClimateWell AB. The measurements at SERC were performed on a prototype version 7:1 and showed that this prototype had several problems resulting in poor and unreliable performance. The main results were that: there was significant corrosion leading to non-condensable gases that in turn caused very poor performance; unwanted crystallisation caused blockages as well as inconsistent behaviour; poor wetting of the heat exchangers resulted in relatively high temperature drops there. A measured thermal COP for cooling of 0.46 was found, which is significantly lower than the theoretical value. These findings resulted in a thorough redesign for the new prototype, called ClimateWell 10 (CW10), which was tested briefly by the authors at ClimateWell. The data collected here was not large, but enough to show that the machine worked consistently with no noticeable vacuum problem s. It was also sufficient for identifying the main parameters in a simulation model developed for the TRNSYS simulation environment, but not enough to verify the model properly. This model was shown to be able to simulate the dynamic as well as static performance of the CW10, and was then used in a series of system simulations. A single system model was developed as the basis

  1. Simulation of Forced Expiration in a Biophysical Model, With Homogeneous and Clustered Bronchoconstriction.

    Science.gov (United States)

    Hedges, Kerry L; Tawhai, Merryn H

    2016-06-01

    One limitation of forced spirometry is that it integrates the contribution of the complex and dynamic behavior of all of the airways and tissue of the lung into a single exhaling unit, hence, it is not clear how spirometric measures are affected by local changes to the airways or tissue such as the presence of "ventilation defects." Here, we adapt a wave-speed limitation model to a spatially distributed and anatomically based airway tree that is embedded within a deformable parenchyma, to simulate forced expiration in 1 s (FEV1). This provides a model that can be used to assess the consequence of imposed constrictions on FEV1. We first show how the model can be parameterized to represent imaging and forced spirometry data from nonasthmatic healthy young adults. We then compare the effect of homogeneous and clustered bronchoconstriction on FEV1 in six subject-specific models (three male and three female). The model highlights potential sources of normal subject variability in response to agonist challenge, including the interaction between sites of airway constriction and sites of flow limitation at baseline. The results support earlier studies which proposed that the significant constriction of nondefect airways must be present in order to match to clinical measurements of lung function. PMID:27109169

  2. The human simulation lab-dissecting sex in the simulator lab: the clinical lacuna of transsexed embodiment.

    Science.gov (United States)

    Singer, Ben

    2013-06-01

    This article begins with an ethnographically documented incident whereby nursing students dissected a medical human simulator model and rearranged it so that the "male" head and torso was attached to the "female" lower half. They then joked about the embodiment of the model, thus staging a scene of anti-trans ridicule. The students' lack of ability, or purposeful refusal, to recognize morphological biodiversity in medical settings indicates a lacuna in clinical imaginaries. Even as trans-identified and gender nonconforming people increasingly access care in the clinic, the lacuna of transsex-as a proxy term for non-binary embodiment-persists at the heart of clinical practice. This article concludes that we might engage in more ethical clinical practice if we recognize and affirm the trace of multiple forms of human being in the non-human simulator. PMID:23475454

  3. Structural biophysics

    International Nuclear Information System (INIS)

    Summaries of research projects conducted during 1978 and 1979 are presented. The structural biophysics group explores the high-resolution structure of biological macromolecules and cell organelles. Specific subject areas include: the basic characteristics of photosynthesis in plants; the chemical composition of individual fly ash particles at the site of their damaging action in tissues; direct analysis of frozen-hydrated biological samples by scanning electron microscopy; yeast genetics; the optical activity of DNA aggregates; measurement and characterization of lipoproteins; function of lipoproteins; and the effect of radiation and pollutants on mammalian cells

  4. Thermal Simulation of Biogas Plants Using Mat Lab

    Directory of Open Access Journals (Sweden)

    Shaheen.M.Sain

    2014-10-01

    Full Text Available The major prerequisite for the optimum production of methane from a biogas plant is the sustenance of digester temperature within the narrow limits (300C-350C. It is experimentally investigated that, the MIT biogas plant is not maintaining optimum temperature, this decreases the efficiency and increases the detention time for charge. To maintain the plant in optimum temperature, it is necessary to find out the heat losses from the biogas plant and the external energy inputs need to operate the plant. Rate of gas yield, and the detention time (time necessary to anaerobically digest organic wastes in a biogas reactor, are favorable functions of the temperature in the digester. A thermal simulation for MIT biogas plant has developed using matlab in order to understand the heat transfer from the slurry and the gas holder to the surrounding earth and air respectively. The computation has been performed when the slurry is maintained at 200C and 300C, optimum temperature of anaerobic fermentation. If the slurry is considered to be at 350C, the optimum temperature of anaerobic fermentation, the total heat loss from the plant is higher than the heat loss when the slurry is maintained at 200C. The heat calculations provide an appraisal for the heat which has to be supplied by external means to compensate for the net heat losses which occur if the slurry is to be maintained at 350C. A solar system with auxiliary electric heater is designed for maintaining the slurry at 350C.In conclusion; the results of thermal analysis are used to define a strategy for operating biogas plant at optimum temperatures. .

  5. Radiation biophysics

    International Nuclear Information System (INIS)

    Summaries of research projects conducted during 1978 and 1979 are presented. The overall thrust of the research is aimed at understanding the effects of radiation on organisms. Specific subject areas include: the effects of heavy-particle beam nuclear interactions in tissue on dosimetry; tracer studies with radioactive fragments of heavy-ion beams; the effects of heavy/ions on human kidney cells and Chinese hamster cells; the response of a rhabdomyosarcoma tumor system in rats to heavy-ion beams; the use of heavy charged particles in radiotherapy of human cancer; heavy-ion radiography; the biological effects of high magnetic fields; central nervous system neurotoxicity; and biophysical studies on cell membranes

  6. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

  7. Development of LabVIEW web-based simulator for RELAP5

    International Nuclear Information System (INIS)

    This work presents the development of a LabVIEW web-based simulator using the output results of the best estimate nuclear system analysis code, RELAP5, for graphical user interfaces and web-casting. A numerical based model designed for natural circulation studies on the thermal hydraulic experimental facility called Natural Circulation Circuit, was developed with RELAP5 code. Specific output results from RELAP5 simulation are displayed in a user friendly graphical format. The temperatures are shown as a function of time in a XY graphic. Temperatures, levels and void fractions are displayed in color-coded scale which change in time on the graphical interface representing the circuit. An alarm is set for the case of onset boiling temperature occurrence at the heater outlet. This simulator allows an easy visual understanding of the thermal hydraulic circuit behavior. It can be shared, via Web, with researchers in any geographical location and, at the same time, it can be used in learning for distance educational purposes. In future work, this LabVIEW simulator will be coupled with RELAP5 code through dll's. Simultaneous graphical displaying and code calculations will be possible. Results are presented and discussed. (author)

  8. Development of LabVIEW web-based simulator for RELAP5

    Energy Technology Data Exchange (ETDEWEB)

    Macedo, Luiz A.; Torres, Walmir M.; Sabundjian, Gaiane; Andrade, Delvonei A.; Belchior Junior, Antonio; Umbehaun, Pedro E.; Conti, Thadeu N.; Mesquita, Roberto N. de; Masotti, Paulo H.F.; Angelo, Gabriel, E-mail: lamacedo@ipen.b, E-mail: wmtorres@ipen.b, E-mail: gdjian@ipen.b, E-mail: delvonei@ipen.b, E-mail: abelchior@ipen.b, E-mail: umbehaun@ipen.b, E-mail: tnconti@ipen.b, E-mail: rnavarro@ipen.b, E-mail: , E-mail: masotti@ipen.b, E-mail: gabriel.angelo@usp.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2011-07-01

    This work presents the development of a LabVIEW web-based simulator using the output results of the best estimate nuclear system analysis code, RELAP5, for graphical user interfaces and web-casting. A numerical based model designed for natural circulation studies on the thermal hydraulic experimental facility called Natural Circulation Circuit, was developed with RELAP5 code. Specific output results from RELAP5 simulation are displayed in a user friendly graphical format. The temperatures are shown as a function of time in a XY graphic. Temperatures, levels and void fractions are displayed in color-coded scale which change in time on the graphical interface representing the circuit. An alarm is set for the case of onset boiling temperature occurrence at the heater outlet. This simulator allows an easy visual understanding of the thermal hydraulic circuit behavior. It can be shared, via Web, with researchers in any geographical location and, at the same time, it can be used in learning for distance educational purposes. In future work, this LabVIEW simulator will be coupled with RELAP5 code through dll's. Simultaneous graphical displaying and code calculations will be possible. Results are presented and discussed. (author)

  9. The "Virtual ChemLab" Project: A Realistic and Sophisticated Simulation of Organic Synthesis and Organic Qualitative Analysis

    Science.gov (United States)

    Woodfield, Brian F.; Andrus, Merritt B.; Waddoups, Gregory L.; Moore, Melissa S.; Swan, Richard; Allen, Rob; Bodily, Greg; Andersen, Tricia; Miller, Jordan; Simmons, Bryon; Stanger, Richard

    2005-01-01

    A set of sophisticated and realistic laboratory simulations is created for use in freshman- and sophomore-level chemistry classes and laboratories called 'Virtual ChemLab'. A detailed assessment of student responses is provided and the simulation's pedagogical utility is described using the organic simulation.

  10. The Virtual ChemLab Project: A Realistic and Sophisticated Simulation of Inorganic Qualitative Analysis

    Science.gov (United States)

    Woodfield, Brian F.; Catlin, Heidi R.; Waddoups, Gregory L.; Moore, Melissa S.; Swan, Richard; Allen, Rob; Bodily, Greg

    2004-11-01

    We have created a set of sophisticated and realistic laboratory simulations for use in freshman- and sophomore-level chemistry classes and laboratories called Virtual ChemLab. We have completed simulations for Inorganic Qualitative Analysis, Organic Synthesis and Organic Qualitative Analysis, Experiments in Quantum Chemistry, Gas Properties, Titration Experiments, and Calorimetric and Thermochemical Experiments. The purpose of our simulations is to reinforce concepts taught in the classroom, provide an environment for creative learning, and emphasize the thinking behind instructional laboratory experiments. We have used the inorganic simulation extensively with thousands of students in our department at Brigham Young University. We have learned from our evaluation that: (i) students enjoy using these simulations and find them to be an asset in learning effective problem-solving strategies, (ii) students like the fact that they can both reproduce experimental procedures and explore various topics in ways they choose, and (iii) students naturally divide themselves into two groups: creative learners, who excel in an open-ended environment of virtual laboratories, and structured learners, who struggle in this same environment. In this article, we describe the Inorganic Qualitative Analysis simulation; we also share specific evaluation findings from using the inorganic simulation in classroom and laboratory settings.

  11. MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies

    Science.gov (United States)

    Gourlé, Hadrien; Bongcam-Rudloff, Erik; Hayer, Juliette

    2016-01-01

    Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens’ theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab. PMID:27479078

  12. MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

    Science.gov (United States)

    Norling, Martin; Karlsson-Lindsjö, Oskar E; Gourlé, Hadrien; Bongcam-Rudloff, Erik; Hayer, Juliette

    2016-01-01

    Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens' theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab. PMID:27479078

  13. MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

    Science.gov (United States)

    Norling, Martin; Karlsson-Lindsjö, Oskar E; Gourlé, Hadrien; Bongcam-Rudloff, Erik; Hayer, Juliette

    2016-01-01

    Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens' theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab.

  14. 2. biophysical work meeting

    International Nuclear Information System (INIS)

    The report comprises 18 papers held at the 2nd Biophysical Work Meeting, 11 - 13 September 1991 in Schlema, Germany. The history of biophysics in Germany particularly of radiation biophysics and radon research, measurements of the radiation effects of radon and the derivation of limits, radon balneotherapy and consequences of uranium ore mining are dealt with. (orig.)

  15. Biophysics conference 1978

    International Nuclear Information System (INIS)

    The main subject on the biophysics meeting was the biophysics of membranes with practical subjects from photosynthesis and the transfer processes on membranes. In radiation biophysics, problems of radiation sensitisation, immunological problems after radiation exposure, the oxygen effect and inhibitory processes in RNS synthesis after radiation exposure were discussed with a view to tumour therapy. (AJ)

  16. Simulation study based on the single-point temperature monitoring system of LabVIEW

    Science.gov (United States)

    Wu, Yongling; Yang, Na; Liu, Shuping; Pan, Xiaohui; Wang, Wenjiang

    2014-12-01

    This paper takes LabVIEW2012 as a development platform, creating a J-type thermocouple sensor and the NI USB-6229 data acquisition card and other hardware emulation circuitry which combined with the PC designed a single-point temperature monitoring system. Through simulation experiments, the system has a collection interval, the sampling rate per channel sampling on the temperature limit set by the user function and it also has the function of real-time display the current temperature, the temperature limit alarm, maximum temperature, minimum temperature display and a temperature history data query. This system can be used for temperature monitoring of life, research, industrial control, environmental monitoring, biomedical, tobacco processing, greenhouse cultivation, livestock breeding and other fields, which has important significance and practical value.

  17. Realization of a Web Simulation Sensor Laboratory by LabVIEW%LabVIEW实现的网络化仿真传感器实验室

    Institute of Scientific and Technical Information of China (English)

    梁胜祥; 王照伟; 栾海峰; 侯永飞; 刘晓旻

    2012-01-01

    The simulation sensor laboratory based on virtual technology provided a novel sensor experimental device which can be upgraded easily. It enriched the experimental teaching resources, expanded the experiment content and solved the problem of ageing and inadequate of the experimental teaching equipment in colleges and universities. The realization of network simulation laboratory broke the time-space limit of the traditional laboratory and promoted the openness of the curriculum resources. An on-line simulation sensor laboratory based on B/S structure was built by the Web publishing and remote access functions of LabVIEW. The database technology strengthened management of the lab and provided secure remote assessments. So the simulation sensor laboratory can be accessed remotely and securely at any authorized terminal. The all-weather on-line simulation sensor laboratory improved students ' interest in active learning, thereby contributing to the development of students' abilities such as autonomous learning, engineering application, innovation and modern engineering thinking.%虚拟技术构筑的仿真传感器实验室丰富了实验教学资源,拓展了实验内容,弥补了高校实验教学设备不足、设备老化等问题,提供了便于升级的“新型传感器实验仪”.仿真实验室网络化的实现,打破了传统实验室的时空局限性,促进了课程资源的开放性.利用LabVIEW的Web发布和远程访问功能,构筑B/S结构的在线仿真传感器实验室,采用数据库技术加强其管理,可以为任意授权的终端提供安全的远程访问机制.全天候在线的仿真传感器实验室,提高了学生主动学习的兴趣,探索了实验教学的新模式,有利于培养学生现代工程思维、自主学习能力、工程应用和创新能力.

  18. Design of two-channel oscilloscope and basic circuit simulations in LabView

    Science.gov (United States)

    Balzhiev, Plamen; Makal, Jaroslaw

    2008-01-01

    The project is realized as a diploma thesis in Bialystok Technical University, Poland). The main aim is to develop a useful educational tool which presents the time and frequency characteristics in basic electrical circuits. It is designed as a helpful instrument for lectures and laboratory classes. The predominant audience will be students of electrical engineering from first semester of the higher education. Therefore the level of knowledge at this stage of education is not high enough and different techniques are necessary to increase the students' interest and the efficiency of teaching process. This educational instrument provides the needed knowledge concerning the basic circuits and its parameters. Graphics and animations of the general processes in the electrical circuits make the problems more interesting, comprehensive and easier to understand. For designing such an instrument the National Instruments' programming environment LabView is used. It is preferred to the other simulation software because of its simplicity flexibility and also availability (the free demo version is sufficient to make a simple virtual instrument). LabView uses graphical programming language and has powerful mathematical functions for analysis and simulations. The useful visualization tools for presenting different diagrams are worth recommending, too. It is also specialized in measurement and control and it supports a wide variety of hardware. Therefore this software is suitable for laboratory classes to present the dependencies between the simulated characteristics in basic electrical circuits and the real one measured with the hardware device. For this purpose a two-channel oscilloscope is designed as part of the described project. The main purpose of this instrument as part of the educational process is to present the desired characteristics of the electrical circuits and to become familiar with the general functions of the oscilloscope. This project combines several important

  19. Radiation and Ionization Energy Loss Simulation for GDH Sum Rule Experiment in Hall-A at Jefferson Lab

    CERN Document Server

    Yan, Xin-Hu; LV, Hai-Jiang; Zhu, Pengjia; Jiang, Fengjian

    2014-01-01

    We studied the radiation and ionization energy loss based on single arm Monte Carlo simulation for GDH sum rule experiment in Hall-A at Jefferson Lab. The radiation length and ionization energy loss calculation methods were discussed in detail for 12C elastic scattering simulation. The relative momentum ratio \\Delta p/p and 12C elastic cross section were compared without and with Radiation Energy Loss and got reasonable shape by simulation. The total energy loss distribution were obtained reasonably with landau shape for 12C elastic scattering. This simulation work will give a good support for radiation correction analysis of GDH sum rule experiment.

  20. Radiation and ionization energy loss simulation for the GDH sum rule experiment in Hall-A at Jefferson Lab

    Institute of Scientific and Technical Information of China (English)

    YAN Xin-Hu; YE Yun-Xiu; CHEN Jian-Ping; LU Hai-Jiang; ZHU Peng-Jia; JIANG Feng-Jian

    2015-01-01

    The radiation and ionization energy loss are presented for single arm Monte Carlo simulation for the GDH sum rule experiment in Hall-A at the Jefferson Lab.Radiation and ionization energy loss are discussed for 12C elastic scattering simulation.The relative momentum ratio-Ap and 12C elastic cross section are compared without and with radiative energy loss and a reasonable shape is obtained by the simulation.The total energy loss distribution is obtained,showing a Landau shape for 12C elastic scattering.This simulation work will give good support for radiation correction analysis of the GDH sum rule experiment.

  1. Methods in Modern Biophysics

    CERN Document Server

    Nölting, Bengt

    2010-01-01

    Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and about 270 illustrations to fully detail the techniques and their underlying mechanisms. Methods in Modern Biophysics is written for advanced undergraduate and graduate students, postdocs, researchers, lecturers, and professors in biophysics, biochemistry and related fields. Special features in the 3rd edition: Introduces rapid partial protein ladder sequencing - an important...

  2. Biophysics of olfaction

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Fabio Marques Simoes de [Cell and Developmental Biology, University of Colorado at Denver and Health Science Center, Campus Box 6511, PO Box 6511, 12801 East 17th Avenue, Aurora, CO 80045 (United States); Antunes, Gabriela [Psychobiology Sector and Department of Chemistry, Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Av. Bandeirantes, 3900, 14040-901, Ribeirao Preto, SP (Brazil)

    2007-03-15

    The majority of the biophysical models of olfaction have been focused on the electrical properties of the system, which is justified by the relative facility of recording the electrical activity of the olfactory cells. However, depending on the level of detail utilized, a biophysical model can explore molecular, cellular and network phenomena. This review presents the state of the art of the biophysical approach to understanding olfaction. The reader is introduced to the principal problems involving the study of olfaction and guided gradually to comprehend why it is important to develop biophysical models to investigate olfaction. A large number of representative biophysical efforts in olfaction, their main contributions, the trends for the next generations of biophysical models and the improvements that may be explored by future biophysicists of olfaction have been reviewed.

  3. Methods in Modern Biophysics

    CERN Document Server

    Nölting, Bengt

    2006-01-01

    Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and 267 illustrations to fully detail the techniques and their underlying mechanisms. Methods in Modern Biophysics is written for advanced undergraduate and graduate students, postdocs, researchers, lecturers and professors in biophysics, biochemistry and related fields. Special features in the 2nd edition: • Illustrates the high-resolution methods for ultrashort-living protei...

  4. New horizons in Biophysics

    Directory of Open Access Journals (Sweden)

    Moylan Elizabeth C

    2011-03-01

    Full Text Available Abstract This editorial celebrates the re-launch of PMC Biophysics previously published by PhysMath Central, in its new format as BMC Biophysics published by BioMed Central with an expanded scope and Editorial Board. BMC Biophysics will fill its own niche in the BMC series alongside complementary companion journals including BMC Bioinformatics, BMC Medical Physics, BMC Structural Biology and BMC Systems Biology.

  5. Auto-control system for artificial rainfall simulation based on LabVIEW%基于LabVIEW的人工模拟降雨自动控制系统

    Institute of Scientific and Technical Information of China (English)

    周奇; 岑国平; 张亮; 敦晓; 郭明威

    2011-01-01

    介绍一种基于LabVIEW语言开发的针对道路水分运移研究的人工模拟降雨自动控制系统.该系统采用闭环控制算法,通过涡轮流量计、电动执行器和PPC(可编程计算机控制器)来控制各种雨型.试验结果显示:设计雨强和检测雨强的相对误差在5%以下;全套系统的重现性、稳定性和降雨空间分布的均匀性在97%以上;渐变降雨的线性率在85%以上.%An auto-control system for artificial rainfall simulation based on LabVIEW to study water migration in road structures was introduced. The closed-loop control algorithm was adopted in the system, and the rain types were controlled by a turboflowmeter, electrical regulated valve and programmable computer controller. The test results indicate that the relative deviation between the design and practical rain intensities is below 5%. Tne fidelity and stability of the whole set of system as well as the uniformity of spatial distribution of the rainfall are all above 97%. The linearity rate of the shadowed rainfall is above 85%.

  6. The Virtual ChemLab Project: A Realistic and Sophisticated Simulation of Inorganic Qualitative Analysis

    Science.gov (United States)

    Woodfield, Brian F.; Catlin, Heidi R.; Waddoups, Gregory L.; Moore, Melissa S.; Swan, Richard; Bodily, Greg; Allen, Rob

    2004-01-01

    Virtual ChemLab project is an instructional laboratory involved in providing a practical experience by connecting the theory and laboratory practicals, teaching laboratory techniques and teaching the cognitive processes. This lab provides the students with the freedom to explore, repeat the procedures again, focuses on the underlying principles of…

  7. Assessment of the dose distribution inside a cardiac cath lab using TLD measurements and Monte Carlo simulations

    International Nuclear Information System (INIS)

    Over the last decade, there was a substantial increase in the number of interventional cardiology procedures worldwide, and the corresponding ionizing radiation doses for both the medical staff and patients became a subject of concern. Interventional procedures in cardiology are normally very complex, resulting in long exposure times. Also, these interventions require the operator to work near the patient and, consequently, close to the primary X-ray beam. Moreover, due to the scattered radiation from the patient and the equipment, the medical staff is also exposed to a non-uniform radiation field that can lead to a significant exposure of sensitive body organs and tissues, such as the eye lens, the thyroid and the extremities. In order to better understand the spatial variation of the dose and dose rate distributions during an interventional cardiology procedure, the dose distribution around a C-arm fluoroscopic system, in operation in a cardiac cath lab at Portuguese Hospital, was estimated using both Monte Carlo (MC) simulations and dosimetric measurements. To model and simulate the cardiac cath lab, including the fluoroscopic equipment used to execute interventional procedures, the state-of-the-art MC radiation transport code MCNPX 2.7.0 was used. Subsequently, Thermo-Luminescent Detector (TLD) measurements were performed, in order to validate and support the simulation results obtained for the cath lab model. The preliminary results presented in this study reveal that the cardiac cath lab model was successfully validated, taking into account the good agreement between MC calculations and TLD measurements. The simulated results for the isodose curves related to the C-arm fluoroscopic system are also consistent with the dosimetric information provided by the equipment manufacturer (Siemens). The adequacy of the implemented computational model used to simulate complex procedures and map dose distributions around the operator and the medical staff is discussed, in

  8. Recirculation of reverse osmosis concentrate in lab-scale anaerobic and aerobic landfill simulation reactors.

    Science.gov (United States)

    Morello, Luca; Cossu, Raffaello; Raga, Roberto; Pivato, Alberto; Lavagnolo, Maria Cristina

    2016-10-01

    Leachate treatment is a major issue in the context of landfill management, particularly in view of the consistent changes manifested over time in the quality and quantity of leachate produced, linked to both waste and landfill characteristics, which renders the procedure technically difficult and expensive. Leachate recirculation may afford a series of potential advantages, including improvement of leachate quality, enhancement of gas production, acceleration of biochemical processes, control of moisture content, as well as nutrients and microbe migration within the landfill. Recirculation of the products of leachate treatment, such as reverse osmosis (RO) concentrate, is a less common practice, with widespread controversy relating to its suitability, potential impacts on landfill management and future gaseous and leachable emissions. Scientific literature provides the results of only a few full-scale applications of concentrate recirculation. In some cases, an increase of COD and ammonium nitrogen in leachate was observed, coupled with an increase of salinity; which, additionally, might negatively affect performance of the RO plant itself. In other cases, not only did leachate production not increase significantly but the characteristics of leachate extracted from the well closest to the re-injection point also remained unchanged. This paper presents the results of lab-scale tests conducted in landfill simulation reactors, in which the effects of injection of municipal solid waste (MSW) landfill leachate RO concentrate were evaluated. Six reactors were managed with different weekly concentrate inputs, under both anaerobic and aerobic conditions, with the aim of investigating the short and long-term effects of this practice on landfill emissions. Lab-scale tests resulted in a more reliable identification of compound accumulation and kinetic changes than full-scale applications, further enhancing the development of a mass balance in which gaseous emissions and waste

  9. Assessment of the dose distribution inside a cardiac cath lab using TLD measurements and Monte Carlo simulations

    Science.gov (United States)

    Baptista, M.; Teles, P.; Cardoso, G.; Vaz, P.

    2014-11-01

    Over the last decade, there was a substantial increase in the number of interventional cardiology procedures worldwide, and the corresponding ionizing radiation doses for both the medical staff and patients became a subject of concern. Interventional procedures in cardiology are normally very complex, resulting in long exposure times. Also, these interventions require the operator to work near the patient and, consequently, close to the primary X-ray beam. Moreover, due to the scattered radiation from the patient and the equipment, the medical staff is also exposed to a non-uniform radiation field that can lead to a significant exposure of sensitive body organs and tissues, such as the eye lens, the thyroid and the extremities. In order to better understand the spatial variation of the dose and dose rate distributions during an interventional cardiology procedure, the dose distribution around a C-arm fluoroscopic system, in operation in a cardiac cath lab at Portuguese Hospital, was estimated using both Monte Carlo (MC) simulations and dosimetric measurements. To model and simulate the cardiac cath lab, including the fluoroscopic equipment used to execute interventional procedures, the state-of-the-art MC radiation transport code MCNPX 2.7.0 was used. Subsequently, Thermo-Luminescent Detector (TLD) measurements were performed, in order to validate and support the simulation results obtained for the cath lab model. The preliminary results presented in this study reveal that the cardiac cath lab model was successfully validated, taking into account the good agreement between MC calculations and TLD measurements. The simulated results for the isodose curves related to the C-arm fluoroscopic system are also consistent with the dosimetric information provided by the equipment manufacturer (Siemens). The adequacy of the implemented computational model used to simulate complex procedures and map dose distributions around the operator and the medical staff is discussed, in

  10. Biophysics An Introduction

    CERN Document Server

    Glaser, Roland

    2012-01-01

    Biophysics is the science of physical principles underlying all processes of life, including the dynamics and kinetics of biological systems. This fully revised 2nd English edition is an introductory text that spans all steps of biological organization, from the molecular, to the organism level, as well as influences of environmental factors. In response to the enormous progress recently made, especially in theoretical and molecular biophysics, the author has updated the text, integrating new results and developments concerning protein folding and dynamics, molecular aspects of membrane assembly and transport, noise-enhanced processes, and photo-biophysics. The advances made in theoretical biology in the last decade call for a fully new conception of the corresponding sections. Thus, the book provides the background needed for fundamental training in biophysics and, in addition, offers a great deal of advanced biophysical knowledge.

  11. Design and implementation progress of multi-purpose simulator for nuclear research reactor using LabVIEW

    Energy Technology Data Exchange (ETDEWEB)

    Arafa, Amany Abdel Aziz; Saleh, Hassan Ibrahim [Atomic Energy Authority, Cairo (Egypt). Radiation Engineering Dept.; Ashoub, Nagieb [Atomic Energy Authority, Cairo (Egypt). Nuclear Research Center

    2015-11-15

    This paper illustrates the neutronic and thermal hydraulic models that were implemented in the nuclear research reactor simulator based on LabVIEW. It also describes the system and transient analysis of the simulator that takes into consideration the temperature effects and poisoning. This simulator is designed to be a multi-purpose in which the operator could understand the effects of the input parameters on the reactor. A designer can study different solutions for virtual reactor accident scenarios. The main features of the simulator are the flexibility to design and maintain the interface and the ability to redesign and remodel the reactor core engine. The developed reactor simulator permits to acquire hands-on the experience of the physics and technology of nuclear reactors including reactivity control, thermodynamics, technology design and safety system design. This simulator can be easily customizable and upgradable and new opportunities for collaboration between academic groups could be conducted.

  12. 基于LabVIEW/Matlab的AUV半实物仿真系统设计%Design of AUV simulation system based on LabVIEW/Matlab

    Institute of Scientific and Technical Information of China (English)

    赵兴; 李健; 李一博

    2014-01-01

    In order to solve the problem of the establishment of actual experimental environment of large AUV(Autono-mous Underwater Vehicle), and for the testing need of different units of AUV control system, a new AUV semi-physical simulation system is designed based on LabVIEW/Matlab under Windows platform. The simulation system realizes the real-time calculation of AUV’s position and posture based on three-dimensional hydrodynamic model; meanwhile, it makes serial port and Ethernet communication with deck system and master control system by imitating Phins, GAPS, fixed high altimeter, obstacle avoidance sonar, and other sensors, which realizes AUV’s motion simulation and also pro-vides evidences for determining motion control strategy. Experimentation shows that the system model is reasonable, and the given software design is feasible. The established simulation system is flexible to be extended or reduced, which is used successfully in testing experiment of AUV’s control system.%为解决大型自主式水下航行器(Autonomous Underwater Vehicle,AUV)实际实验环境搭建的困难,以及AUV控制系统各单元功能测试的需要,设计了一套新的Windows平台下基于LabVIEW/Matlab的AUV半实物仿真系统。该仿真系统基于三维空间的水动力模型,来实时计算AUV的位置和姿态等信息;同时,模仿Phins、GAPS、定高高度计、避障声呐等传感器,和AUV甲板、主控以及运动控制单元进行串行和以太网络通信,实现了AUV的运动仿真,同时也为制定运动控制策略提供相关依据。大量实验表明,该系统模型较合理,软件设计可行,具有灵活的扩展性和伸缩性,在AUV控制系统测试实验中成功应用。

  13. Virtual Simulations as Preparation for Lab Exercises: Assessing Learning of Key Laboratory Skills in Microbiology and Improvement of Essential Non-Cognitive Skills

    DEFF Research Database (Denmark)

    Makransky, Guido; Warming Thisgaard, Malene; Gadegaard, Helen

    2016-01-01

    bacteria on agar plates. All students were blindly assessed on their ability to perform the streaking technique in the physical lab, and were administered a pre and post-test to determine their knowledge of microbiology, intrinsic motivation to study microbiology, and self-efficacy in the field......Objective To investigate if a virtual laboratory simulation (vLAB) could be used to replace a face to face tutorial (demonstration) to prepare students for a laboratory exercise in microbiology. Methods A total of 189 students who were participating in an undergraduate biology course were randomly...... selected into a vLAB or demonstration condition. In the vLAB condition students could use a vLAB at home to 'practice' streaking out bacteria on agar plates in a virtual environment. In the demonstration condition students were given a live demonstration from a lab tutor showing them how to streak out...

  14. Simulation of Sampling Theroem Based on LabVIEW%基于LabVIEW的抽样定理仿真研究

    Institute of Scientific and Technical Information of China (English)

    王怀兴

    2012-01-01

    与连续时间信号相比,离散时间信号的处理更加灵活、方便,应用更加广泛。在实际应用中,通常先将连续时间信号转换成离散时间信号,前提是抽样过程必须满足抽样定理。抽样定理在连续时间信号与离散时间信号之间架起了一座桥梁。本文利用LabVIEW对抽样过程进行仿真,并对抽样定理的条件与结论进行验证和讨论,通过研究可以得到符合实际应用的结论,同时加深对抽样定理的理解和把握。%The processing for discrete-time signal is more flexible,convenient,and more widely used,compared with continuous-time signal.In practice,continuous-time signal is usually changed into discrete-time signal firstly,provided that the sampling process meets the sampling theorem.Sampling theorem sets up a bridge between continuous-time signal and discrete-time signal.But must the restrictions and conclusion of the sampling theorem coincide with the actual application? In this paper,sampling process is simulated by using LabVIEW,and the conditions and conclusion of sampling theorem is validated and discussion,through which shows that the restrictions and the conclusion of sampling theorem agrees with the practice;meanwhile,understanding and grasp of sampling theorem is deepened.

  15. Towards a Better Understanding of Forest Biophysical Parameters - Combining High Fidelity Simulations, Airborne Waveform Lidar, and Terrestrial Lidar Sensing

    Science.gov (United States)

    van Aardt, J. A.; Kelbe, D.; Romanczyk, P.; van Leeuwen, M.; Cawse-Nicholson, K.; Krause, K.; Kampe, T. U.

    2015-12-01

    The science community has come a long way from traditional, 2D imaging approaches to the assessment of ecosystem structure, function and composition. For example, waveform- (wlidar) and terrestrial lidar systems (TLS) present us with exciting opportunities for detailed, accurate and precise, and scalable structural characterization of vegetation. wlidar and TLS generally can be regarded as complementary i.e., airborne wlidar typically digitizes the entire backscattered energy profile at high spatial and vertical resolutions, while TLS samples dense 3D point clouds of the bottom-up vegetation structure. Research teams at Rochester Institute of Technology (RIT) have been collaborating with the National Ecological Observation Network (NEON) to assess vegetation structure and variation in the Pacific-Southwest (San Joaquin Experimental Range and Soaproot Saddle sites, CA) and Northeast (Harvard Forest, MA) domains. The teams collected airborne small-footprint wlidar data and in-situ TLS data for these sites and is taking a two-tiered (top-down and bottom-up) approach to forest structural assessment. We will present our work where we (i) studied wlidar signal attenuation throughout the canopy in a simulation environment - the attenuation correction factor was linearly proportional to the sum of the area under the proceeding Gaussians - and (ii) used the fine-scale stem structure extracted via TLS to reconstruct complex, but realistic, 3D forest environments for refined simulation studies. These studies indicate that we can potentially assess vegetation canopies remotely using a vertically-stratified approach with wlidar and use rapid-scan TLS technology to calibrate models predicated upon synoptic airborne systems. Other outputs of our approaches can be used for typical forest inventory, ecological parameter extraction, and new algorithm validation.

  16. Advanced Techniques in Biophysics

    CERN Document Server

    Arrondo, José Luis R

    2006-01-01

    Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.

  17. Virtual Environment User Interfaces to Support RLV and Space Station Simulations in the ANVIL Virtual Reality Lab

    Science.gov (United States)

    Dumas, Joseph D., II

    1998-01-01

    Several virtual reality I/O peripherals were successfully configured and integrated as part of the author's 1997 Summer Faculty Fellowship work. These devices, which were not supported by the developers of VR software packages, use new software drivers and configuration files developed by the author to allow them to be used with simulations developed using those software packages. The successful integration of these devices has added significant capability to the ANVIL lab at MSFC. In addition, the author was able to complete the integration of a networked virtual reality simulation of the Space Shuttle Remote Manipulator System docking Space Station modules which was begun as part of his 1996 Fellowship. The successful integration of this simulation demonstrates the feasibility of using VR technology for ground-based training as well as on-orbit operations.

  18. Virtual Simulations as Preparation for Lab Exercises: Assessing Learning of Key Laboratory Skills in Microbiology and Improvement of Essential Non-Cognitive Skills

    Science.gov (United States)

    Makransky, Guido; Thisgaard, Malene Warming; Gadegaard, Helen

    2016-01-01

    Objective To investigate if a virtual laboratory simulation (vLAB) could be used to replace a face to face tutorial (demonstration) to prepare students for a laboratory exercise in microbiology. Methods A total of 189 students who were participating in an undergraduate biology course were randomly selected into a vLAB or demonstration condition. In the vLAB condition students could use a vLAB at home to ‘practice’ streaking out bacteria on agar plates in a virtual environment. In the demonstration condition students were given a live demonstration from a lab tutor showing them how to streak out bacteria on agar plates. All students were blindly assessed on their ability to perform the streaking technique in the physical lab, and were administered a pre and post-test to determine their knowledge of microbiology, intrinsic motivation to study microbiology, and self-efficacy in the field of microbiology prior to, and after the experiment. Results The results showed that there were no significant differences between the two groups on their lab scores, and both groups had similar increases in knowledge of microbiology, intrinsic motivation to study microbiology, as well as self-efficacy in the field of microbiology. Conclusion Our data show that vLABs function just as well as face to face tutorials in preparing students for a physical lab activity in microbiology. The results imply that vLABs could be used instead of face to face tutorials, and a combination of virtual and physical lab exercises could be the future of science education. PMID:27253395

  19. Virtual Simulations as Preparation for Lab Exercises: Assessing Learning of Key Laboratory Skills in Microbiology and Improvement of Essential Non-Cognitive Skills.

    Directory of Open Access Journals (Sweden)

    Guido Makransky

    Full Text Available To investigate if a virtual laboratory simulation (vLAB could be used to replace a face to face tutorial (demonstration to prepare students for a laboratory exercise in microbiology.A total of 189 students who were participating in an undergraduate biology course were randomly selected into a vLAB or demonstration condition. In the vLAB condition students could use a vLAB at home to 'practice' streaking out bacteria on agar plates in a virtual environment. In the demonstration condition students were given a live demonstration from a lab tutor showing them how to streak out bacteria on agar plates. All students were blindly assessed on their ability to perform the streaking technique in the physical lab, and were administered a pre and post-test to determine their knowledge of microbiology, intrinsic motivation to study microbiology, and self-efficacy in the field of microbiology prior to, and after the experiment.The results showed that there were no significant differences between the two groups on their lab scores, and both groups had similar increases in knowledge of microbiology, intrinsic motivation to study microbiology, as well as self-efficacy in the field of microbiology.Our data show that vLABs function just as well as face to face tutorials in preparing students for a physical lab activity in microbiology. The results imply that vLABs could be used instead of face to face tutorials, and a combination of virtual and physical lab exercises could be the future of science education.

  20. The Biophysics of Infection.

    Science.gov (United States)

    Leake, Mark C

    2016-01-01

    Our understanding of the processes involved in infection has grown enormously in the past decade due in part to emerging methods of biophysics. This new insight has been enabled through advances in interdisciplinary experimental technologies and theoretical methods at the cutting-edge interface of the life and physical sciences. For example, this has involved several state-of-the-art biophysical tools used in conjunction with molecular and cell biology approaches, which enable investigation of infection in living cells. There are also new, emerging interfacial science tools which enable significant improvements to the resolution of quantitative measurements both in space and time. These include single-molecule biophysics methods and super-resolution microscopy approaches. These new technological tools in particular have underpinned much new understanding of dynamic processes of infection at a molecular length scale. Also, there are many valuable advances made recently in theoretical approaches of biophysics which enable advances in predictive modelling to generate new understanding of infection. Here, I discuss these advances, and take stock on our knowledge of the biophysics of infection and discuss where future advances may lead.

  1. Biophysics of molecular gastronomy.

    Science.gov (United States)

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP.

  2. Biophysics of molecular gastronomy.

    Science.gov (United States)

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. PMID:25815978

  3. Recent progress in Biophysics

    International Nuclear Information System (INIS)

    Recent progress in biophysics is reviewed, and three examples of the use of physical techniques and ideas in biological research are given. The first one deals with the oxygen transporting protein-hemoglobin, the second one with photosynthesis, and the third one with image formation, using nuclear magnetic resonance. (Author)

  4. Stochastic biophysical modeling of irradiated cells

    CERN Document Server

    Fornalski, Krzysztof Wojciech

    2014-01-01

    The paper presents a computational stochastic model of virtual cells irradiation, based on Quasi-Markov Chain Monte Carlo method and using biophysical input. The model is based on a stochastic tree of probabilities for each cell of the entire colony. Biophysics of the cells is described by probabilities and probability distributions provided as the input. The adaptation of nucleation and catastrophe theories, well known in physics, yields sigmoidal relationships for carcinogenic risk as a function of the irradiation. Adaptive response and bystander effect, incorporated into the model, improves its application. The results show that behavior of virtual cells can be successfully modeled, e.g. cancer transformation, creation of mutations, radioadaptation or radiotherapy. The used methodology makes the model universal and practical for simulations of general processes. Potential biophysical curves and relationships are also widely discussed in the paper. However, the presented theoretical model does not describe ...

  5. From provocative narrative scenarios to quantitative biophysical model results: Simulating plausible futures to 2070 in an urbanizing agricultural watershed in Wisconsin, USA

    Science.gov (United States)

    Booth, E.; Chen, X.; Motew, M.; Qiu, J.; Zipper, S. C.; Carpenter, S. R.; Kucharik, C. J.; Steven, L. I.

    2015-12-01

    Scenario analysis is a powerful tool for envisioning future social-ecological change and its consequences on human well-being. Scenarios that integrate qualitative storylines and quantitative biophysical models can create a vivid picture of these potential futures but the integration process is not straightforward. We present - using the Yahara Watershed in southern Wisconsin (USA) as a case study - a method for developing quantitative inputs (climate, land use/cover, and land management) to drive a biophysical modeling suite based on four provocative and contrasting narrative scenarios that describe plausible futures of the watershed to 2070. The modeling suite consists of an agroecosystem model (AgroIBIS-VSF), hydrologic routing model (THMB), and empirical lake water quality model and estimates several biophysical indicators to evaluate the watershed system under each scenario. These indicators include water supply, lake flooding, agricultural production, and lake water quality. Climate (daily precipitation and air temperature) for each scenario was determined using statistics from 210 different downscaled future climate projections for two 20-year time periods (2046-2065 and 2081-2100) and modified using a stochastic weather generator to allow flexibility for matching specific climate events within the scenario narratives. Land use/cover for each scenario was determined first by quantifying changes in areal extent every decade for 15 categories at the watershed scale to be consistent with the storyline events and theme. Next, these changes were spatially distributed using a rule-based framework based on land suitability metrics that determine transition probabilities. Finally, agricultural inputs including manure and fertilizer application rates were determined for each scenario based on the prevalence of livestock, water quality regulations, and technological innovations. Each scenario is compared using model inputs (maps and time-series of land use/cover and

  6. Fetal Biophysical Profile Scoring

    Directory of Open Access Journals (Sweden)

    H.R. HaghighatKhah

    2009-01-01

    Full Text Available   "nFetal biophysical profile scoring is a sonographic-based method of fetal assessment first described by Manning and Platt in 1980. "nThe biophysical profile score was developed as a method to integrate real-time observations of the fetus and his/her intrauterine environment in order to more comprehensively assess the fetal condition. These findings must be evaluated in the context of maternal/fetal history (i.e., chronic hypertension, post-dates, intrauterine growth restriction, etc, fetal structural integrity (presence or absence of congenital anomalies, and the functionality of fetal support structures (placental and umbilical cord. For example, acute asphyxia due to placental abruption may result in an absence of the acute variables of the biophysical profile score (fetal breathing movements, fetal movement, fetal tone, and fetal heart rate reactivity with a normal amniotic fluid volume. With post maturity the asphyxial event may be intermittent and chronic resulting in a decrease in amniotic fluid volume, but with the acute variables remaining normal. "nWhile the 5 components of the biophysical profile score have remained unchanged since 1980 (Manning, 1980, the definitions of a normal and abnormal parameter have evolved with increasing experience. "nIn 1984 the definition of oligohydramnios was increased from < 1cm pocket of fluid to < 2.0 x 1.0 cm pocket. Oligohydramnios is now defined as a pocket of amniotic fluid < 2.0 x 2.0 cm (Manning, 1995a "nIf the four ultrasound variables are normal, the accuracy of the biophysical profile score was not found to be significantly improved by adding the non-stress test. As a result, in 1987 the profile score was modified to incorporate the non-stress test only when one of the ultrasound variables was abnormal (Manning 1987. Table 1 outlines the current definitions for quantifying a variable as present or absent. "nEach of the 5 components of the biophysical profile score does not have equal

  7. Thread Group Multithreading: Accelerating the Computation of an Agent-Based Power System Modeling and Simulation Tool -- C GridLAB-D

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Shuangshuang; Chassin, David P.

    2014-01-06

    GridLAB-DTM is an open source next generation agent-based smart-grid simulator that provides unprecedented capability to model the performance of smart grid technologies. Over the past few years, GridLAB-D has been used to conduct important analyses of smart grid concepts, but it is still quite limited by its computational performance. In order to break through the performance bottleneck to meet the need for large scale power grid simulations, we develop a thread group mechanism to implement highly granular multithreaded computation in GridLAB-D. We achieve close to linear speedups on multithreading version compared against the single-thread version of the same code running on general purpose multi-core commodity for a benchmark simple house model. The performance of the multithreading code shows favorable scalability properties and resource utilization, and much shorter execution time for large-scale power grid simulations.

  8. The Virtual Lab System

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A virtual lab system is the simulation of real devices and experiments using computer and network tech-nology. It can make users do experiments easily, observe experiment phenomena and results through the remote termi-nal. Consequently, users can get final results to verify relative theory. The article analyses the features of virtual labsystems. A real virtual lab system named "Multimedia Virtual Lab for Digital Circuit Logic Design (MVLDCLD) "which has been developed by the authors and their group is also presented.

  9. Developing an International Combined Applied Surgical Science and Wet Lab Simulation Course as an Undergraduate Teaching Model

    Directory of Open Access Journals (Sweden)

    Michail Sideris

    2015-01-01

    Full Text Available Background. Essential Skills in the Management of Surgical Cases (ESMSC is an international, animal model-based course. It combines interactive lectures with basic ex vivo stations and more advanced wet lab modules, that is, in vivo dissections and Heart Transplant Surgery on a swine model. Materials and Methods. Forty-nine medical students (male, N=27, female N=22, and mean age = 23.7 years from King’s College London (KCL and Greek Medical Schools attended the course. Participants were assessed with Direct Observation of Procedural Skills (DOPS, as well as Multiple Choice Questions (MCQs. Paired t-test associations were used to evaluate whether there was statistically significant improvement in their performance. Aim. To evaluate the effectiveness of a combined applied surgical science and wet lab simulation course as a teaching model for surgical skills at the undergraduate level. Results. The mean MCQ score was improved by 2.33/32 (P<0.005. Surgical skills competences, as defined by DOPS scores, were improved in a statically significant manner (P<0.005 for all paired t-test correlations. Conclusions. ESMSC seems to be an effective teaching model, which improves the understanding of the surgical approach and the basic surgical skills. In vivo models could be used potentially as a step further in the Undergraduate Surgical Education.

  10. Vision Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Vision Lab personnel perform research, development, testing and evaluation of eye protection and vision performance. The lab maintains and continues to develop...

  11. Modelling and simulation of passive Lab-on-a-Chip (LoC) based micromixer for clinical application

    Science.gov (United States)

    Saikat, Chakraborty; Sharath, M.; Srujana, M.; Narayan, K.; Pattnaik, Prasant Kumar

    2016-03-01

    In biomedical application, micromixer is an important component because of many processes requires rapid and efficient mixing. At micro scale, the flow is Laminar due to small channel size which enables controlled rapid mixing. The reduction in analysis time along with high throughput can be achieved with the help of rapid mixing. In LoC application, micromixer is used for mixing of fluids especially for the devices which requires efficient mixing. Micromixer of this type of microfluidic devices with a rapid mixing is useful in application such as DNA/RNA synthesis, drug delivery system & biological agent detection. In this work, we design and simulate a microfluidic based passive rapid micromixer for lab-on-a-chip application.

  12. Theoretical Molecular Biophysics

    CERN Document Server

    Scherer, Philipp

    2010-01-01

    "Theoretical Molecular Biophysics" is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in mechanics, electrostatics, quantum theory and statistical physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. Basic concepts such as phase transitions of biopolymers, electrostatics, protonation equilibria, ion transport, radiationless transitions as well as energy- and electron transfer are discussed within the frame of simple models.

  13. Structure and biophysics

    CERN Document Server

    Puglisi, Joseph D

    2007-01-01

    This volume is a collection of articles from the proceedings of the ISSBMR 7th Course: Structure and Biophysics - New Technologies for Current Challenges in Biology and Beyond. This NATO Advanced Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture on 22 June through 3 July 2005. The ASI brought together a diverse group of experts in the fields of Structural Biology, Biophysics and Physics. Prominent lecturers, from seven different countries, and students from around the world participated in the NATO ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU). Advances in nuclear magnetic resonance spectroscopy (NMR) and x-ray crystallography have allowed the three-dimensional structures of many biological macromolecules and their complexes, including the ribosome and RNA polymerase to be solved. Fundamental principles of NMR spectroscopy and dynamics, x-ray crystallography, computation and experimental dynamics we...

  14. Biophysics an introduction

    CERN Document Server

    Cotteril, Rodney

    2002-01-01

    Biophysics: An Introduction, is a concise balanced introduction to this subject. Written in an accessible and readable style, the book takes a fresh, modern approach with the author successfully combining key concepts and theory with relevant applications and examples drawn from the field as a whole. Beginning with a brief introduction to the origins of biophysics, the book takes the reader through successive levels of complexity, from atoms to molecules, structures, systems and ultimately to the behaviour of organisms. The book also includes extensive coverage of biopolymers, biomembranes, biological energy, and nervous systems. The text not only explores basic ideas, but also discusses recent developments, such as protein folding, DNA/RNA conformations, molecular motors, optical tweezers and the biological origins of consciousness and intelligence.

  15. Simulating thick atmospheric turbulence in the lab with application to orbital angular momentum communication

    International Nuclear Information System (INIS)

    We describe a procedure by which a long (≳1 km) optical path through atmospheric turbulence can be experimentally simulated in a controlled fashion and scaled down to distances easily accessible in a laboratory setting. This procedure is then used to simulate a 1 km long free-space communication link in which information is encoded in orbital angular momentum spatial modes. We also demonstrate that standard adaptive optics methods can be used to mitigate many of the effects of thick atmospheric turbulence. (paper)

  16. Thermal Manikins & Clothing Biophysics Laboratories

    Data.gov (United States)

    Federal Laboratory Consortium — Five biophysical evaluation chambers containing fully sensored, articulated, moveable copper manikins, and other metallic models of feet and hands are available for...

  17. Application of network communication in simulation systems based on LabVIEW virtual instrument%网络通信在基于LabVIEW虚拟仪器仿真系统中的应用

    Institute of Scientific and Technical Information of China (English)

    刘艳莉; 金文; 陈志敏; 刘宏军; 程泽

    2011-01-01

    The network communication function of virtual Instruments LabVIEW simulation software supplies the experimental teaching with open teaching and learning environment , which is a combination of personalized learning and interactive sharing of resources in practice. With the combination of database technology and software programming techniques and based on LabVIEW, the virtual instrument simulation of electrical and electronic systems can achieve the organization and process management of the groups of students’ experiments in a virtual laboratory, as well as educate innovation and self-design capability of students. At the same time, it can help students solve the practical problems encountered in the experiment through an online interactive features.%虚拟仪器仿真软件LabVIEW所具有的网络通信功能,为实验教学提供了个性化学习与交互式资源共享相结合的开放式实践教学环境.结合数据库技术和软件编程技术所开发的基于LabVIEW"电工电子虚拟仪器仿真系统",在培养学生的创新意识和自主设计能力的同时,可实现虚拟实验室多组学生实验的组织和过程管理,并通过在线交互功能帮助学生解决实验中遇到的实际问题.

  18. System-level network simulation for robust centrifugal-microfluidic lab-on-a-chip systems.

    Science.gov (United States)

    Schwarz, I; Zehnle, S; Hutzenlaub, T; Zengerle, R; Paust, N

    2016-05-10

    Centrifugal microfluidics shows a clear trend towards a higher degree of integration and parallelization. This trend leads to an increase in the number and density of integrated microfluidic unit operations. The fact that all unit operations are processed by the same common spin protocol turns higher integration into higher complexity. To allow for efficient development anyhow, we introduce advanced lumped models for network simulations in centrifugal microfluidics. These models consider the interplay of centrifugal and Euler pressures, viscous dissipation, capillary pressures and pneumatic pressures. The simulations are fast and simple to set up and allow for the precise prediction of flow rates as well as switching and valving events. During development, channel and chamber geometry variations due to manufacturing tolerances can be taken into account as well as pipetting errors, variations of contact angles, compliant chamber walls and temperature variations in the processing device. As an example of considering these parameters during development, we demonstrate simulation based robustness analysis for pneumatic siphon valving in centrifugal microfluidics. Subsequently, the influence of liquid properties on pumping and valving is studied for four liquids relevant for biochemical analysis, namely, water (large surface tension), blood plasma (large contact angle hysteresis), ethanol/water (highly wetting) and glycerine/water (highly viscous). In a second example, we derive a spin protocol to attain a constant flow rate under varying pressure conditions. Both examples show excellent agreement with experimental validations. PMID:27095248

  19. System-level network simulation for robust centrifugal-microfluidic lab-on-a-chip systems.

    Science.gov (United States)

    Schwarz, I; Zehnle, S; Hutzenlaub, T; Zengerle, R; Paust, N

    2016-05-10

    Centrifugal microfluidics shows a clear trend towards a higher degree of integration and parallelization. This trend leads to an increase in the number and density of integrated microfluidic unit operations. The fact that all unit operations are processed by the same common spin protocol turns higher integration into higher complexity. To allow for efficient development anyhow, we introduce advanced lumped models for network simulations in centrifugal microfluidics. These models consider the interplay of centrifugal and Euler pressures, viscous dissipation, capillary pressures and pneumatic pressures. The simulations are fast and simple to set up and allow for the precise prediction of flow rates as well as switching and valving events. During development, channel and chamber geometry variations due to manufacturing tolerances can be taken into account as well as pipetting errors, variations of contact angles, compliant chamber walls and temperature variations in the processing device. As an example of considering these parameters during development, we demonstrate simulation based robustness analysis for pneumatic siphon valving in centrifugal microfluidics. Subsequently, the influence of liquid properties on pumping and valving is studied for four liquids relevant for biochemical analysis, namely, water (large surface tension), blood plasma (large contact angle hysteresis), ethanol/water (highly wetting) and glycerine/water (highly viscous). In a second example, we derive a spin protocol to attain a constant flow rate under varying pressure conditions. Both examples show excellent agreement with experimental validations.

  20. Anaerobic Digestion and Biogas Potential: Simulation of Lab and Industrial-Scale Processes

    Directory of Open Access Journals (Sweden)

    Ihsan Hamawand

    2015-01-01

    Full Text Available In this study, a simulation was carried out using BioWin 3.1 to test the capability of the software to predict the biogas potential for two different anaerobic systems. The two scenarios included: (1 a laboratory-scale batch reactor; and (2 an industrial-scale anaerobic continuous lagoon digester. The measured data related to the operating conditions, the reactor design parameters and the chemical properties of influent wastewater were entered into BioWin. A sensitivity analysis was carried out to identify the sensitivity of the most important default parameters in the software’s models. BioWin was then calibrated by matching the predicted data with measured data and used to simulate other parameters that were unmeasured or deemed uncertain. In addition, statistical analyses were carried out using evaluation indices, such as the coefficient of determination (R-squared, the correlation coefficient (r and its significance (p-value, the general standard deviation (SD and the Willmott index of agreement, to evaluate the agreement between the software prediction and the measured data. The results have shown that after calibration, BioWin can be used reliably to simulate both small-scale batch reactors and industrial-scale digesters with a mean absolute percentage error (MAPE of less than 10% and very good values of the indexes. Furthermore, by changing the default parameters in BioWin, which is a way of calibrating the models in the software, as well, this may provide information about the performance of the digester. Furthermore, the results of this study showed there may be an over estimation for biogas generated from industrial-scale digesters. More sophisticated analytical devices may be required for reliable measurements of biogas quality and quantity.

  1. Population heterogeneity in Saccharomyces cerevisiae and Escherichia coli lab scale cultivations simulating industrial scale bioprocesses

    DEFF Research Database (Denmark)

    Heins, Anna-Lena

    . This thesis aimed at reaching a deeper understanding of how microbial physiology and cell dynamics are affected by the spatial heterogeneity in a bioreactor. Therefore large scale fermentation was simulated in laboratory scale using two of the most industrially relevant organisms E. coli and S. cerevisiae...... in a quantitative manner through newly developed parameters, using percentile analysis followed by multivariate statistics as well as using a modeling approach. In general the applied reporter strains as well as fluorescence stains in combination with flow cytometry showed to be valuable tools to study population...

  2. Modeling and simulation of lab-scale anaerobic co-digestion of MEA waste

    Directory of Open Access Journals (Sweden)

    Shuai Wang

    2014-01-01

    Full Text Available Anaerobic digestion model No.1 (ADM1 was applied and expanded in this study to model and simulate anaerobic digestion (AD of an industrial carbon capture reclaimer MEA (monoethanolamine waste (MEAw together with easily degradable organics. The general structure of ADM1 was not changed except for introducing state variables of MEA and complex organics (CO in the waste and biochemical reactions of MEA uptake and CO hydrolysis in the model ADM1_MEAw. Experimental batch test results were used for calibrating kinetics variables. The obtained kinetics were employed in the ADM1_MEAw to simulate semi-continuously fed experimental test for 486 days at room temperature (22 +/- 2oC. The validation results show that the ADM1_MEAw was able to predict the process performance with reasonable accuracy, including process pH, biogas generation and inorganic nitrogen concentrations, for a wide range of feed scenarios. Free ammonia inhibition, was observed to be the main inhibitory effects on acetoclastic methanogenesis, leading to volatile fatty acids (VFA accumulation at high loads. Inhibition assumed to be caused by potentially toxic constituents of MEAw appears to be much less important than ammonia, suggesting that such constituents were broken down by AD.

  3. Aeration of the teuftal landfill: Field scale concept and lab scale simulation.

    Science.gov (United States)

    Ritzkowski, Marco; Walker, Beat; Kuchta, Kerstin; Raga, Roberto; Stegmann, Rainer

    2016-09-01

    Long lasting post-closure care (PCC) is often the major financial burden for operators of municipal solid waste (MSW) landfills. Beside costs for the installation and maintenance of technical equipment and barriers, in particular long term treatment of leachate and landfill gas has to be paid from capital surplus. Estimations based on laboratory experiments project time periods of many decades until leachate quality allows for direct discharge (i.e. no need for further purification). Projections based on leachate samples derived from the last 37years for 35 German landfills confirm these assumption. Moreover, the data illustrate that in particular ammonium nitrogen concentrations are likely to fall below limit values only after a period of 300years. In order to avoid long lasting PCC the operator of Teuftal landfill, located in the Swiss canton Bern, decided to biologically stabilize the landfill by means of a combined in situ aeration and moisturization approach. In December 2014 the aeration started at a landfill section containing approximately 30% of the total landfill volume. From summer 2016 onwards the remaining part of the landfill will be aerated. Landfill aeration through horizontal gas and leachate drains is carried out for the first time in field scale in Europe. The technical concept is described in the paper. Parallel to field scale aeration, investigations for the carbon and nitrogen turnover are carried out by means of both simulated aerated landfills and simulated anaerobic landfills. The results presented in this paper demonstrate that aeration is capable to enhance, both carbon mobilization and discharge via the gas phase. This effect comes along with a significant increase in bio-stabilization of the waste organic fraction, which positively affects the landfill emission behavior in the long run. In terms of leachate pollution reduction it could be demonstrated that the organic load decrease fast and widely independent of the adjusted aeration

  4. Aeration of the teuftal landfill: Field scale concept and lab scale simulation.

    Science.gov (United States)

    Ritzkowski, Marco; Walker, Beat; Kuchta, Kerstin; Raga, Roberto; Stegmann, Rainer

    2016-09-01

    Long lasting post-closure care (PCC) is often the major financial burden for operators of municipal solid waste (MSW) landfills. Beside costs for the installation and maintenance of technical equipment and barriers, in particular long term treatment of leachate and landfill gas has to be paid from capital surplus. Estimations based on laboratory experiments project time periods of many decades until leachate quality allows for direct discharge (i.e. no need for further purification). Projections based on leachate samples derived from the last 37years for 35 German landfills confirm these assumption. Moreover, the data illustrate that in particular ammonium nitrogen concentrations are likely to fall below limit values only after a period of 300years. In order to avoid long lasting PCC the operator of Teuftal landfill, located in the Swiss canton Bern, decided to biologically stabilize the landfill by means of a combined in situ aeration and moisturization approach. In December 2014 the aeration started at a landfill section containing approximately 30% of the total landfill volume. From summer 2016 onwards the remaining part of the landfill will be aerated. Landfill aeration through horizontal gas and leachate drains is carried out for the first time in field scale in Europe. The technical concept is described in the paper. Parallel to field scale aeration, investigations for the carbon and nitrogen turnover are carried out by means of both simulated aerated landfills and simulated anaerobic landfills. The results presented in this paper demonstrate that aeration is capable to enhance, both carbon mobilization and discharge via the gas phase. This effect comes along with a significant increase in bio-stabilization of the waste organic fraction, which positively affects the landfill emission behavior in the long run. In terms of leachate pollution reduction it could be demonstrated that the organic load decrease fast and widely independent of the adjusted aeration

  5. 'Virtual' monitoring in LabVIEW 8 and process simulation of the cryogenic pilot plant

    International Nuclear Information System (INIS)

    Full text: The implementation of the new software and hardware's technologies for tritium processing nuclear plants, and especially those with an experimental character or of new technology developments shows a coefficient of complexity due to issues raised by the use of the performing instrumentation and equipment into a unitary monitoring system of the nuclear technological process of tritium removal. Keeping the system's flexibility is a demand of the nuclear experimental plants for which the change of configuration, process and parameters is something usual. The big amount of data that needs to be processed, stored and accessed for real time simulation and optimization demands the achievement of the virtual technologic platform where the data acquiring, control and analysis systems of the technological process can be integrated with a developed technological monitoring system. Thus, integrated computing and monitoring systems needed for the supervising of the technological process will be carried out, and continued with the optimization of the system, by choosing new and performing methods corresponding to the technological processes within the tritium removal processing nuclear plants. The developing software applications is carried out by means of the program packages dedicated to industrial processes and they will include acquisition and monitoring sub-modules, named 'virtual' as well as the storage sub-module of the process data later required for the software of optimization and simulation of the technological process for tritium removal. The system plays an important role in the environment protection and sustainable development through new technologies, that is - the reduction of and fight against industrial accidents in the case of tritium processing nuclear plants. Research for monitoring optimization of nuclear processes is also a major driving force for economic and social development. (authors)

  6. Sensor-Augmented Virtual Labs: Using Physical Interactions with Science Simulations to Promote Understanding of Gas Behavior

    Science.gov (United States)

    Chao, Jie; Chiu, Jennifer L.; DeJaegher, Crystal J.; Pan, Edward A.

    2016-02-01

    Deep learning of science involves integration of existing knowledge and normative science concepts. Past research demonstrates that combining physical and virtual labs sequentially or side by side can take advantage of the unique affordances each provides for helping students learn science concepts. However, providing simultaneously connected physical and virtual experiences has the potential to promote connections among ideas. This paper explores the effect of augmenting a virtual lab with physical controls on high school chemistry students' understanding of gas laws. We compared students using the augmented virtual lab to students using a similar sensor-based physical lab with teacher-led discussions. Results demonstrate that students in the augmented virtual lab condition made significant gains from pretest and posttest and outperformed traditional students on some but not all concepts. Results provide insight into incorporating mixed-reality technologies into authentic classroom settings.

  7. Digital Controller Development Methodology Based on Real-Time Simulations with LabVIEW FPGA Hardware-Software Toolset

    Directory of Open Access Journals (Sweden)

    Tommaso Caldognetto

    2013-12-01

    Full Text Available In this paper, we exemplify the use of NI Lab-VIEW FPGA as a rapid prototyping environment for digital controllers. In our power electronics laboratory, it has been successfully employed in the development, debugging, and test of different power converter controllers for microgrid applications.The paper shows how this high level programming language,together with its target hardware platforms, including CompactRIO and Single Board RIO systems, allows researchers and students to develop even complex applications in reasonable times. The availability of efficient drivers for the considered hardware platforms frees the users from the burden of low level programming. At the same time, the high level programming approach facilitates software re-utilization, allowing the laboratory know-how to steadily grow along time. Furthermore, it allows hardware-in-the-loop real-time simulation, that proved to be effective, and safe, in debugging even complex hardware and software co-designed controllers. To illustrate the effectiveness of these hardware-software toolsets and of the methodology based upon them, two case studies are

  8. The Virtual Anatomy Lab: an eDemonstrator pedagogical agent can simulate student-faculty interaction and promote student engagement

    Directory of Open Access Journals (Sweden)

    Jonathan Weber

    2012-07-01

    Full Text Available As medical curricula evolve, many universities have adopted a clinical case-centered medical curriculum with a strong focus on small group learning and reduction of traditional lectures such that anatomy has become a self-taught subject supported by e-learning modules. One caveat of this approach is decreased student-faculty interaction and reduced student engagement. Thus use of e-learning must be balanced with the need for continued student-faculty interaction to promote healthy student engagement. To both support self-directed learning of anatomy and to simulate student-faculty interaction, we created the Virtual Anatomy Lab (VAL that features a human pedagogical agent, called the eDemonstrator, who guides student navigation through the available learning resources. The VAL was evaluated using a mixed methods approach (usage statistics and focus groups by two medical student populations at the University of Ottawa: first year medical students in a revised curriculum where anatomy lectures were abolished and laboratory sessions were self-taught, and second year medical students in the former curriculum in which anatomy lectures were given in advance of each laboratory session. We conclude that online modules such as the VAL, well designed with a human pedagogical agent, can be used within the curriculum without negatively impacting student engagement. Ethical Approval for this study was obtained from the Ottawa Hospital Research Ethics Board (protocol number #2009055-01H.

  9. NaI (Tl) calorimeter calibration and simulation for Coulomb sum rule experiment in Hall-A at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Xinhu; Chen, Jian-Ping; Choi, Seonho; Lu, Hai-Jiang; Meziani, Zein-Eddine; Oh, Yoomin; Sulkosky, Vince; Ye, Yunxiu; Yao, Huan

    2011-05-01

    A precision measurment of inclusive electron scattering cross sections is carried out at Jefferson Lab in the quasi-elastic region for 4He, 12C, 56Fe and 208Pb targets. The longitudinal (RL) and transverse (RT) response functions of the nucleon need to be extracted precisely in the momentum transfer range 0.55 GeV/c ≤ |q| ≤ 1.0 GeV/c. To achieve the above goal, a NaI (Tl) calorimeter is used to distinguish good electrons from background, including pions and low energy electrons rescattered from the walls of the spectrometer magnets. Due to a large set of kinematics and changes in HV settings, a number of calibrations are performed for the NaI (Tl) detector. Corrections for a few blocks of NaI (Tl) with bad or no signal are applied. The resolution of the NaI (Tl) detector after calibration reached ɤE/√E ≈ 3% at E = 1 GeV. The performance of the NaI (Tl) detector is compared with a simulation.

  10. 利用LabVieW的G语言对控制系统的虚拟仿真%A Virtual Simulation of Control System by G- Languge of LabView

    Institute of Scientific and Technical Information of China (English)

    刘怡

    2009-01-01

    LabView具有功能强大的G语言,给控制系统的虚拟仿真带来很大方便.介绍开发的控制系统虚拟实验中用Labview的G语言对控制系统结构图进行虚拟仿真的方法,对控制系统的原理研究和设计以及培养学生的动手能力有很大帮助.%LabView has a powerful G-language, which provides incredible amount of con-viniences for control system's virtual simulation function. This report will use a sample control system to demonstrate how to use G-language in the control system's virtual simulation experiment, which devel-oped by the author, to virtually simulate the control system's structure diagram. The method is very be-nificial for the studying and designing of the control system's theory and it's helpful for student's hands-on skills.

  11. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  12. Biophysics and cancer

    CERN Document Server

    Nicolini, Claudio

    1986-01-01

    Since the early times of the Greek philosophers Leucippus and Democritus, and later of the Roman philosopher Lucretius, a simple, fundamental idea emerged that brought the life sciences into the realm of the physical sciences. Atoms, after various interactions, were assumed to acquire stable configurations that corresponded either to the living or to the inanimate world. This simple and unitary theory, which has evolved in successive steps to our present time, remarkably maintained its validity despite several centuries of alternative vicissitudes, and is the foundation of modern biophysics. Some of the recent developments of this ancient idea are the discovery of the direct relationship between spatial structures and chemical activity of such molecules as methane and benzene, and the later discovery of the three-dimensional structure of double-helical DNA, and of its relationship with biological activity. The relationship between the structure of various macromolecules and the function of living cells was on...

  13. Simulation and Control Lab Development for Power and Energy Management for NASA Manned Deep Space Missions

    Science.gov (United States)

    McNelis, Anne M.; Beach, Raymond F.; Soeder, James F.; McNelis, Nancy B.; May, Ryan; Dever, Timothy P.; Trase, Larry

    2014-01-01

    The development of distributed hierarchical and agent-based control systems will allow for reliable autonomous energy management and power distribution for on-orbit missions. Power is one of the most critical systems on board a space vehicle, requiring quick response time when a fault or emergency is identified. As NASAs missions with human presence extend beyond low earth orbit autonomous control of vehicle power systems will be necessary and will need to reliably function for long periods of time. In the design of autonomous electrical power control systems there is a need to dynamically simulate and verify the EPS controller functionality prior to use on-orbit. This paper presents the work at NASA Glenn Research Center in Cleveland, Ohio where the development of a controls laboratory is being completed that will be utilized to demonstrate advanced prototype EPS controllers for space, aeronautical and terrestrial applications. The control laboratory hardware, software and application of an autonomous controller for demonstration with the ISS electrical power system is the subject of this paper.

  14. LabVIEW在蒸汽发生器动态仿真研究的应用%Labview Applied in Dynamic Simulation of Steam Generators

    Institute of Scientific and Technical Information of China (English)

    张琴舜; 李剑

    2001-01-01

    由于蒸汽发生器是压水堆的核心部件,而且蒸汽发生器的故障概率也比较高,因此蒸汽发生器的仿真研究是现今核电厂控制领域的重要课题之一。本文重点介绍一种新型仿真语言LabVIEW在蒸汽发生器仿真中的应用,对比以前所用到的仿真语言,这种语言带来许多的便利与强大的功能。%Steam generator, a key component of the PWR, has high malfunctionrate in operation. That is why its simulation becomes one of the most important topics in the area of nuclear power plant control. This paper introduces a new type simulation language of LabVIEW for simulation of steam generators. Compared with traditional simulation languages, LabVIEW proves more powerful and advantageous.

  15. VIBA-Lab 3.0: Computer program for simulation and semi-quantitative analysis of PIXE and RBS spectra and 2D elemental maps

    Science.gov (United States)

    Orlić, Ivica; Mekterović, Darko; Mekterović, Igor; Ivošević, Tatjana

    2015-11-01

    VIBA-Lab is a computer program originally developed by the author and co-workers at the National University of Singapore (NUS) as an interactive software package for simulation of Particle Induced X-ray Emission and Rutherford Backscattering Spectra. The original program is redeveloped to a VIBA-Lab 3.0 in which the user can perform semi-quantitative analysis by comparing simulated and measured spectra as well as simulate 2D elemental maps for a given 3D sample composition. The latest version has a new and more versatile user interface. It also has the latest data set of fundamental parameters such as Coster-Kronig transition rates, fluorescence yields, mass absorption coefficients and ionization cross sections for K and L lines in a wider energy range than the original program. Our short-term plan is to introduce routine for quantitative analysis for multiple PIXE and XRF excitations. VIBA-Lab is an excellent teaching tool for students and researchers in using PIXE and RBS techniques. At the same time the program helps when planning an experiment and when optimizing experimental parameters such as incident ions, their energy, detector specifications, filters, geometry, etc. By "running" a virtual experiment the user can test various scenarios until the optimal PIXE and BS spectra are obtained and in this way save a lot of expensive machine time.

  16. Biophysics of protein evolution and evolutionary protein biophysics

    OpenAIRE

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for ...

  17. Lab-on-a-bird: biophysical monitoring of flying birds.

    Directory of Open Access Journals (Sweden)

    Abdurrahman Gumus

    Full Text Available The metabolism of birds is finely tuned to their activities and environments, and thus research on avian systems can play an important role in understanding organismal responses to environmental changes. At present, however, the physiological monitoring of bird metabolism is limited by the inability to take real-time measurements of key metabolites during flight. In this study, we present an implantable biosensor system that can be used for continuous monitoring of uric acid levels of birds during various activities including flight. The system consists of a needle-type enzymatic biosensor for the amperometric detection of uric acid in interstitial fluids. A lightweight two-electrode potentiostat system drives the biosensor, reads the corresponding output current and wirelessly transfers the data or records to flash memory. We show how the device can be used to monitor, in real time, the effects of short-term flight and rest cycles on the uric acid levels of pigeons. In addition, we demonstrate that our device has the ability to measure uric acid level increase in homing pigeons while they fly freely. Successful application of the sensor in migratory birds could open up a new way of studying birds in flight which would lead to a better understanding of the ecology and biology of avian movements.

  18. [Biophysics of nerve excitation].

    Science.gov (United States)

    Kol'e, O R; Maksimov, G V

    2010-01-01

    The studies testifying to the presence of the interrelation between the physiological functions of the organism and physical and chemical processes in nerves are discussed. Changes in some physical and chemical parameters observed both upon elicited rhythmic exaltation of nerves and during the spontaneous rhythmic activity of neurons are analyzed. Upon rhythmic exaltation, a complex of physical and chemical processes is triggered, and reversible structural and metabolic rearrangements at the subcellular and molecular levels occur that do not take place during the generation of a single action potential. Thus, only in conditions of rhythmic exaltation of a nerve, it is possible to reveal those processes that provide exaltation of nerves in the organism. The future possibilities of the investigations combining the biophysical and physiological approaches are substantiated. Characteristic changes in physicochemical parameters are observed in nerves during the generation of a series of action potentials of different frequency and duration ("frequency dependence") under normal physiological conditions, as well as in extreme situations and in nerve pathology. The structural and metabolic rearrangements are directly related to the mode of rhythmic exaltation and proceed both in the course of rhythmic exaltation and after its termination. Participation and the basic components of the nervous fulcrum (an axon, Shwan cell, myelin, subcellular organelles) in the realization of rhythmic exaltation is shown. In the coordination of all processes involved in rhythmic exaltation, the main role is played by the systems of redistribution and transport of intercellular and endocellular calcium. The idea is put forward that myelin of nerve fibers is not only an isolator, but also an "intercellular depot" of calcium and participates in the redistribution of different ions. Thus, the rhythmic excitation is of great importance in the realization of some physiological functions, the

  19. Virtual Labs.

    Science.gov (United States)

    Russo, Ruth

    1997-01-01

    Discusses the potential of computers in teaching laboratories to spare the lives of animals; however, it is felt that in areas of physiology education, virtual labs are not as desirable a learning experience for advanced students as live animal labs. (Author/AIM)

  20. Sensor-Augmented Virtual Labs: Using Physical Interactions with Science Simulations to Promote Understanding of Gas Behavior

    Science.gov (United States)

    Chao, Jie; Chiu, Jennifer L.; DeJaegher, Crystal J.; Pan, Edward A.

    2016-01-01

    Deep learning of science involves integration of existing knowledge and normative science concepts. Past research demonstrates that combining physical and virtual labs sequentially or side by side can take advantage of the unique affordances each provides for helping students learn science concepts. However, providing simultaneously connected…

  1. Advanced LabVIEW Labs

    International Nuclear Information System (INIS)

    In the world of computer-based data acquisition and control, the graphical interface program LabVIEW from National Instruments is so ubiquitous that in many ways it has almost become the laboratory standard. To date, there have been approximately fifteen books concerning LabVIEW, but Professor Essick's treatise takes on a completely different tack than all of the previous discussions. In the more standard treatments of the ways and wherefores of LabVIEW such as LabVIEW Graphical Programming: Practical Applications in Instrumentation and Control by Gary W. Johnson (McGraw Hill, NY 1997), the emphasis has been instructing the reader how to program LabVIEW to create a Virtual Instrument (VI) on the computer for interfacing to a particular instruments. LabVIEW is written in ''G'' a graphical programming language developed by National Instruments. In the past the emphasis has been on training the experimenter to learn ''G''. Without going into details here, ''G'' incorporates the usual loops, arithmetic expressions, etc., found in many programming languages, but in an icon (graphical) environment. The net result being that LabVIEW contains all of the standard methods needed for interfacing to instruments, data acquisition, data analysis, graphics, and also methodology to incorporate programs written in other languages into LabVIEW. Historically, according to Professor Essick, he developed a series of experiments for an upper division laboratory course for computer-based instrumentation. His observation was that while many students had the necessary background in computer programming languages, there were students who had virtually no concept about writing a computer program let alone a computer- based interfacing program. Thus the beginnings of a concept for not only teaching computer- based instrumentation techniques, but aiso a method for the beginner to experience writing a com- puter program. Professor Essick saw LabVIEW as the ''perfect environment in which to

  2. From hadron therapy to cosmic rays: a life in biophysics

    CERN Multimedia

    Christine Sutton

    2014-01-01

    In 1954 – the year CERN was founded – another scientific journey began at what is now the Lawrence Berkeley National Laboratory. Beams of protons from a particle accelerator were used for the first time by John Lawrence – a doctor and the brother of Ernest Lawrence, the physicist after whom the Berkeley lab is named – to treat patients with cancer. For many years, Eleanor Blakely has been one of the leaders of that journey. She visited CERN last week and spoke with the Bulletin about her life in biophysics.   Use of the cylcotron beam to mimic "shooting stars" seen by astronauts. Black hood on subject Cornelius Tobias keeps out light during neutron irradiation experiment at the 184-inch accelerator. Helping to position Tobias in the beam line are (left to right) John Lyman of Biomedical Division, and Ralph Thomas of Health Physics. (Photo courtesy of Lawrence Berkeley National Laboratory.) Interested in biophysics, which was still a new...

  3. Understanding Statistical Mechanics and Biophysics Using Excel

    Science.gov (United States)

    Nelson, Peter

    2009-03-01

    A new approach to teaching statistical mechanics and biophysics is presented using the classic two-box system from statistical mechanics as an example. This approach makes advanced physics concepts accessible to a broad audience including undergraduates with no calculus background. Students develop a simple Excel spreadsheet that implements a kinetic Monte Carlo (kMC) simulation algorithm ``from scratch''. The students discover for themselves the properties of the system by analyzing the simulation output in a directed, activity-based exercise. By changing the number and initial distribution of the particles, students see how the system approaches equilibrium and how system variability changes with system size. A finite difference solution is also implemented in Excel, and students compare its predictions with the kMC results. This approach is quite different from using ``canned'' computer demonstrations, as students design, implement and debug the simulation themselves -- ensuring that they understand the model system intimately.

  4. Integrated Molecular and Cellular Biophysics

    CERN Document Server

    Raicu, Valerica

    2008-01-01

    This book integrates concepts and methods from physics, biology, biochemistry and physical chemistry into a standalone, unitary text of biophysics that aims to provide a quantitative description of structures and processes occurring in living matter. The book introduces graduate physics students and physicists interested in biophysics research to 'classical' as well as emerging areas of biophysics. The advanced undergraduate physics students and the life scientists are also invited to join in, by building on their knowledge of basic physics. Essential notions of biochemistry and biology are introduced, as necessary, throughout the book, while the reader's familiarity with basic knowledge of physics is assumed. Topics covered include interactions between biological molecules, physical chemistry of phospholipids association into bilayer membranes, DNA and protein structure and folding, passive and active electrical properties of the cell membrane, classical as well as fractal aspects of reaction kinetics and di...

  5. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with the design and measurement of physical parameters used in theory or to support biological experiments. The radiation biophysics program tests and uses the theoretical developments for experimental design, and provides information for further theoretical development through experiments on cellular systems

  6. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with design and measurement of those physical parameters used in the theory or to support biological experiments. The radiation biophysics program tests and makes use of the theoretical developments for experimental design. Also, this program provides information for further theoretical development through experiments on cellular systems

  7. The biophysics of neuronal growth

    Science.gov (United States)

    Franze, Kristian; Guck, Jochen

    2010-09-01

    For a long time, neuroscience has focused on biochemical, molecular biological and electrophysiological aspects of neuronal physiology and pathology. However, there is a growing body of evidence indicating the importance of physical stimuli for neuronal growth and development. In this review we briefly summarize the historical background of neurobiophysics and give an overview over the current understanding of neuronal growth from a physics perspective. We show how biophysics has so far contributed to a better understanding of neuronal growth and discuss current inconsistencies. Finally, we speculate how biophysics may contribute to the successful treatment of lesions to the central nervous system, which have been considered incurable until very recently.

  8. Simulating Two-way Interactive Vegetation-Biophysical Processes and Atmospheric- Mesoscale Circulations During 2001 Santarem Field Campaign Using SiB-RAMS Model

    Science.gov (United States)

    Lu, L.; Denning, S. A.; Baker, I.; Uliasz, M.

    2008-12-01

    The Simple Biosphere Model Version 2.5 (SiB2.5) is coupled with the Colorado State University Regional Atmospheric Modeling System (RAMS) to study the two-way interactions between the land surface and atmosphere during the dry season 2001 Santarem field campaign. The evaluations against flux tower and nearby meteorological station observations show that the SiB-RAMS is able to capture the variability in observed meteorology and CO2 concentration, as well as surface fluxes of CO2, H, and LE, during the 15- day simulation time period, 1 through 15 August 2001. The mechanically forced low-level convergence on the eastside of Tapajos" river has significant impact on observed ecosystem carbon fluxes, and is taken into account when tower fluxes are generalized to a large region. The impact of CO2 source from the Tapajos River was also examined by performing numerical sensitivity experiments with and without specifying river CO2 effluxes. The magnitude of these fluxes is 5 umol/m2/s, which is determined by boat measurement. The results show that the river CO2 effluxes modify the spatial and temporal distributions of atmospheric CO2 concentrations, especially at night. Our simulation also indicated the Amazon Basin continues to be a carbon sink even when the additional CO2 from the river to the atmosphere is accounted for. The additional CO2 source enhances carbon uptake over vegetated land on the lee side of Tapajos" river. Furthermore, a Lagrangian Particle Dispersion Model (LPDM) was used to quantify the contribution of river CO2 effluxes to tower observed variability in CO2 flux and concentration. A transect of 10 virtual towers was placed across the Tapajos River with 4-km spacing between each tower in the east-west direction. The particles were released and tracked backward in time at each tower. The influence function was calculated and integrated with the surface CO2 fluxes simulated by SiB-RAMS. The experiment demonstrates that LPDM is capable to determine when

  9. Fundamental Concepts in Biophysics Volume 1

    CERN Document Server

    Jue, Thomas

    2009-01-01

    HANDBOOK OF MODERN BIOPHYSICS Series Editor Thomas Jue, PhD Handbook of Modern Biophysics brings current biophysics topics into focus, so that biology, medical, engineering, mathematics, and physical-science students or researchers can learn fundamental concepts and the application of new techniques in addressing biomedical challenges. Chapters explicate the conceptual framework of the physics formalism and illustrate the biomedical applications. With the addition of problem sets, guides to further study, and references, the interested reader can continue to explore independently the ideas presented. Volume I: Fundamental Concepts in Biophysics Editor Thomas Jue, PhD In Fundamental Concepts in Biophysics, prominent professors have established a foundation for the study of biophysics related to the following topics: Mathematical Methods in Biophysics Quantum Mechanics Basic to Biophysical Methods Computational Modeling of Receptor–Ligand Binding and Cellular Signaling Processes Fluorescence Spectroscopy Elec...

  10. TELECOM LAB

    CERN Multimedia

    IT-CS-TEL Section

    2001-01-01

    The Telecom Lab is moving from Building 104 to Building 31 S-026, with its entrance via the ramp on the side facing Restaurant n°2. The help desk will thus be closed to users on Tuesday 8 May. On May 9, the Lab will only be able to deal with problems of a technical nature at the new address and it will not be able to process any new subscription requests throughout the week from 7 to 11 May. We apologise for any inconvenience this may cause and thank you for your understanding.

  11. 基于RT-LAB的半实物仿真系统研究%Research of Hardware-in-the-Loop Simulation Based on RT-LAB

    Institute of Scientific and Technical Information of China (English)

    晁鲁静; 赵晓蓓; 黄勇; 常晓飞

    2011-01-01

    Hardware-in-the-loop simulation plays a very important role in missile design. Simulation can test the per formance and harmony of each part of the missile at minimum cost. This paper presents the development method and programming essentials of PCI card driver under QNX based on simulation of X-type IR seeker. Some problems that may be encountered in the process are described in detail. The paper also presents a guide to RT-LAB and how to design the simulation model. The research shows that RT-LAB can apply Simulink model in hardware-in-the-loop simulation system conveniently and rapidly. The system takes QNX as the target node and improves stability, reliability and the real-time performance of the simulation. The result indicates that the simulation system is stable and reliable in simulation of X-type IR seeker.%半实物仿真是导弹研制过程中的一个重要环节,仿真实验可以最小的成本检验导弹各个部件的性能及工作的协调性.本文基于某型红外导引头半实物仿真系统,详细介绍了QNX下自制板卡驱动程序的开发方法、编程要点以及可能遇到的问题,给出了RT-LAB软件的使用方法以及仿真模型的搭建方法.研究表明,RT-LAB可以方便快捷地将Simulink模型应用于半实物仿真系统,使用QNX系统作为目标节点,提高了仿真系统的实时性、稳定性和可靠性.某型红外导引头的半实物仿真系统中的运行结果表明该系统运行稳定、可靠.

  12. Biotic games and cloud experimentation as novel media for biophysics education

    Science.gov (United States)

    Riedel-Kruse, Ingmar; Blikstein, Paulo

    2014-03-01

    First-hand, open-ended experimentation is key for effective formal and informal biophysics education. We developed, tested and assessed multiple new platforms that enable students and children to directly interact with and learn about microscopic biophysical processes: (1) Biotic games that enable local and online play using galvano- and photo-tactic stimulation of micro-swimmers, illustrating concepts such as biased random walks, Low Reynolds number hydrodynamics, and Brownian motion; (2) an undergraduate course where students learn optics, electronics, micro-fluidics, real time image analysis, and instrument control by building biotic games; and (3) a graduate class on the biophysics of multi-cellular systems that contains a cloud experimentation lab enabling students to execute open-ended chemotaxis experiments on slimemolds online, analyze their data, and build biophysical models. Our work aims to generate the equivalent excitement and educational impact for biophysics as robotics and video games have had for mechatronics and computer science, respectively. We also discuss how scaled-up cloud experimentation systems can support MOOCs with true lab components and life-science research in general.

  13. Mechanical Implementation and Simulation of MoboLab, A Mobile Robot for Inspection of Power Transmission Lines

    Directory of Open Access Journals (Sweden)

    Mahmud Saadat Foumani

    2008-11-01

    Full Text Available This paper describes the first phase in development of a mobile robot that can navigate aerial power transmission lines completely unattended by human operator. Its ultimate purpose is to automate inspection of power transmission lines and their equipments. The authors have developed a scaled functional model of such a mobile robot with a preliminary simple computer based on-off controller. MoboLab (Mobile Laboratory navigates a power transmission line between two strain towers. It can maneuver over obstructions created by line equipments such as insulators, warning spheres, dampers, and spacer dampers. It can also easily negotiate the towers by its three flexible arms. MoboLab has an internal main screw which enables the robot to move itself or its two front and rear arms independently through changing gripped points. When the front arm gets close to an obstacle, the arm detaches from the line and goes down, the robot moves forward, the arm passes the obstacle and grippes the line again. In a same way another arms pass the obstacle.

  14. Biophysical science in Italy: SIBPA turns 40.

    Science.gov (United States)

    Giacomazza, Daniela; Musio, Carlo

    2013-12-01

    This Special Issue of Biophysical Chemistry includes a selection of the papers presented at the XXI Congress of the Italian Society of Pure and Applied Biophysics (i.e., SIBPA, Società Italiana di Biofisica Pura ed Applicata) held on September 2012 at the University of Ferrara, Ferrara, Italy. Topics cover all biophysical disciplines, from molecular to cellular, to integrative biophysics giving an almost comprehensive view of the interdisciplinary and multidisciplinary approaches, proper of the modern biophysics. SIBPA, which celebrates its 40th anniversary in 2013, has steadily grown and appeals to both specialists and a wider general audience.

  15. Leukocyte biophysics. An invited review.

    Science.gov (United States)

    Schmid-Schönbein, G W

    1990-10-01

    The biophysical properties of leukocytes in the passive and active state are discussed. In the passive unstressed state, leukocytes are spherical with numerous membrane folds. Passive leukocytes exhibit viscoelastic properties, and the stress is carried largely by the cell cytoplasm and the nucleus. The membrane is highly deformable in shearing and bending, but resists area expansion. Membrane tension can usually be neglected but plays a role in cases of large deformation when the membrane becomes unfolded. The constant membrane area constraint is a determinant of phagocytic capacity, spreading of cells, and passage through narrow pores. In the active state, leukocytes undergo large internal cytoplasmic deformation, pseudopod projection, and granule redistribution. Several different measurements for assessment of biophysical properties and the internal cytoplasmic deformation in form of strain and strain rate tensors are presented. The current theoretical models for active cytoplasmic motion in leukocytes are discussed in terms of specific macromolecular reactions. PMID:1705479

  16. Space Biophysics: Accomplishments, Trends, Challenges

    Science.gov (United States)

    Smith, Jeffrey D.

    2015-01-01

    Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond

  17. Lab architecture

    Science.gov (United States)

    Crease, Robert P.

    2008-04-01

    There are few more dramatic illustrations of the vicissitudes of laboratory architecturethan the contrast between Building 20 at the Massachusetts Institute of Technology (MIT) and its replacement, the Ray and Maria Stata Center. Building 20 was built hurriedly in 1943 as temporary housing for MIT's famous Rad Lab, the site of wartime radar research, and it remained a productive laboratory space for over half a century. A decade ago it was demolished to make way for the Stata Center, an architecturally striking building designed by Frank Gehry to house MIT's computer science and artificial intelligence labs (above). But in 2004 - just two years after the Stata Center officially opened - the building was criticized for being unsuitable for research and became the subject of still ongoing lawsuits alleging design and construction failures.

  18. Workspace: LAB

    DEFF Research Database (Denmark)

    Binder, Thomas; Lundsgaard, Christina; Nørskov, Eva-Carina

    2007-01-01

    På mange arbejdspladser viger man tilbage fra at inddrage medarbejderne når der igangsættes større forandringer. Workspace:lab er et bud på en inddragende udviklingsproces hvor dialog og eksperimenter står i centrum. Ved at samle såvel medarbejdere som ledelse og rådgivere på et mindre antal...

  19. Simulation of Digital Trapezoidal Shaping Algorithm Based LabVIEW%基于 LabVIEW 的数字梯形成形算法仿真研究

    Institute of Scientific and Technical Information of China (English)

    朱玉玉; 杨露; 杨民

    2014-01-01

    成形滤波技术是核能谱测量的关键技术,数字梯形滤波是实现核能谱仪数字化的关键环节。论文基于数字多道系统中核信号处理要求,对梯形成形滤波技术进行了理论研究。利用LabVIEW软件平台实现了梯形滤波器仿真,讨论了滤波器参数对系统性能或输出的影响。仿真结果表明,数字梯形滤波成形器能够根据实际信号特性灵活进行参数优化和配置,以有效地适应后续测量。%Shaping filter technique is the key technique of nuclear energy spectrum measurements , digital trape-zoidal filter is the key to realize nuclear spectrometer digitizing .For the processing requirement of the nuclear signal in digital multi -channel system , this article did a study about trapezoidal shaping and filtering tech-nique .And it has realized the simulation of this filter , discussed the impact on system performance or output caused by filter parameters .The result showed the parameters of digital trapezoidal filter can be optimized flexi -bly in accordance with actual signal characteristic to effectively adapt to subsequent measurements .

  20. Innovations in STEM education: the Go-Lab federation of online labs

    NARCIS (Netherlands)

    Jong, de Ton; Sotiriou, Sofoklis; Gillet, Dennis

    2014-01-01

    The Go-Lab federation of online labs opens up virtual laboratories (simulation), remote laboratories (real equipment accessible at distance) and data sets from physical laboratory experiments (together called “online labs”) for large-scale use in education. In this way, Go-Lab enables inquiry-based

  1. Networking Online Labs within the ISA Framework

    Directory of Open Access Journals (Sweden)

    Danilo Garbi Zutin

    2009-11-01

    Full Text Available The proposed paper focuses in outlining the implementation of online laboratories within the framework of the iLab Shared Architecture (ISA in order to facilitate sharing those labs among several institutions and managing laboratory users. The laboratories are compliant with the ISA batched architecture, which is based on Web services to mediate the communication between Lab Servers and Lab Clients. The first laboratory presented is a Hybrid Lab that allows for the realization of real experiments as well as simulations with an analog programmable device.

  2. Quantum Nanobiology and Biophysical Chemistry

    DEFF Research Database (Denmark)

    2013-01-01

    An introduction was provided in the first issue by way of an Editorial to this special two issue volume of Current Physical Chemistry – “Quantum Nanobiology and Biophysical Chemistry” [1]. The Guest Editors would like to thank all the authors and referees who have contributed to this second issue...... and Jalkanen et al. provide a theoretical and experimental investigation of the infrared and Raman spectra of Leu- Enkephalin in dimethylsulfoxide will be published in the August 2013 issue, Volume 3, Issue 3. In place of these two contributions, two General Articles from Esalmi et al., and Liu et al...

  3. Molecular Biophysics Symposium, November 6, 2014

    OpenAIRE

    Capelluto, Daniel

    2014-01-01

    Virginia Tech hosted the first Molecular Biophysics Symposium focusing on structural biology studies of proteins. The event pursued two goals. First, it was designed to enrich the interaction among biophysical research groups located in southwest Virginia. Second, the symposium offered undergraduate students, interested in continuing their graduate studies in biophysics, the opportunity to meet with local and invited biophysicists and structural biologists. Four speakers were selected from su...

  4. Evolution and Biophysics of the Escherichia coli lac Operon

    Science.gov (United States)

    Ray, J. Christian; Igoshin, Oleg; Quan, Selwyn; Monds, Russell; Cooper, Tim; Balázsi, Gábor

    2011-03-01

    To understand, predict, and control the evolution of living organisms, we consider biophysical effects and molecular network architectures. The lactose utilization system of E. coli is among the most well-studied molecular networks in biology, making it an ideal candidate for such studies. Simulations show how the genetic architecture of the wild-type operon attenuates large metabolic intermediate fluctuations that are predicted to occur in an equivalent system with the component genes on separate operons. Quantification of gene expression in the lac operon evolved in growth conditions containing constant lactose, alternating with glucose, or constant glucose, shows characteristic gene expression patterns depending on conditions. We are simulating these conditions to show context-dependent biophysical sources and costs of different lac operon architectures.

  5. Airliner cabin air quality: emissions of organophosphates originating from aircraft engine oil. Experimental lab simulation and measurements on flight

    NARCIS (Netherlands)

    Houtzager, M.M.G.; Havermans, J.B.G.A.; Bos, J.G.H.; Makarem Akhlaghi, H.; Hijman, W.C.; Renesse van Duivenbode, J.A.D.; Jedynska, A.D.

    2014-01-01

    In our simulation experiments, using e.g., a dedicated emission chamber, the emission of organophosphates as tricresyl phosphate (TCP) was studied using turbine oil. Experiments were carried out at 250°C and 370°C. Subsequently field studies were carried out to detect the presence of TCPs in the coc

  6. Computer Simulations of Quantum Theory of Hydrogen Atom for Natural Science Education Students in a Virtual Lab

    Science.gov (United States)

    Singh, Gurmukh

    2012-01-01

    The present article is primarily targeted for the advanced college/university undergraduate students of chemistry/physics education, computational physics/chemistry, and computer science. The most recent software system such as MS Visual Studio .NET version 2010 is employed to perform computer simulations for modeling Bohr's quantum theory of…

  7. A Simulation of Energy Storage System for Improving the Power System Stability with Grid-Connected PV using MCA Analysis and LabVIEW Tool

    Directory of Open Access Journals (Sweden)

    Jindrich Stuchly

    2015-01-01

    Full Text Available The large-scale penetration of distributed, Renewable power plants require transfers of large amounts of energy. This, in turn, puts a high strain on the energy delivery infrastructure. In particular, photovoltaic power plants supply energy with high intermittency, possibly affecting the stability of the grid by changing the voltage at the plant connection point. In this contribution, we summarize the main negative effects of selected and real-operated grid connected photovoltaic plant. Thereafter a review of suitable Energy storage systems to mitigate the negative effects has been carried out, compared and evaluated using Multi-criterion analysis. Based on this analysis, data collected at the plant and the grid, are used to design the energy storage systems to support connection of the plant to the grid. The cooperation of these systems is then analysed and evaluated using simulation tools created in LabVIEW for this purpose. The simulation results demonstrate the capability of energy storage system solutions to significantly reduce the negative feedback effects of Photovoltaic Power Plan to the low voltage grid.

  8. NeuroLab: A Set of Graphical Computer Simulations to Support Neuroscience Instruction at the High School and Undergraduate Level

    OpenAIRE

    Schettino, Luis F.

    2014-01-01

    Young students struggle with concepts that involve the parallel activity of large numbers of similar entities, precisely the kind of concepts that abound in neuroscience. While a direct experience to laboratory work cannot be replaced, such activities include a steep learning curve and may be impractical in certain course settings. This article describes a set of computer simulations of a number of neural processes using NetLogo (Wilensky, 1999), a software environment for the design and impl...

  9. The Mechanics and Biophysics of Hearing

    CERN Document Server

    Geisler, C; Matthews, John; Ruggero, Mario; Steele, Charles

    1990-01-01

    Proceedings of a workshop on the physics and biophysics of hearing that brought together experimenters and modelers working on all aspects of audition. Topics covered include: cochlear mechanical measurements, cochlear models, mechanicals and biophysics of hair cells, efferent control, and ultrastructure.

  10. Linking Gap Model with MODIS Biophysical Products for Biomass Estimation

    Science.gov (United States)

    Wang, D.; Sun, G.; Cai, Y.; Guo, Z.; Fu, A.; Ni, W.; Liu, D.

    With the development of earth observation technology and data processing technology biophysical data from remote sensing means such as MODIS LAI and NPP are accessible now However it is still difficult for direct measurement of biomass from remote sensors One possibility for overcoming this problem is using ecological models to link the vegetation parameters currently available from remote sensing to biomass In this paper a combined work is done for estimating forest biomass A calibrated gap model ZELIG was run to simulate the forest development in a temperate forested area in NE China The output relationship between age and biomass was linked to registered MODIS LAI NPP and land cover type images of the same area From the above work forest age or biomass was estimated from existing remote sensed data Obviously there is a lot of work to be done such as optimal combination of biophysical parameters to improve the linkage between MODIS product and ecological modeling

  11. Numerical simulation of competitive aerobic / anaerobic hydrocarbon plume biodegradation in two-dimensional bench scale lab-experiments

    Science.gov (United States)

    Beyer, C.; Ballarini, E.; Bauer, R.; Griebler, C.; Bauer, S.

    2011-12-01

    profiles perpendicular to the flow direction along the plume. Simulated microbial growth was strongest near the central tank inlet, where both, oxygen and ethylbenzene were available at high concentrations, and along the transverse mixing zone at the fringe of the developed ethylbenzene plume. Model based interpretation of the aerobic/anaerobic phase with competitive biodegradation proved to be ambiguous due to uncertainties regarding the actual stoichiometry of the specific denitrification reaction. Also, the simulated isotopic patterns were very sensitive to the assumed initial distribution of the A. aromaticum EbN1 biomass. Ethylbenzene concentrations and isotopic patterns predicted by the numerical model match the measurements quite well for the first half of the aerobic/anaerobic phase. A distinct increase in biodegradation dynamics later on hints at a change in biodegradation dynamics during the course of the experiment.

  12. Historical and Critical Review on Biophysical Economics

    Science.gov (United States)

    Adigüzel, Yekbun

    2016-07-01

    Biophysical economics is initiated with the long history of the relation of economics with ecological basis and biophysical perspectives of the physiocrats. It inherently has social, economic, biological, environmental, natural, physical, and scientific grounds. Biological entities in economy like the resources, consumers, populations, and parts of production systems, etc. could all be dealt by biophysical economics. Considering this wide scope, current work is a “biophysical economics at a glance” rather than a comprehensive review of the full range of topics that may just be adequately covered in a book-length work. However, the sense of its wide range of applications is aimed to be provided to the reader in this work. Here, modern approaches and biophysical growth theory are presented after the long history and an overview of the concepts in biophysical economics. Examples of the recent studies are provided at the end with discussions. This review is also related to the work by Cleveland, “Biophysical Economics: From Physiocracy to Ecological Economics and Industrial Ecology” [C. J. Cleveland, in Advances in Bioeconomics and Sustainability: Essay in Honor of Nicholas Gerogescu-Roegen, eds. J. Gowdy and K. Mayumi (Edward Elgar Publishing, Cheltenham, England, 1999), pp. 125-154.]. Relevant parts include critics and comments on the presented concepts in a parallelized fashion with the Cleveland’s work.

  13. Virtual Labs and Virtual Worlds

    Science.gov (United States)

    Boehler, Ted

    2006-12-01

    Virtual Labs and Virtual Worlds Coastline Community College has under development several virtual lab simulations and activities that range from biology, to language labs, to virtual discussion environments. Imagine a virtual world that students enter online, by logging onto their computer from home or anywhere they have web access. Upon entering this world they select a personalized identity represented by a digitized character (avatar) that can freely move about, interact with the environment, and communicate with other characters. In these virtual worlds, buildings, gathering places, conference rooms, labs, science rooms, and a variety of other “real world” elements are evident. When characters move about and encounter other people (players) they may freely communicate. They can examine things, manipulate objects, read signs, watch video clips, hear sounds, and jump to other locations. Goals of critical thinking, social interaction, peer collaboration, group support, and enhanced learning can be achieved in surprising new ways with this innovative approach to peer-to-peer communication in a virtual discussion world. In this presentation, short demos will be given of several online learning environments including a virtual biology lab, a marine science module, a Spanish lab, and a virtual discussion world. Coastline College has been a leader in the development of distance learning and media-based education for nearly 30 years and currently offers courses through PDA, Internet, DVD, CD-ROM, TV, and Videoconferencing technologies. Its distance learning program serves over 20,000 students every year. sponsor Jerry Meisner

  14. Supercharging Lessons with a Virtual Lab

    Science.gov (United States)

    Stewart, Jefferson; Vincent, Daniel

    2013-01-01

    The authors describes their experiences incorporating the virtual lab into a simple circuit lesson during an energy unit in a sixth-grade class. The lesson included a hands-on group experiment using wire, batteries, and light bulbs to make a circuit and an online simulation, using a virtual lab. Class discussions, student inquiries, and the study…

  15. An introduction to environmental biophysics

    CERN Document Server

    Campbell, Gaylon S

    1977-01-01

    The study of environmental biophysics probably began earlier in man's history than that of any other science. The study of organism-environment interaction provided a key to survival and progress. Systematic study of the science and recording of experimental results goes back many hundreds of years. Ben­ jamin Franklin, the early American statesman, inventor, printer, and scientist studied conduction, evaporation, and radiation. One of his observations is as follows: My desk on which I now write, and the lock of my desk, are both exposed to the same temperature of the air, and have therefore the same degree of heat or cold; yet if I lay my hand successively on the wood and on the metal, the latter feels much the coldest, not that it is really so, but being a better conductor, it more readily than the wood takes away and draws into itself the fire that was in my skin. 1 Franklin probably was not the first to discover this principle, and certainly was not the last. Modem researchers rediscover this principle f...

  16. Applications of synchrotron radiation in Biophysics

    International Nuclear Information System (INIS)

    A short introduction to the generation of the synchrotron radiation is made. Following, the applications of such a radiation in biophysics with emphasis to the study of the hemoglobin molecule are presented. (L.C.)

  17. Biophysics software for interdisciplinary education and research

    OpenAIRE

    Deutsch, J. M.

    2013-01-01

    Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching undergraduates biophysics in an interdisciplinary manner. Projects have been devised on topics that range from x-ray diffraction to the Hodgkin Huxley equations. They are team-based and encourage collaboration. The projects make extensive use of software writt...

  18. Biophysical regulation of stem cell differentiation.

    Science.gov (United States)

    Govey, Peter M; Loiselle, Alayna E; Donahue, Henry J

    2013-06-01

    Bone adaptation to its mechanical environment, from embryonic through adult life, is thought to be the product of increased osteoblastic differentiation from mesenchymal stem cells. In parallel with tissue-scale loading, these heterogeneous populations of multipotent stem cells are subject to a variety of biophysical cues within their native microenvironments. Bone marrow-derived mesenchymal stem cells-the most broadly studied source of osteoblastic progenitors-undergo osteoblastic differentiation in vitro in response to biophysical signals, including hydrostatic pressure, fluid flow and accompanying shear stress, substrate strain and stiffness, substrate topography, and electromagnetic fields. Furthermore, stem cells may be subject to indirect regulation by mechano-sensing osteocytes positioned to more readily detect these same loading-induced signals within the bone matrix. Such paracrine and juxtacrine regulation of differentiation by osteocytes occurs in vitro. Further studies are needed to confirm both direct and indirect mechanisms of biophysical regulation within the in vivo stem cell niche.

  19. Biophysical Regulation of Vascular Differentiation and Assembly

    CERN Document Server

    Gerecht, Sharon

    2011-01-01

    The ability to grow stem cells in the laboratory and to guide their maturation to functional cells allows us to study the underlying mechanisms that govern vasculature differentiation and assembly in health and disease. Accumulating evidence suggests that early stages of vascular growth are exquisitely tuned by biophysical cues from the microenvironment, yet the scientific understanding of such cellular environments is still in its infancy. Comprehending these processes sufficiently to manipulate them would pave the way to controlling blood vessel growth in therapeutic applications. This book assembles the works and views of experts from various disciplines to provide a unique perspective on how different aspects of its microenvironment regulate the differentiation and assembly of the vasculature. In particular, it describes recent efforts to exploit modern engineering techniques to study and manipulate various biophysical cues. Biophysical Regulation of Vascular Differentiation and Assembly provides an inter...

  20. Exploring the Impact of TeachME™ Lab Virtual Classroom Teaching Simulation on Early Childhood Education Majors' Self-Efficacy Beliefs

    Science.gov (United States)

    Bautista, Nazan Uludag; Boone, William J.

    2015-01-01

    The purpose of this study was to investigate the impact of a mixed-reality teaching environment, called TeachME™ Lab (TML), on early childhood education majors' science teaching self-efficacy beliefs. Sixty-two preservice early childhood teachers participated in the study. Analysis of the quantitative (STEBI-b) and qualitative (journal entries)…

  1. Global energy modeling - A biophysical approach

    Energy Technology Data Exchange (ETDEWEB)

    Dale, Michael

    2010-09-15

    This paper contrasts the standard economic approach to energy modelling with energy models using a biophysical approach. Neither of these approaches includes changing energy-returns-on-investment (EROI) due to declining resource quality or the capital intensive nature of renewable energy sources. Both of these factors will become increasingly important in the future. An extension to the biophysical approach is outlined which encompasses a dynamic EROI function that explicitly incorporates technological learning. The model is used to explore several scenarios of long-term future energy supply especially concerning the global transition to renewable energy sources in the quest for a sustainable energy system.

  2. Are Remote Labs Worth the Cost? Insights From a Study of Student Perceptions of Remote Labs

    Directory of Open Access Journals (Sweden)

    David Uttal

    2011-05-01

    Full Text Available Remote online laboratories enable students to conduct scientific investigations using real experimental equipment. However, scaling up remote labs may require significant costs in purchasing and maintaining expensive equipment compared to scaling simulated labs. While these costs are a consequence of using physical equipment, we argue that there are unique educational advantages to remote labs. This paper presents the results of a preliminary study of student perceptions of a remote lab in comparison to an identical lab experience with simulated data. The findings reveal several intriguing themes that highlight the pedagogical value of remote laboratories. In addition, we provide recommendations for the design and pedagogy of online laboratory experiences based on our findings.

  3. Biophysical Evaluation of SonoSteam®:

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan R.;

    /response relationship between SonoSteam treatment time and changes in collagen I, and a depth dependency in bacterial reduction, which points toward CFU counts overestimating total bacterial reduction. In conclusion the biophysical methods provide a less biased, reproducible and highly detailed system description...

  4. Agriculture sector resource and environmental policy analysis: an economic and biophysical approach.

    Science.gov (United States)

    House, R; McDowell, H; Peters, M; Heimlich, R

    1999-01-01

    Agricultural pollution of the environment is jointly determined by economic decisions driving land use, production practices, and stochastic biophysical processes associated with agricultural production, land and climate characteristics. It follows that environmental and economic statistics, traditionally collected independently of each other, offer little insight into non-point pollutant loadings. We argue that effective policy development would be facilitated by integrating environmental and economic data gathering, combined with simulation modelling linking economic and biophysical components. Integrated data collection links economics, land use, production methods and environmental loadings. An integrated economic/biophysical modelling framework facilitates policy analysis because monetary incentives to reduce pollution can be evaluated in the context of market costs and returns that influence land use and production activity. This allows prediction of environmental and economic outcomes from alternative policies to solve environmental problems. We highlight steps taken to merge economic and biophysical modelling for policy analysis within the Economic Research Service of the United States Department of Agriculture. An example analysis of a policy to reduce agricultural nitrogen pollution is presented, with the economic and environmental results illustrating the value of linked economic and biophysical analysis. PMID:10231835

  5. Lidar remote sensing of savanna biophysical attributes

    Science.gov (United States)

    Gwenzi, David

    plot level biomass into wall-to-wall maps that provide more ecological information. We evaluated the utility of three spatial modeling approaches to address this problem: deterministic methods, geostatistical methods and an image segmentation approach. Overall, the mean pixel biomass estimated by the 3 approaches did not differ significantly but the output maps showed marked differences in the estimation precision and ability of each model to mimic the primary variable's trend across the landscape. The results emphasized the need for future satellite lidar missions to consider increasing the sampling intensity across track so that biomass observations are made and characterized at the scale at which they vary. We used data from the Multiple Altimeter Beam Experimental Lidar (MABEL), an airborne photon counting lidar sensor developed by NASA Goddard to simulate ICESat-2 data. We segmented each transect into different block sizes and calculated canopy top and mean ground elevation based on the structure of the histogram of the block's aggregated photons. Our algorithm was able to compute canopy height and generate visually meaningful vegetation profiles at MABEL's signal and noise levels but a simulation of the expected performance of ICESat-2 by adjusting MABEL data's detected number of signal and noise photons to that predicted using ATLAS instrument model design cases indicated that signal photons will be substantially lower. The lower data resolution reduces canopy height estimation precision especially in areas of low density vegetation cover. Given the clear difficulties in processing simulated ATLAS data, it appears unlikely that it will provide the kind of data required for mapping of the biophysical properties of savanna vegetation. Rather, resources are better concentrated on preparing for the Global Ecosystem Dynamics Investigation (GEDI) mission, a waveform lidar mission scheduled to launch by the end of this decade. In addition to the full waveform technique

  6. Biophysical influence of airborne carbon nanomaterials on natural pulmonary surfactant.

    Science.gov (United States)

    Valle, Russell P; Wu, Tony; Zuo, Yi Y

    2015-05-26

    Inhalation of nanoparticles (NP), including lightweight airborne carbonaceous nanomaterials (CNM), poses a direct and systemic health threat to those who handle them. Inhaled NP penetrate deep pulmonary structures in which they first interact with the pulmonary surfactant (PS) lining at the alveolar air-water interface. In spite of many research efforts, there is a gap of knowledge between in vitro biophysical study and in vivo inhalation toxicology since all existing biophysical models handle NP-PS interactions in the liquid phase. This technical limitation, inherent in current in vitro methodologies, makes it impossible to simulate how airborne NP deposit at the PS film and interact with it. Existing in vitro NP-PS studies using liquid-suspended particles have been shown to artificially inflate the no-observed adverse effect level of NP exposure when compared to in vivo inhalation studies and international occupational exposure limits (OELs). Here, we developed an in vitro methodology called the constrained drop surfactometer (CDS) to quantitatively study PS inhibition by airborne CNM. We show that airborne multiwalled carbon nanotubes and graphene nanoplatelets induce a concentration-dependent PS inhibition under physiologically relevant conditions. The CNM aerosol concentrations controlled in the CDS are comparable to those defined in international OELs. Development of the CDS has the potential to advance our understanding of how submicron airborne nanomaterials affect the PS lining of the lung.

  7. Commentary on “Biophysical Economics” and Evolving Areas

    Science.gov (United States)

    Flomenbom, Ophir; Coban, Gul Unal; Adigüzel, Yekbun

    2016-07-01

    In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area.

  8. Crystallization Formulation Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Crystallization Formulation Lab fills a critical need in the process development and optimization of current and new explosives and energetic formulations. The...

  9. USNA DIGITAL FORENSICS LAB

    Data.gov (United States)

    Federal Laboratory Consortium — To enable Digital Forensics and Computer Security research and educational opportunities across majors and departments. Lab Mission Establish and maintain a Digital...

  10. Fabrication and Prototyping Lab

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The Fabrication and Prototyping Lab for composite structures provides a wide variety of fabrication capabilities critical to enabling hands-on research and...

  11. Teaching wave phenomena via biophysical applications

    Science.gov (United States)

    Reich, Daniel; Robbins, Mark; Leheny, Robert; Wonnell, Steven

    2014-03-01

    Over the past several years we have developed a two-semester second-year physics course sequence for students in the biosciences, tailored in part to the needs of undergraduate biophysics majors. One semester, ``Biological Physics,'' is based on the book of that name by P. Nelson. This talk will focus largely on the other semester, ``Wave Phenomena with Biophysical Applications,'' where we provide a novel introduction to the physics of waves, primarily through the study of experimental probes used in the biosciences that depend on the interaction of electromagnetic radiation with matter. Topic covered include: Fourier analysis, sound and hearing, diffraction - culminating in an analysis of x-ray fiber diffraction and its use in the determination of the structure of DNA - geometrical and physical optics, the physics of modern light microscopy, NMR and MRI. Laboratory exercises tailored to this course will also be described.

  12. Biophysics of α-synuclein membrane interactions.

    Science.gov (United States)

    Pfefferkorn, Candace M; Jiang, Zhiping; Lee, Jennifer C

    2012-02-01

    Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson's disease (PD) related protein, α-synuclein (α-syn). We give particular focus to studies that have led to the current understanding of membrane-bound α-syn structure and the elucidation of specific membrane properties that affect α-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and α-syn in PD pathogenesis. This article is part of a Special Issue entitled: Membrane protein structure and function.

  13. Biophysics and the Challenges of Emerging Threats

    CERN Document Server

    Puglisi, Joseph D

    2009-01-01

    This volume is a collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 8th Course: Biophysics and the Challenges of Emerging Threats. This NATO Advance Study Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture on 19 through 30 June 2007. The ASI brought together a diverse group of experts who bridged the fields of virology and biology, biophysics, chemistry and physics. Prominent lecturers and students from around the world representant a total of 24 countries participated in the NATO ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU). The central hypothesis underlying this ASI was that interdisciplinary research, merging principles of physics, chemistry and biology, can drive new discovery in detecting and fighting bioterrorism agents, lead to cleaner environments, and help propel development in NATO partner countries. The ASI merged the relat...

  14. RoboLab and virtual environments

    Science.gov (United States)

    Giarratano, Joseph C.

    1994-01-01

    A useful adjunct to the manned space station would be a self-contained free-flying laboratory (RoboLab). This laboratory would have a robot operated under telepresence from the space station or ground. Long duration experiments aboard RoboLab could be performed by astronauts or scientists using telepresence to operate equipment and perform experiments. Operating the lab by telepresence would eliminate the need for life support such as food, water and air. The robot would be capable of motion in three dimensions, have binocular vision TV cameras, and two arms with manipulators to simulate hands. The robot would move along a two-dimensional grid and have a rotating, telescoping periscope section for extension in the third dimension. The remote operator would wear a virtual reality type headset to allow the superposition of computer displays over the real-time video of the lab. The operators would wear exoskeleton type arms to facilitate the movement of objects and equipment operation. The combination of video displays, motion, and the exoskeleton arms would provide a high degree of telepresence, especially for novice users such as scientists doing short-term experiments. The RoboLab could be resupplied and samples removed on other space shuttle flights. A self-contained RoboLab module would be designed to fit within the cargo bay of the space shuttle. Different modules could be designed for specific applications, i.e., crystal-growing, medicine, life sciences, chemistry, etc. This paper describes a RoboLab simulation using virtual reality (VR). VR provides an ideal simulation of telepresence before the actual robot and laboratory modules are constructed. The easy simulation of different telepresence designs will produce a highly optimum design before construction rather than the more expensive and time consuming hardware changes afterwards.

  15. Making Real Virtual Labs

    Science.gov (United States)

    Keller, Harry E.; Keller, Edward E.

    2005-01-01

    Francis Bacon began defining scientific methodology in the early 17th century, and secondary school science classes began to implement science labs in the mid-19th century. By the early 20th century, leading educators were suggesting that science labs be used to develop scientific thinking habits in young students, and at the beginning of the 21st…

  16. 基于虚拟仪器LabView的数字相敏检波算法仿真研究%Simulation Study of Digital Phase Sensitive Detector Algorithm Based on LabView Virtual Instrument

    Institute of Scientific and Technical Information of China (English)

    梁培艳

    2012-01-01

    Weak signal detection play a crucial role in the development of science and technology.Its detection accuracy affect the astronomical,biochemical,physics and other science development progress directly.This paper introduces weak signal detection of square wave based on virtual instrument technology and digital detection phase sensitive algorithm of subsection accumulating and relating.This method can be used to detect weak dc signal.Through simulation this method can detect the amplitude effectively of weak square wave signal and can be used to detect amplitude of weak dc signal.%微弱信号检测在现在科技发展中起着至关重要的作用,它的检测精度直接影响着天文,生化,物理等科技的发展进度。该文介绍了基于虚拟仪器技术和分段累加相关数字相敏检波算法对于微弱方波信号的检测,用于检测微弱直流信号。通过仿真此方法能有效地检测到微弱方波信号的幅值,进而可以用于检测微弱直流信号的幅值。

  17. Unusual biophysics of intrinsically disordered proteins.

    Science.gov (United States)

    Uversky, Vladimir N

    2013-05-01

    Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue

  18. Coupling Biophysical and Socioeconomic Models for Coral Reef Systems in Quintana Roo, Mexican Caribbean

    Directory of Open Access Journals (Sweden)

    Elizabeth A. Fulton

    2011-09-01

    Full Text Available Transdisciplinary approaches that consider both socioeconomic and biophysical processes are central to understanding and managing rapid change in coral reef systems worldwide. To date, there have been limited attempts to couple the two sets of processes in dynamic models for coral reefs, and these attempts are confined to reef systems in developed countries. We present an approach to coupling existing biophysical and socioeconomic models for coral reef systems in the Mexican state of Quintana Roo. The biophysical model is multiscale, using dynamic equations to capture local-scale ecological processes on individual reefs, with reefs connected at regional scales by the ocean transport of larval propagules. The agent-based socioeconomic model simulates changes in tourism, fisheries, and urbanization in the Quintana Roo region. Despite differences in the formulation and currencies of the two models, we were able to successfully modify and integrate them to synchronize and define information flows and feedbacks between them. A preliminary evaluation of the coupled model system indicates that the model gives reasonable predictions for fisheries and ecological variables and can be used to examine scenarios for future social–ecological change in Quintana Roo. We provide recommendations for where efforts might usefully be focused in future attempts to integrate models of biophysical and socioeconomic processes, based on the limitations of our coupled system.

  19. OpenLabNotes

    DEFF Research Database (Denmark)

    List, Markus; Franz, Michael; Tan, Qihua;

    2015-01-01

    Framework, a powerful and flexible laboratory information management system. In contrast to comparable solutions, it allows to protect the intellectual property of its users by offering data protection with digital signatures. OpenLabNotes effectively Closes the gap between research documentation and sample management...... be advantageous if an ELN was Integrated with a laboratory information management system to allow for a comprehensive documentation of experimental work including the location of samples that were used in a particular experiment. Here, we present OpenLabNotes, which adds state-of-the-art ELN capabilities to OpenLab......, thus making Open-Lab Framework more attractive for laboratories that seek to increase productivity through electronic data management....

  20. Deciphering Your Lab Report

    Science.gov (United States)

    Advertisement Proceeds from website advertising help sustain Lab Tests Online. AACC is a not-for-profit organization and does not endorse non-AACC products and services. Advertising & Sponsorship: Policy | Opportunities PLEASE NOTE: Your web browser ...

  1. Advanced Lab Consortium ``Conspiracy''

    Science.gov (United States)

    Reichert, Jonathan F.

    2006-03-01

    Advanced Laboratory instruction is a time-honored and essential element of an undergraduate physics education. But, from my vantage point, it has been neglected by the two major professional societies, APS and AAPT. At some schools, it has been replaced by ``research experiences,'' but I contend that very few of these experiences in the research lab, particularly in the junior year, deliver what they promise. It is time to focus the attention of APS, AAPT, and the NSF on the advanced lab. We need to create an Advanced Lab Consortium (ALC) of faculty and staff to share experiments, suppliers, materials, pedagogy, ideas, in short to build a professional network for those committed to advanced lab instruction. The AAPT is currently in serious discussions on this topic and my company stands ready with both financial and personnel resources to support the effort. This talk is a plea for co-conspirators.

  2. The Udall Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Udall lab is interested in genome evolution and cotton genomics.The cotton genus ( Gossypium) is an extraordinarily diverse group with approximately 50 species...

  3. Virtual labs: a substitute for traditional labs?

    Science.gov (United States)

    Scheckler, Rebecca K

    2003-01-01

    Current technologies give us the ability to enhance and replace developmental biology classes with computer-based resources, often called virtual labs. In the process of using these resources, teachers may be tempted to neglect the simpler technologies and lab bench activities, which can be labor intensive. In this paper, I take a critical look at the role of computer-based materials for the teaching of developmental biology in order to aid teachers in assessing their value. I conclude that while digital tools have value, they should not replace all of the traditional laboratory activities. Clearly, both computer-enhanced activities and traditional labs must be included in laboratory exercises. Reliance on only one or the other is inappropriate. In order to determine when it is appropriate to use a particular educational tool, the goals of the course and the needs of biology students for an education that gives them a realistic and engaged view of biology must be understood. In this paper, I dispel some of the myths of computer tools and give specific guidelines for assessing their usage, taking into account the special needs of a developmental biology class and the difficulties of observing all the developmental stages of subject organisms in the timescale of class meetings. PMID:12705675

  4. Biophysics of Magnetic Orientation: Radical Pairs, Biogenic Magnetite, or both?

    Science.gov (United States)

    Kirschvink, Joe

    2011-03-01

    Two major biophysical mechanisms for magnetoreception in terrestrial animals, one based on biogenic magnetite and another on radical-pair biochemical reactions, have been the subject of experiment and debate for the past 30 years. The magnetite hypothesis has stood the test of time: biogenic magnetite is synthesized biochemically in Bacteria, Protists, and numerous Animal phyla, as well as in some plants. Chains of single-domain crystals have been detected by clean-lab based SQUID magnetometry in animal tissues in all major phyla, followed by high-resolution TEM in selected model organisms, as well as by electrophysiological studies demonstrating the role of the ophthalmic branch of the trigeminal nerve in the magnetoreceptive process. Pulse-remagnetization - configured to uniquely flip the polarity of single-domain ferromagnets - has dramatic effects on the behavior of many birds, honeybees, mole rats, turtles, and bats, to cite a growing list. Magnetite-containing cells in the vicinity of these neurons in fish are now the subject of intense study by our consortium. The existence of a specialized class of magnetite-containing magnetoreceptor cells in animal tissues is no longer controversial. In contrast, less success has been achieved in gaining experimental support across a range of taxa for the radical-pair hypothesis. Although this mechanism was proposed to explain an early observation that birds would not respond to complete inversion of the magnetic vector, many organisms (even some birds) do indeed respond to the field polarity. We also note that few, if any, of these critical experiments have been done using fully double-blind methods. This is joint work with: M. M. Walker (University of Auckland, New Zealand) and M. Winklhofer (LMU Munich, Germany).

  5. Testing the Simple Biosphere model (SiB) using point micrometeorological and biophysical data

    Science.gov (United States)

    Sellers, P. J.; Dorman, J. L.

    1987-01-01

    The suitability of the Simple Biosphere (SiB) model of Sellers et al. (1986) for calculation of the surface fluxes for use within general circulation models is assessed. The structure of the SiB model is described, and its performance is evaluated in terms of its ability to realistically and accurately simulate biophysical processes over a number of test sites, including Ruthe (Germany), South Carolina (U.S.), and Central Wales (UK), for which point biophysical and micrometeorological data were available. The model produced simulations of the energy balances of barley, wheat, maize, and Norway Spruce sites over periods ranging from 1 to 40 days. Generally, it was found that the model reproduced time series of latent, sensible, and ground-heat fluxes and surface radiative temperature comparable with the available data.

  6. Exploring the Impact of TeachME™ Lab Virtual Classroom Teaching Simulation on Early Childhood Education Majors' Self-Efficacy Beliefs

    Science.gov (United States)

    Bautista, Nazan Uludag; Boone, William J.

    2015-04-01

    The purpose of this study was to investigate the impact of a mixed-reality teaching environment, called TeachME™ Lab (TML), on early childhood education majors' science teaching self-efficacy beliefs. Sixty-two preservice early childhood teachers participated in the study. Analysis of the quantitative (STEBI-b) and qualitative (journal entries) data revealed that personal science teaching efficacy and science teaching outcome expectancy beliefs increased significantly after one semester of participation in TML. Three key factors impacted preservice teachers' (PST) self-efficacy beliefs in the context of participation in TML: PSTs' perceptions of their science content knowledge, their familiarity with TML technology and avatars, and being observed by peers. Cognitive pedagogical mastery (TML practices), effective/actual modeling, cognitive self-modeling, and emotional arousal were the primary sources that increased the PSTs' perceived self-efficacy beliefs. Overall, the results of this study suggest that the TML is a worthwhile technology for learning to teach in teacher education. It provides a way for PSTs to have a highly personalized learning experience that enables them to improve their understanding and confidence related to teaching science, so that ideally someday they may translate such an experience into their classroom practices.

  7. Biophysical and structural considerations for protein sequence evolution

    Directory of Open Access Journals (Sweden)

    Grahnen Johan A

    2011-12-01

    Full Text Available Abstract Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.

  8. Surface-Enhanced Raman Scattering and Biophysics

    Science.gov (United States)

    Kneipp, Katrin

    2001-03-01

    Surface-enhanced Raman scattering (SERS) is a phenomenon resulting in strongly increased Raman signals from molecules which have been attached to metallic nanostructures such as colloidal silver or gold particles. The effect combines the structural information content of a vibrational spectroscopy with extremely high sensitivity and in some cases, it showes promise in overcoming the low-sensitivity problems inherent in Raman spectroscopy. Cross sections effective in SERS can reach 10 16 to 10 15 cm2 per molecule corresponding to enhancement factors of about fourteen orders of magnitude compared with “normal” non-resonant Raman scattering. Such extremely large cross sections are sufficient for single molecule Raman spectroscopy. The high sensitivity and particularly the single molecule capabilities open up exciting perspectives for SERS as tool for basic research in biophysics, biochemistry and in laboratory medicine, where it allows to study extremely small amounts of biolomedically relevant molecules in order to understand development of diseases, treatment and therapy control based on molecular structural information at the single molecule level. The most spectacular applications might appear in rapidly spectroscopic characterization of specific DNA fragments down to structurally sensitive detection of single bases in order to elucidate the human genome sequence without any labeling technology. I will briefly introduce the SERS effect and report experiments with Raman scattering of single molecules. Potential and limitations of surface-enhanced Raman techniques as a tool in biophysics and biomedical spectroscopy will be considered.

  9. Modeling the effects of noninvasive transcranial brain stimulation at the biophysical, network, and cognitive Level

    DEFF Research Database (Denmark)

    Hartwigsen, Gesa; Bergmann, Til Ole; Herz, Damian Marc;

    2015-01-01

    these approaches advance the scientific potential of NTBS as an interventional tool in cognitive neuroscience. (i) Leveraging the anatomical information provided by structural imaging, the electric field distribution in the brain can be modeled and simulated. Biophysical modeling approaches generate testable...... predictions regarding the impact of interindividual variations in cortical anatomy on the injected electric fields or the influence of the orientation of current flow on the physiological stimulation effects. (ii) Functional brain mapping of the spatiotemporal neural dynamics during cognitive tasks can...

  10. Lab Attendance and Academic Performance

    OpenAIRE

    Kirk Adair; Swinton, Omari H

    2012-01-01

    The benefits from attendance of lectures have been established in the literature. This paper focuses on attendance not of the lecture, but of smaller labs. These labs are 50 minutes one-day-a-week sessions to emphasis material covered during lecture. Using a 200-student Principles of Economics class that covers microeconomics with six different labs, we investigate the effect of lab attendance on exam performance by taking into account individual characteristics. We find that lab attendance b...

  11. Lessons from an α-Helical Membrane Enzyme: Expression, Purification, and Detergent Optimization for Biophysical and Structural Characterization.

    Science.gov (United States)

    Johnson, Jennifer L; Kalyoncu, Sibel; Lieberman, Raquel L

    2016-01-01

    This chapter outlines the protocol developed in our lab to produce a multipass α-helical membrane protein. We present our work flow, from ortholog selection to protein purification, including molecular biology for plasmid construction, protein expression in E. coli, membrane isolation and detergent solubilization, protein purification and tag removal, biophysical assessment of protein stability in different detergents, and detergent concentration determination using thin-layer chromatography. We focus on results from our ongoing work with intramembrane aspartyl proteases from archaeal organisms. PMID:27485343

  12. Application of biophysical technologies in dental research

    Science.gov (United States)

    Higham, Susan M.; Pender, Neil; de Josselin de Jong, Elbert; Smith, Philip W.

    2009-05-01

    There is a wealth of evidence to indicate that if dental caries can be recognized at an early stage, it is possible to halt its progression or even reverse it. This has led to an increased interest in the development of diagnostic techniques capable of visualizing caries at an early stage in addition to providing clinicians with an aid to diagnosis. Several techniques are available for research and clinical applications for detecting early demineralization. This manuscript has reviewed some of the techniques currently available to determine their advantages, whether they have any limitations and their applicability to dental research and clinical dentistry. Not one method is the perfect choice in all situations, but what is clear is that the development and application of biophysical technologies have allowed major advances to be made in dental research as well as in clinical dentistry. With continued developments these technologies will play an important role in the future management of dental disease.

  13. [Biophysical Characterization of Biopharmaceuticals, Including Antibody Drugs].

    Science.gov (United States)

    Uchiyama, Susumu

    2016-01-01

    Biopharmaceuticals, including antibody drugs, are now popular because of their high specificity with low adverse effects, especially in the treatment of cancer and autoimmune diseases. However, because the active pharmaceutical ingredients of biopharmaceuticals are proteins, biophysical characterization of these therapeutic proteins should be required. In this manuscript, methods of chemical and physical characterization of therapeutic proteins are described. In terms of chemical characterization, analysis of chemical modifications of the constituent amino acids is explained. Physical characterization includes higher order structural analysis and assessment of protein aggregates. Quantification methods of aggregates with different sizes, recently encouraged by the U.S. Food and Drug Administration (FDA), are introduced. As for the stability of therapeutic proteins, the importance of chemical and physical stability is explained. Finally, the contribution of colloidal and structural stability to the production of an antibody drug less prone to aggregation is introduced.

  14. Biophysics of NASA radiation quality factors

    International Nuclear Information System (INIS)

    NASA has implemented new radiation quality factors (QFs) for projecting cancer risks from space radiation exposures to astronauts. The NASA QFs are based on particle track structure concepts with parameters derived from available radiobiology data, and NASA introduces distinct QFs for solid cancer and leukaemia risk estimates. The NASA model was reviewed by the US National Research Council and approved for use by NASA for risk assessment for International Space Station missions and trade studies of future exploration missions to Mars and other destinations. A key feature of the NASA QFs is to represent the uncertainty in the QF assessments and evaluate the importance of the QF uncertainty to overall uncertainties in cancer risk projections. In this article, the biophysical basis for the probability distribution functions representing QF uncertainties was reviewed, and approaches needed to reduce uncertainties were discussed. (author)

  15. CDC Lab Values

    Centers for Disease Control (CDC) Podcasts

    2015-02-02

    More than fifteen hundred scientists fill the lab benches at CDC, logging more than four million hours each year. CDC’s laboratories play a critical role in the agency’s ability to find, stop, and prevent disease outbreaks. This podcast provides a brief overview of what goes on inside CDC’s labs, and why this work makes a difference in American’s health.  Created: 2/2/2015 by Office of the Associate Director for Communication (OADC).   Date Released: 2/2/2015.

  16. The NOAO Data Lab

    Science.gov (United States)

    Fitzpatrick, M.; Olsen, K.; Stobie, E. B.; Mighell, K. J.; Norris, P.

    2015-09-01

    We describe the NOAO Data Lab to help community users take advantage of current large surveys and prepare them even larger surveys in the era of LSST. The Data Lab will allow users to efficiently utilize catalogs of billions of objects, combine traditional telescope image and spectral data with external archives, share custom results with collaborators, publish data products to other users, and experiment with analysis toolkits. Specific science cases will be used to develop a prototype framework and tools, allowing us to work directly with scientists from survey teams to ensure development remains focused on scientifically productive tasks.

  17. Simulation and Implementation of Typical Optical Path Adjustments Involved in an Optical Virtual Lab%光学虚拟实验室中典型光路调试的仿真实现

    Institute of Scientific and Technical Information of China (English)

    林远芳; 李拓宇; 郑晓东; 刘旭; 刘向东

    2011-01-01

    在Visual Studio 2005下,将面向对象的方法应用于虚拟器材建模,基于C用程序以仿真各种实验场景和实验状态.通过操作鼠标和键盘,可以进行使激光光束平行于工作台面、使激光光束的主光线通过透镜光学面中心、使针孔位于扩束镜后焦点处,基于剪切干涉法使透过准直透镜的激光为平行光、使光栅光谱仪中的光栅位于与光轴垂直的平面内并且栅线平行于狭缝5种典型光路的交互式实时虚拟调试.这种所见即所得的虚拟实验方式无需真实实验设备支撑,有助于增强感性认识,加深对光学基础理论的理解.%To avoid the limits of traditional optical real lab on the opening, hours, space and equipments, an object oriented approach was applied to the modeling of virtual equipments and the simulation of various experimental scenes and status were realized through developing of "event driven" applications based on C# language in Visual Studio 2005.Real-time interactive virtual adjustments of optical paths which include adjusting the laser beam to be parallel to the work platform ,adjusting the chief ray of the laser beam to go through the center of the lens optical surface, adjusting the pinhole to position in the focus of the extender lens,adjusting the collimating lens based on shearing interferometry to get collimated laser beam, adjusting the grating in spectrometer to locate in the plane perpendicular to the optical axis and the grating line to be parallel to the slit, could be simulated through operations of the mouse and keyboard. This WYSIWYG way of virtual experiment needs no real experimental equipment support, can realize concept of "if users can' t come to the lab…, the lab without walls will come to users!", is helpful to enhance perceptual knowledge and deepen the understanding of the optical basic theory.

  18. A Big Bang Lab

    Science.gov (United States)

    Scheider, Walter

    2005-01-01

    The February 2005 issue of The Science Teacher (TST) reminded everyone that by learning how scientists study stars, students gain an understanding of how science measures things that can not be set up in lab, either because they are too big, too far away, or happened in a very distant past. The authors of "How Far are the Stars?" show how the…

  19. Elemental Chem Lab

    Science.gov (United States)

    Franco Mariscal, Antonio Joaquin

    2008-01-01

    This educative material uses the symbols of 45 elements to spell the names of 32 types of laboratory equipment usually found in chemical labs. This teaching material has been divided into three puzzles according to the type of the laboratory equipment: (i) glassware as reaction vessels or containers; (ii) glassware for measuring, addition or…

  20. Skills Labs: workshop EMERGO toolkit

    NARCIS (Netherlands)

    Kurvers, Hub; Slootmaker, Aad

    2009-01-01

    Kurvers, H. J., & Slootmaker, A. (2009). Skills Labs: workshop EMERGO toolkit. Presentation given at project members of Skills Labs. March, 31, 2009 and April, 24, 2009, Heerlen, The Netherlands: Open University of the Netherlands.

  1. Bridging the gap : with a new CHOPS simulation model leading the way, the Alberta Research Council is helping close the gap between the lab and the field

    Energy Technology Data Exchange (ETDEWEB)

    Collison, M.

    2007-04-15

    Heavy oil is more difficult and costly to produce and refine than conventional light oil. Almost 50 per cent of the oil currently produced in Canada is classified as heavy oil. This article provided details of a heavy oil technology pilot project conducted by the Alberta Research Council (ARC) and Husky Energy. The ARC has now formed a steering committee of industry members to analyze new technologies and find ways to implement them. As part of their technology program, ARC hired, trained and placed an engineer with Husky Energy to execute a field application at Lloydminster of a heavy oil reservoir simulation software program. The biggest barrier to production in the Lloydminster play is the sand mixed throughout the viscous oil. In order to address the problem, Husky has spent 20 years developing a process known as cold heavy oil production with sand (CHOPS). The process employs a cavity pump which can tolerate extremely large amounts of sand in viscous oil. The pump has a corkscrew metal rotor placed inside a rubber covering, which rotates and pumps up the heavy oil, sand, natural gas, and water. The sand and oil are pumped into huge settling tanks which are heated by the natural gas that is stripped out of the oil. The sand sinks out the warm floating oil and settles in the tanks. Although it is very difficult to model a situation where sand flows from the reservoir along with the oil, ARC has developed a model of the process using data collected by Husky throughout its use of the CHOPS technique. A number of wells have been successfully modelled using the simulation tool. It was concluded that use of the CHOPS model has allowed researchers to test different operating strategies and extrapolate them to the field to predict possible oil production for various heavy oil recovery processes. 1 fig.

  2. Rhizosphere biophysics and root water uptake

    Science.gov (United States)

    Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

    2016-04-01

    The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its

  3. An Integrated Biogeochemical and Biophysical Analysis of Bioenergy Crops

    Science.gov (United States)

    Liang, M.; Song, Y.; Barman, R.; Jain, A. K.

    2010-12-01

    Bioenergy crops are becoming increasingly important with growing concerns about the energy demand and climate change and the need to replace fossil fuels with carbon-neutral renewable sources of energy. The transition to a biofuel-based energy supply raises many questions such as: how and where to grow energy crops, what will be the impacts of growing large scale biofuel crops on climate system, the hydrological cycle and soil biogeochemistry. We are developing and applying an integrated system modeling framework to investigate the biophysical, physiological, and biogeochemical systems governing important processes that regulate crop growth such as water, energy and nutrient cycles. The framework has a two-big-leaf canopy scheme for photosynthesis, stomatal conductance, leaf temperature and energy fluxes. The soil/snow hydrology consists of 10 layers for soil and up to 5 layers for snow. The biogeochemistry component explicitly accounts for coupled carbon and nitrogen dynamics. The feedstocks currently considered include corn stover, Miscanthus and switchgrass. The parameters used for simulation of each crop have been calibrated using field experimental data from the US. The use of this modeling capability will be demonstrated through its applications to study the environmental effects (through changes in albedo and evapotranspiration) of biofuel production as well as the effective management practice in the United States.

  4. A biophysical understanding of the applications and implications of nanomaterials

    Science.gov (United States)

    Geitner, Nicholas K.

    The last few decades have seen an explosion in the study and application of nanomaterials that continues to grow at a dizzying pace. Despite exciting applications in nano-enabled electronics, materials, medicine, and environmental remediation, an understanding of the interactions of these materials with natural materials and systems and the resulting implications lags severely behind. The purpose of this dissertation is to illuminate these interactions as well as develop novel environmental applications from a biophysical perspective. Following an introduction and literature review in Chapter 1, Chapters 2-4 will explore the application of dendritic polymers as novel and biocompatible oil dispersants for more environmentally conscious response to catastrophic oil spills. Chapter 2 will serve as a proof-of-concept, exploring the interactions between two model dendritic polymers and two model oil hydrocarbons. Next, the biocompatibility of these nanoscale dispersing agents is addressed in Chapter 3, using a soil amoeba as the primary model organism with emphasis on the mechanisms of any observed toxicity. Finally, in an effort to minimize cationic charge-induced cytotoxicity, the cationic terminal functional groups of poly(amidoamine) (PAMAM) dendrimers are replaced with either anionic or neutral functional groups. The resulting changes in structure and oil-dispersing function of the original and modified dendrimers are then investigated. Chapter 5 details a study of the applications and implications of graphene derivatives. Specifically, the environmental persistence of graphene and graphene oxide are assessed by studying their interactions with natural amphiphiles using synergistic experiments and molecular dynamics simulations. The application of graphene oxide for the removal of polyaromatic hydrocarbons from aquatic systems is also investigated and compared to the efficacy of PAMAM dendrimers in the same application. Finally, Chapter 6 explores the interactions

  5. Contribution to researches in biophysics and biology

    International Nuclear Information System (INIS)

    In this accreditation to supervise research, the author indicates its curriculum and scientific works which mainly dealt with the different agents used in chemotherapy. Scientific works addressed anti-carcinogenic pharmacology, applied biophysics, and researches in oncology and radiobiology. Current research projects deal with mechanisms of cellular transformation and the implication of the anti-oxidising metabolism and of nucleotide metabolism in cell radio-sensitivity. Teaching and research supervising activities are also indicated. Several articles are proposed in appendix: Average quality factor and dose equivalent meter based on microdosimetry techniques; Activity of thymidylate synthetase, thymidine kinase and galactokinase in primary and xenografted human colorectal cancers in relation to their chromosomal patterns; Nucleotide metabolism in human gliomas, relation to the chromosomal profile; Pyrimidine nucleotide metabolism in human colon carcinomas: comparison of normal tissues, primary tumors and xenografts; Modifications of the antioxidant metabolism during proliferation and differentiation of colon tumours cell lines; Modulation of the antioxidant enzymes, p21 and p53 expression during proliferation and differentiation of human melanoma cell lines; Purine metabolism in 2 human melanoma cell lines, relation with proliferation and differentiation; Radiation-induced changes in nucleotide metabolism of 2 colon cancer cell lines with different radio-sensitivities

  6. Review of FEWS NET Biophysical Monitoring Requirements

    Science.gov (United States)

    Ross, K. W.; Brown, Molly E.; Verdin, J.; Underwood, L. W.

    2009-01-01

    The Famine Early Warning System Network (FEWS NET) provides monitoring and early warning support to decision makers responsible for responding to famine and food insecurity. FEWS NET transforms satellite remote sensing data into rainfall and vegetation information that can be used by these decision makers. The National Aeronautics and Space Administration has recently funded activities to enhance remote sensing inputs to FEWS NET. To elicit Earth observation requirements, a professional review questionnaire was disseminated to FEWS NET expert end-users: it focused upon operational requirements to determine additional useful remote sensing data and; subsequently, beneficial FEWS NET biophysical supplementary inputs. The review was completed by over 40 experts from around the world, enabling a robust set of professional perspectives to be gathered and analyzed rapidly. Reviewers were asked to evaluate the relative importance of environmental variables and spatio-temporal requirements for Earth science data products, in particular for rainfall and vegetation products. The results showed that spatio-temporal resolution requirements are complex and need to vary according to place, time, and hazard: that high resolution remote sensing products continue to be in demand, and that rainfall and vegetation products were valued as data that provide actionable food security information.

  7. Biophysical and biomathematical adventures in radiobiology

    International Nuclear Information System (INIS)

    Highlights of my biophysical and biomathematical adventures in radiobiology is presented. Early adventures involved developing ''state-vector models'' for specific harmful effects (cell killing, life shortening) of exposure to radiation. More recent adventures led to developing ''hazard-function models'' for predicting biological effects (e.g., cell killing, mutations, tumor induction) of combined exposure to different toxicants. Hazard-function models were also developed for predicting harm to man from exposure to large radiation doses. Major conclusions derived from the modeling adventures are as follows: (1) synergistic effects of different genotoxic agents should not occur at low doses; (2) for exposure of the lung or bone marrow to large doses of photon radiation, low rates of exposure should be better tolerated than high rates; and (3) for some types of radiation (e.g., alpha particles and fission neutrons), moderate doses delivered at a low rate may be more harmful than the same dose given at a high rate. 53 refs., 7 figs

  8. Biophysically realistic minimal model of dopamine neuron

    Science.gov (United States)

    Oprisan, Sorinel

    2008-03-01

    We proposed and studied a new biophysically relevant computational model of dopaminergic neurons. Midbrain dopamine neurons are involved in motivation and the control of movement, and have been implicated in various pathologies such as Parkinson's disease, schizophrenia, and drug abuse. The model we developed is a single-compartment Hodgkin-Huxley (HH)-type parallel conductance membrane model. The model captures the essential mechanisms underlying the slow oscillatory potentials and plateau potential oscillations. The main currents involved are: 1) a voltage-dependent fast calcium current, 2) a small conductance potassium current that is modulated by the cytosolic concentration of calcium, and 3) a slow voltage-activated potassium current. We developed multidimensional bifurcation diagrams and extracted the effective domains of sustained oscillations. The model includes a calcium balance due to the fundamental importance of calcium influx as proved by simultaneous electrophysiological and calcium imaging procedure. Although there are significant evidences to suggest a partially electrogenic calcium pump, all previous models considered only elecrtogenic pumps. We investigated the effect of the electrogenic calcium pump on the bifurcation diagram of the model and compared our findings against the experimental results.

  9. Brain Mapping Center Opens at Institute of Biophysics

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ Agroup of world-class scie, ntists in brain imaging came to China's capital to .witness the inauguration of the Beijing MRI Center for Brain Research, which was officially opened on May 25 at the CAS Institute of Biophysics.

  10. Developing spatial biophysical accounting for multiple ecosystem services

    NARCIS (Netherlands)

    Remme, R.P.; Schroter, M.; Hein, L.G.

    2014-01-01

    Ecosystem accounting is receiving increasing interest as a way to systematically monitor the conditions of ecosystems and the ecosystem services they provide. A critical element of ecosystem accounting is understanding spatially explicit flows of ecosystem services. We developed spatial biophysical

  11. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop “From Computational Biophysics to Systems Biology (CBSB12)” which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  12. Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  13. Signatures of protein biophysics in coding sequence evolution

    OpenAIRE

    Wilke, Claus O; Drummond, D Allan

    2010-01-01

    Since the early days of molecular evolution, the conventional wisdom has been that the evolution of protein-coding genes is primarily determined by functional constraints. Yet recent evidence indicates that the evolution of these genes is strongly shaped by the biophysical processes of protein synthesis, protein folding, and specific as well as non-specific protein–protein interactions. Selection pressures related to these biophysical processes affect primarily the amino-acid sequence of gene...

  14. Biophysics of Human Hair Structural, Nanomechanical, and Nanotribological Studies

    CERN Document Server

    Bhushan, Bharat

    2010-01-01

    This book presents the biophysics of hair. It deals with the structure of hair, its mechanical properties, the nanomechanical characterization, tensile deformation, tribological characterization, the thickness distribution and binding interactions on hair surface. Another important topic of the book is the health of hair, human hair and skin, hair care, cleaning and conditioning treatments and damaging processes. It is the first book on the biophysical properties of hair.

  15. Characterising the biophysical properties of normal and hyperkeratotic foot skin

    OpenAIRE

    Hashmi, Farina; Nester, Christopher; Wright, Ciaran; Newton, Veronica; Lam, Sharon

    2015-01-01

    Background Plantar foot skin exhibits unique biophysical properties that are distinct from skin on other areas of the body. This paper characterises, using non-invasive methods, the biophysical properties of foot skin in healthy and pathological states including xerosis, heel fissures, calluses and corns. Methods Ninety three people participated. Skin hydration, elasticity, collagen and elastin fibre organisation and surface texture was measured from plantar calluses, corns, fissured heel ski...

  16. The relationship between fetal biophysical profile and cord blood PH

    Directory of Open Access Journals (Sweden)

    Valadan M

    2009-02-01

    Full Text Available "nBackground: The Biophysical Profile (BPP is a noninvasive test that predicts the presence or absence of fetal asphyxia and, ultimately, the risk of fetal death in the antenatal period. Intervention on the basis of an abnormal biophysical profile result has been reported to yield a significant reduction in prenatal mortality, and an association exists between biophysical profile scoring and a decreased cerebral palsy rate in a given population. The BPP evaluates five characteristics: fetal movement, tone, breathing, heart reactivity, and amniotic fluid (AF volume estimation. The purpose of study was to determine whether there are different degree of acidosis at which the biophysical activity (acute marker are affected. "nMethods: In a prospective study of 140 patients undergoing cesarean section before onset of labor, the fetal biophysical profile was performed 24h before the time of cesarean and was matched with cord arterial PH that was obtained from a cord segment (10-20cm that was double clamped after delivery of newborn. (using cord arterial PH less than 7.20 for the diagnosis of acidosis. "nResults: The fetal biophysical profile was found to have a significant relationship with umbilical blood PH. The sensitivity, specificity, positive predictive value, negative predictive value of fetal biophysical profile score were: 88.9%, 88.6%, 50%, 98.1%. "nConclusion: The first manifestations of fetal acidosis are nonreactive nonstress testing and fetal breathing loss; in advanced acidemia fetal movements and fetal tone are compromised. A protocol of antepartum fetal evaluation is suggested based upon the individual biophysical components rather than the score alone.

  17. Do frogs have to croak? Comparing academic performance of students in traditional dissection labs on campus with students using virtual simulations via distance education

    Science.gov (United States)

    Humphries, Susie Annette

    This quantitative study was designed to determine whether there were any significant differences in students and their understanding of animal anatomy and basic physiology in introductory biology and anatomy courses when instructed using self-directed, virtual simulation dissections in a distance-learning format rather than by teacher-directed, hands-on dissections in traditional on-campus classes. Two different courses at Snead State Community College, a small, rural 2-year institution in north Alabama, participated in this study. Principles of Biology II (BIO 104) was a course taken by students not planning a career in a health field, while Human Anatomy and Physiology I (BIO 201) was a course designed for students who plan to pursue a health-related degree. A total of 44 students participated in the online versions of their respective anatomy courses, 11 in BIO 104 and 33 in BIO 201, whereas a total of 132 students participated in the on-campus versions of their anatomy courses, 28 in BIO 104 and 104 in BIO 201. At the outset of their anatomy courses, all participants were given a presurvey to obtain basic demographics and background information used in the final analyses. A pretest/posttest laboratory practicum evaluation was used to determine students' academic performance in their anatomy courses over a semester. The results indicated that for the BIO 104 students there were no significant differences between those students taking the course online and those taking the course on campus. The BIO 201 students, on the other hand, did indicate a significant difference in the overall academic performance on their laboratory practicums, with the on-campus students achieving statistically higher than the online students. However, it is important to note that the BIO 104 students were not taking their exams as a part of their course grade as were the BIO 201 students. It was also ascertained through this study that students with prior online experience and/or with

  18. Modeling crop water use in an irrigated maize cropland using a biophysical process-based model

    Science.gov (United States)

    Ding, Risheng; Kang, Shaozhong; Du, Taisheng; Hao, Xinmei; Tong, Ling

    2015-10-01

    Accurate modeling of crop water use or evapotranspiration (ET) is needed to understand the hydrologic cycle and improve water use efficiency. Biophysical process-based multilayer models can capture details of the nonlinear interaction between microclimate and physiology within the canopy and thus accurately simulate ET. In this study, we extended a process-based multilayer model, ACASA, which explicitly simulated many of the nonlinear biophysical processes within each of ten crop canopy sublayers and then integrated to represent the complete crop canopy. Based on the original ACASA model, we made the improved modifications including four added modules (C4 crop photosynthesis, water stress response of stomatal conductance, crop morphological changes, and heterogeneous root water uptake), and two adjusted calculation procedures (soil evaporation resistance and hydraulic characteristic parameters). Key processes were parameterized for the improved ACASA model using observations. The simulated canopy ET was validated using eddy covariance measurements over an irrigated maize field in an arid inland region of northwest China. The improved ACASA model predicted maize ET for both half-hourly and daily time-scales. The improved model also predicted the reduction in maize ET under the condition of soil water deficit. Soil evaporation, an important component of maize ET, was also satisfactorily simulated in the improved model. Compared to the original ACASA model, the improved model yielded an improved estimation of maize ET. Using the improved model, we found that maize ET was nonlinearly affected by changes in leaf area index and photosynthetic capacity through canopy conductance. In general, the improved ACASA model, a biophysical process-based multilayer model, can be used to diagnose and predict crop ET, and draw some insights into the nonlinear interactions between crop canopy and ambient environment.

  19. Archimedes Remote Lab for Secondary Schools

    NARCIS (Netherlands)

    Garcia Zubia, J.; Angulo Martinez, I.; Martinez Pieper, G.; Lopez de Ipina Gonzalez de Artaza, D.; Hernandez Jayo, U.; Orduna Fernandez, P.; Dziabenko, O.; Rodriguez Gil, L.; Riesen, van S.A.N.; Anjewierden, A.A.; Kamp, E.; Jong, de A.J.M.

    2015-01-01

    This paper presents a remote lab designed for teaching the Archimedes’ principle to secondary school students, as well as an online virtual lab on the general domain of buoyancy. The Archimedes remote lab is integrated into WebLab-Deusto. Both labs are promoted for usage in frame of the Go-Lab Europ

  20. Estimation efficiency of usage satellite derived and modelled biophysical products for yield forecasting

    Science.gov (United States)

    Kolotii, Andrii; Kussul, Nataliia; Skakun, Sergii; Shelestov, Andrii; Ostapenko, Vadim; Oliinyk, Tamara

    2015-04-01

    Efficient and timely crop monitoring and yield forecasting are important tasks for ensuring of stability and sustainable economic development [1]. As winter crops pay prominent role in agriculture of Ukraine - the main focus of this study is concentrated on winter wheat. In our previous research [2, 3] it was shown that usage of biophysical parameters of crops such as FAPAR (derived from Geoland-2 portal as for SPOT Vegetation data) is far more efficient for crop yield forecasting to NDVI derived from MODIS data - for available data. In our current work efficiency of usage such biophysical parameters as LAI, FAPAR, FCOVER (derived from SPOT Vegetation and PROBA-V data at resolution of 1 km and simulated within WOFOST model) and NDVI product (derived from MODIS) for winter wheat monitoring and yield forecasting is estimated. As the part of crop monitoring workflow (vegetation anomaly detection, vegetation indexes and products analysis) and yield forecasting SPIRITS tool developed by JRC is used. Statistics extraction is done for landcover maps created in SRI within FP-7 SIGMA project. Efficiency of usage satellite based and modelled with WOFOST model biophysical products is estimated. [1] N. Kussul, S. Skakun, A. Shelestov, O. Kussul, "Sensor Web approach to Flood Monitoring and Risk Assessment", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 815-818. [2] F. Kogan, N. Kussul, T. Adamenko, S. Skakun, O. Kravchenko, O. Kryvobok, A. Shelestov, A. Kolotii, O. Kussul, and A. Lavrenyuk, "Winter wheat yield forecasting in Ukraine based on Earth observation, meteorological data and biophysical models," International Journal of Applied Earth Observation and Geoinformation, vol. 23, pp. 192-203, 2013. [3] Kussul O., Kussul N., Skakun S., Kravchenko O., Shelestov A., Kolotii A, "Assessment of relative efficiency of using MODIS data to winter wheat yield forecasting in Ukraine", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 3235 - 3238.

  1. Interactive, Online, Adsorption Lab to Support Discovery of the Scientific Process

    Science.gov (United States)

    Carroll, K. C.; Ulery, A. L.; Chamberlin, B.; Dettmer, A.

    2014-12-01

    Science students require more than methods practice in lab activities; they must gain an understanding of the application of the scientific process through lab work. Large classes, time constraints, and funding may limit student access to science labs, denying students access to the types of experiential learning needed to motivate and develop new scientists. Interactive, discovery-based computer simulations and virtual labs provide an alternative, low-risk opportunity for learners to engage in lab processes and activities. Students can conduct experiments, collect data, draw conclusions, and even abort a session. We have developed an online virtual lab, through which students can interactively develop as scientists as they learn about scientific concepts, lab equipment, and proper lab techniques. Our first lab topic is adsorption of chemicals to soil, but the methodology is transferrable to other topics. In addition to learning the specific procedures involved in each lab, the online activities will prompt exploration and practice in key scientific and mathematical concepts, such as unit conversion, significant digits, assessing risks, evaluating bias, and assessing quantity and quality of data. These labs are not designed to replace traditional lab instruction, but to supplement instruction on challenging or particularly time-consuming concepts. To complement classroom instruction, students can engage in a lab experience outside the lab and over a shorter time period than often required with real-world adsorption studies. More importantly, students can reflect, discuss, review, and even fail at their lab experience as part of the process to see why natural processes and scientific approaches work the way they do. Our Media Productions team has completed a series of online digital labs available at virtuallabs.nmsu.edu and scienceofsoil.com, and these virtual labs are being integrated into coursework to evaluate changes in student learning.

  2. Optimize Sedimentation Tank and Lab Flocculation Unit by CFD

    OpenAIRE

    Zhang, Duo

    2014-01-01

    This work aim at introduce basic knowledge of CFD and it’s application in optimization of sedimentation tank and lab flocculation units. A series of specialized strategies are developed for the simulation of the sedimentation tanks and lab flocculation units. Chapter 1 is general introduction of particle removal in water and wastewater treatment, includes particle separation, as well as particle removal during chemical treatment and biological treatment. In chapter 2, background and appli...

  3. Human Engineering Modeling and Performance Lab Study Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J.

    2014-01-01

    The HEMAP (Human Engineering Modeling and Performance) Lab is a joint effort between the Industrial and Human Engineering group and the KAVE (Kennedy Advanced Visualiations Environment) group. The lab consists of sixteen camera system that is used to capture human motions and operational tasks, through te use of a Velcro suit equipped with sensors, and then simulate these tasks in an ergonomic software package know as Jac, The Jack software is able to identify the potential risk hazards.

  4. e-Learning - Physics Labs

    Science.gov (United States)

    Mohottala, Hashini

    2014-03-01

    The general student population enrolled in any college level class is highly diverse. An increasing number of ``nontraditional'' students return to college and most of these students follow distance learning degree programs while engaging in their other commitments, work and family. However, those students tend to avoid taking science courses with labs, mostly because of the incapability of remotely completing the lab components in such courses. In order to address this issue, we have come across a method where introductory level physics labs can be taught remotely. In this process a lab kit with the critical lab components that can be easily accessible are conveniently packed into a box and distributed among students at the beginning of the semester. Once the students are given the apparatus they perform the experiments at home and gather data All communications with reference to the lab was done through an interactive user-friendly webpage - Wikispaces (WikiS). Students who create pages on WikiS can submit their lab write-ups, embed videos of the experiments they perform, post pictures and direct questions to the lab instructor. The students who are enrolled in the same lab can interact with each other through WikiS to discuss labs and even get assistance.

  5. Modelling Biophysical Parameters of Maize Using Landsat 8 Time Series

    Science.gov (United States)

    Dahms, Thorsten; Seissiger, Sylvia; Conrad, Christopher; Borg, Erik

    2016-06-01

    Open and free access to multi-frequent high-resolution data (e.g. Sentinel - 2) will fortify agricultural applications based on satellite data. The temporal and spatial resolution of these remote sensing datasets directly affects the applicability of remote sensing methods, for instance a robust retrieving of biophysical parameters over the entire growing season with very high geometric resolution. In this study we use machine learning methods to predict biophysical parameters, namely the fraction of absorbed photosynthetic radiation (FPAR), the leaf area index (LAI) and the chlorophyll content, from high resolution remote sensing. 30 Landsat 8 OLI scenes were available in our study region in Mecklenburg-Western Pomerania, Germany. In-situ data were weekly to bi-weekly collected on 18 maize plots throughout the summer season 2015. The study aims at an optimized prediction of biophysical parameters and the identification of the best explaining spectral bands and vegetation indices. For this purpose, we used the entire in-situ dataset from 24.03.2015 to 15.10.2015. Random forest and conditional inference forests were used because of their explicit strong exploratory and predictive character. Variable importance measures allowed for analysing the relation between the biophysical parameters with respect to the spectral response, and the performance of the two approaches over the plant stock evolvement. Classical random forest regression outreached the performance of conditional inference forests, in particular when modelling the biophysical parameters over the entire growing period. For example, modelling biophysical parameters of maize for the entire vegetation period using random forests yielded: FPAR: R² = 0.85; RMSE = 0.11; LAI: R² = 0.64; RMSE = 0.9 and chlorophyll content (SPAD): R² = 0.80; RMSE=4.9. Our results demonstrate the great potential in using machine-learning methods for the interpretation of long-term multi-frequent remote sensing datasets to model

  6. Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures.

    Science.gov (United States)

    Imoto, Sho; Kibies, Patrick; Rosin, Christopher; Winter, Roland; Kast, Stefan M; Marx, Dominik

    2016-08-01

    Biophysics under extreme conditions is the fundamental platform for scrutinizing life in unusual habitats, such as those in the deep sea or continental subsurfaces, but also for putative extraterrestrial organisms. Therefore, an important thermodynamic variable to explore is pressure. It is shown that the combination of infrared spectroscopy with simulation is an exquisite approach for unraveling the intricate pressure response of the solvation pattern of TMAO in water, which is expected to be transferable to biomolecules in their native solvent. Pressure-enhanced hydrogen bonding was found for TMAO in water. TMAO is a molecule known to stabilize proteins against pressure-induced denaturation in deep-sea organisms. PMID:27351995

  7. Inexpensive DAQ based physics labs

    Science.gov (United States)

    Lewis, Benjamin; Clark, Shane

    2015-11-01

    Quality Data Acquisition (DAQ) based physics labs can be designed using microcontrollers and very low cost sensors with minimal lab equipment. A prototype device with several sensors and documentation for a number of DAQ-based labs is showcased. The device connects to a computer through Bluetooth and uses a simple interface to control the DAQ and display real time graphs, storing the data in .txt and .xls formats. A full device including a larger number of sensors combined with software interface and detailed documentation would provide a high quality physics lab education for minimal cost, for instance in high schools lacking lab equipment or students taking online classes. An entire semester’s lab course could be conducted using a single device with a manufacturing cost of under $20.

  8. Simulations

    CERN Document Server

    Ngada, N M

    2015-01-01

    The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.

  9. Biogeochemical and biophysical climate regulation services from converting native grassland to bioenergy production in the US Midwest

    Science.gov (United States)

    Zhang, X.; Zhao, K.; Abraha, M.; Gelfand, I.; Izaurralde, R. C.; Thomson, A. M.; Hamilton, S. K.; Chen, J.; Robertson, P.; Xu, M.; Liang, X. Z.

    2015-12-01

    Land use conversion to bioenergy crops production not only alters biogeochemical cycles, but also modifies surface biophysics, such as albedo and and leaf area. These biophysical perturbations subsequently change radiation budget at land surface and land-atmosphere exchange in water and energy, and ultimately influence local/regional climate. Here, we combine long-term in situ field measurements, remote sensing observations, and regional earth system modeling to improve our understanding of changes in biophysical climate regulation services from converting native grassland to perennial bioenergy crops. In the US Midwest, albedo change as a result of cultivating native grassland for cellulosic bioenergy feedstocks could enhance the net greenhouse gases (GHGs) mitigation benefit of cellulosic bioenergy production (116.5 MgCO2 ha-1) by 20% over a time horizon of 50 years. With an integrated climate-agroecosystem model, parameterized with in situ and remote sensing data, we further demonstrate that cultivating native grassland may result in noticeable difference in simulated regional climate (e.g. precipitation, temperature, and radiation budget), highlighting the importance of additionally including biophysical climate services in evaluating land-based climate mitigation activities, such as bioenergy production.

  10. Modelling the influence of land-use changes on biophysical and biochemical interactions at regional and global scales.

    Science.gov (United States)

    Devaraju, N; Bala, G; Nemani, R

    2015-09-01

    Land-use changes since the start of the industrial era account for nearly one-third of the cumulative anthropogenic CO2 emissions. In addition to the greenhouse effect of CO2 emissions, changes in land use also affect climate via changes in surface physical properties such as albedo, evapotranspiration and roughness length. Recent modelling studies suggest that these biophysical components may be comparable with biochemical effects. In regard to climate change, the effects of these two distinct processes may counterbalance one another both regionally and, possibly, globally. In this article, through hypothetical large-scale deforestation simulations using a global climate model, we contrast the implications of afforestation on ameliorating or enhancing anthropogenic contributions from previously converted (agricultural) land surfaces. Based on our review of past studies on this subject, we conclude that the sum of both biophysical and biochemical effects should be assessed when large-scale afforestation is used for countering global warming, and the net effect on global mean temperature change depends on the location of deforestation/afforestation. Further, although biochemical effects trigger global climate change, biophysical effects often cause strong local and regional climate change. The implication of the biophysical effects for adaptation and mitigation of climate change in agriculture and agroforestry sectors is discussed.

  11. A PROSPECTIVE TRIAL OF THE FETAL BIOPHYSICAL PROFILE VERSUS MODIFIED BIOPHYSICAL PROFILE IN THE MANAGEMENT OF HIGH RISK PREGNANCIES

    Directory of Open Access Journals (Sweden)

    A. Jamal

    2007-07-01

    Full Text Available "nThe original biophysical profile is time consuming and costly. This study was performed to compare diagnostic value of the original fetal biophysical profile to the modified biophysical profile. Patients were selected from high risk pregnancies referred for fetal assessment and were randomly assigned to two groups. The measures of outcomes were perinatal mortality, Cesarean section for abnormal test, meconium-stained amniotic fluid and 5-minute Apgar score < 7. Diagnostic values of tests were assessed in terms of the incidence of abnormal outcome. In addition comparisons between the positive and negative predictive values of each of these tests as well as the sensitivity and specificity of the tests were reviewed. A total of 200 patients were entered into the study; 104 pregnancies were managed by the original biophysical profile and 96 pregnancies by the modified biophysical profile. There were 30 abnormal (31.3% in modified biophysical profile and 24 (23.1% abnormal tests in original one. There was significant difference in the incidence of meconium passage between two groups. Cesarean section for abnormal tests was 27 of 30 abnormal test (90% in modified and 22 of 24 (91.6% in original profile that was similar in both groups. There was not significant difference in Apgar score < 7 between two groups. We did not find significant difference with comparison of the sensitivity, specificity and negative predictive value of two tests for all measures of outcome except the positive predictive value of meconium passage. Original biophysical profile is more costly and time consuming than modified one.

  12. Electron paramagnetic resonance biophysical radiation dosimetry with tooth enamel

    International Nuclear Information System (INIS)

    This thesis deals with the advancements made in the field of Electron Paramagnetic Resonance (EPR) for biophysical dosimetry with tooth enamel for accident, emergency, and retrospective radiation dose reconstruction. A methodology has been developed to measure retrospective radiation exposures in human tooth enamel. This entails novel sample preparation procedures with minimum mechanical treatment to reduce the preparation induced uncertainties, establish optimum measurement conditions inside the EPR cavity, post-process the measured spectrum with functional simulation of dosimetric and other interfering signals, and reconstruct dose. By using this technique, retrospective gamma exposures as low as 80±30 mGy have been successfully deciphered. The notion of dose modifier was introduced in EPR biodosimetry for low dose measurements. It has been demonstrated that by using the modified zero added dose (MZAD) technique for low radiation exposures, doses in 100 mGy ranges can be easily reconstructed in teeth that were previously thought useless for EPR dosimetry. Also, the use of a dose modifier makes robust dose reconstruction possible for higher radiation exposures. The EPR dosimetry technique was also developed for tooth samples extracted from rodents, which represent small tooth sizing. EPR doses in the molars, extracted from the mice irradiated with whole body exposures, were reassessed and shown to be correct within the experimental uncertainty. The sensitivity of human tooth enamel for neutron irradiation, obtained from the 3 MV McMaster K.N. Van de Graaff accelerator, was also studied. For the first time this work has shown that the neutron sensitivity of the tooth enamel is approximately 1/10th of the equivalent gamma sensitivity. Parametric studies for neutron dose rate and neutron energy within the available range of the accelerator, showed no impact on the sensitivity of the tooth enamel. Therefore, tooth enamel can be used as a dosimeter for both neutrons

  13. Estimation of rice biophysical parameters using multitemporal RADARSAT-2 images

    Science.gov (United States)

    Li, S.; Ni, P.; Cui, G.; He, P.; Liu, H.; Li, L.; Liang, Z.

    2016-04-01

    Compared with optical sensors, synthetic aperture radar (SAR) has the capability of acquiring images in all-weather conditions. Thus, SAR images are suitable for using in rice growth regions that are characterized by frequent cloud cover and rain. The objective of this paper was to evaluate the probability of rice biophysical parameters estimation using multitemporal RADARSAT-2 images, and to develop the estimation models. Three RADARSTA-2 images were acquired during the rice critical growth stages in 2014 near Meishan, Sichuan province, Southwest China. Leaf area index (LAI), the fraction of photosynthetically active radiation (FPAR), height, biomass and canopy water content (WC) were observed at 30 experimental plots over 5 periods. The relationship between RADARSAT-2 backscattering coefficients (σ 0) or their ratios and rice biophysical parameters were analysed. These biophysical parameters were significantly and consistently correlated with the VV and VH σ 0 ratio (σ 0 VV/ σ 0 VH) throughout all growth stages. The regression model were developed between biophysical parameters and σ 0 VV/ σ 0 VH. The results suggest that the RADARSAT-2 data has great potential capability for the rice biophysical parameters estimation and the timely rice growth monitoring.

  14. The physical basis of biochemistry the foundations of molecular biophysics

    CERN Document Server

    Bergethon, Peter R

    1998-01-01

    The objective of this book is to provide a unifying approach to the study of biophysical chemistry for the advanced undergraduate who has had a year of physics, organic chem­ istry, calculus, and biology. This book began as a revised edition of Biophysical Chemistry: Molecules to Membranes, which Elizabeth Simons and I coauthored. That short volume was written in an attempt to provide a concise text for a one-semester course in biophysical chemistry at the graduate level. The experience of teaching biophysical chemistry to bi­ ologically oriented students over the last decade has made it clear that the subject requires a more fundamental text that unifies the many threads of modem science: physics, chem­ istry, biology, mathematics, and statistics. This book represents that effort. This volume is not a treatment of modem biophysical chemistry with its rich history and many contro­ versies, although a book on that topic is also needed. The Physical Basis of Biochemistry is an introduction to the philosophy...

  15. Biophysics in drug discovery: impact, challenges and opportunities.

    Science.gov (United States)

    Renaud, Jean-Paul; Chung, Chun-Wa; Danielson, U Helena; Egner, Ursula; Hennig, Michael; Hubbard, Roderick E; Nar, Herbert

    2016-10-01

    Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.

  16. Large-scale biophysical evaluation of protein PEGylation effects

    DEFF Research Database (Denmark)

    Vernet, Erik; Popa, Gina; Pozdnyakova, Irina;

    2016-01-01

    of PEGylation on the thermal stability of a protein based on data generated by circular dichroism (CD), differential scanning calorimetry (DSC), or differential scanning fluorimetry (DSF). In addition, DSF was validated as a fast and inexpensive screening method for thermal unfolding studies of PEGylated...... proteins. Multivariate data analysis revealed clear trends in biophysical properties upon PEGylation for a subset of proteins, although no universal trends were found. Taken together, these findings are important in the consideration of biophysical methods and evaluation of second......-generation biopharmaceutical drug candidates....

  17. The Twilight of Determinism: At Least in Biophysical Novelties

    CERN Document Server

    Gilead, Amihud

    2015-01-01

    In the 1990s, Richard Lewontin referred to what appeared to be the twilight of determinism in biology. He pointed out that DNA determines only a little part of life phenomena, which are very complex. In fact, organisms determine the environment and vice versa in a nonlinear way. Very recently, biophysicists, Shimon Marom and Erez Braun, have demonstrated that controlled biophysical systems have shown a relative autonomy and flexibility in response which could not be predicted. Within the boundaries of some restraints, most of them genetic, this freedom from determinism is well maintained. Marom and Braun have challenged not only biophysical determinism but also reverse-engineering, naive reductionism, mechanism, and systems biology.

  18. Institute of Biochemistry and Biophysics. Research Report 1996-1997

    International Nuclear Information System (INIS)

    Scientific interests of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences have evolved from classical biochemistry, biophysics and physiological chemistry to up-to-date molecular biology. Research interests are focussed on replication, mutagenesis and repair of DNA; regulation of gene expression at various levels; biosynthesis and post-translational modifications of proteins; gene sequencing and functional analysis of open reading frames; structure, function and regulation of enzymes; conformation of proteins and peptides; modelling of structures and prediction of functions of proteins; mechanisms of electron transfer in polypeptides

  19. Biophysical characterization of a model antibody drug conjugate.

    Science.gov (United States)

    Arakawa, Tsutomu; Kurosawa, Yasunori; Storms, Michael; Maruyama, Toshiaki; Okumura, C J; Maluf, Nasib Karl

    2016-01-01

    Antibody drug conjugates (ADC) are important next-generation biopharmaceuticals and thus require stringent structure characterization as is the case for monoclonal antibodies. We have tested several biophysical techniques, i.e., circular dichroism, analytical ultracentrifugation, differential scanning calorimetry and fluorescence spectroscopy, to characterize a fluorescein-labeled monoclonal antibody as a model ADC. These techniques indicated possible small structure and stability changes by the conjugation, while largely retaining the tertiary structure of the antibody, consistent with unaltered biological activities. Thus, the above biophysical techniques are effective at detecting changes in the structural properties of ADC. PMID:27534450

  20. Physics Labs with Flavor II

    Science.gov (United States)

    Agrest, Mikhail M.

    2011-01-01

    This paper was inspired by the numerous requests from "TPT" readers to expand the number of examples of "recurrent study" lab exercises described in my previous paper "Physics Labs with Flavor." I recommend that readers examine it first in order to better understand this one as my attempt here is to be brief. In that paper, one can find details…

  1. GitLab repository management

    CERN Document Server

    Hethey, Jonathan

    2013-01-01

    A simple, easy to understand tutorial guide on how to build teams and efficiently use version control, using GitLab.If you are a system administrator in a company that writes software or are in charge of an infrastructure, this book will show you the most important features of GitLab, including how to speed up the overall process

  2. The lab of fame

    CERN Multimedia

    Antonella Del Rosso

    2014-01-01

    For a third time, CERN is organising the Swiss heat of Famelab, the world’s leading science communication competition that has already gathered over 5,000 young and talented scientists and engineers from all across the planet.   Besides their degrees, the scientists who participate in Famelab have another thing in common: their passion for communicating science. Coming from a variety of scientific fields, from medicine to particle physics and microbiology, the contestants have three minutes to present a science, technology, mathematics or engineering-based talk using only the props he or she can carry onto the stage; PowerPoint presentations are not permitted. The contestants are then judged by a panel of three judges who evaluate the content, clarity and charisma of their talks. What's unique about FameLab is the fact that content is an important aspect of the performance. At the end of their presentation, contestants are often questioned about the scientific relevance of...

  3. Delineating Biophysical Environments of the Sunda Banda Seascape, Indonesia

    Directory of Open Access Journals (Sweden)

    Mingshu Wang

    2015-01-01

    Full Text Available The Sunda Banda Seascape (SBS, located in the center of the Coral Triangle, is a global center of marine biodiversity and a conservation priority. We proposed the first biophysical environmental delineation of the SBS using globally available satellite remote sensing and model-assimilated data to categorize this area into unique and meaningful biophysical classes. Specifically, the SBS was partitioned into eight biophysical classes characterized by similar sea surface temperature, chlorophyll a concentration, currents, and salinity patterns. Areas within each class were expected to have similar habitat types and ecosystem functions. Our work supplemented prevailing global marine management schemes by focusing in on a regional scale with finer spatial resolution. It also provided a baseline for academic research, ecological assessments and will facilitate marine spatial planning and conservation activities in the area. In addition, the framework and methods of delineating biophysical environments we presented can be expanded throughout the whole Coral Triangle to support research and conservation activities in this important region.

  4. Skin Biophysical Characteristics in Patients with Keratoconus: A Controlled Study

    Science.gov (United States)

    Robati, Reza M.; Einollahi, Bahram; Einollahi, Hoda; Younespour, Shima; Fadaifard, Shahed

    2016-01-01

    Background. Keratoconus is a relatively common corneal disease causing significant visual disability. Individuals with connective tissue disorders that affect the skin such as Marfan's syndrome and Ehlers-Danlos syndrome or patients with atopic dermatitis show an increased prevalence of keratoconus. It seems that there are some concurrent alterations of skin and cornea in patients with keratoconus. Objective. We plan to compare skin biophysical characteristics in patients with keratoconus and healthy controls. Methods. Forty patients with keratoconus (18 females and 22 males) with mean (SD) age of 33.32 (9.55) years (range 19–56) and 40 healthy controls were recruited to this study. Skin biophysical characteristics including cutaneous resonance running time (CRRT), stratum corneum hydration, and melanin values were measured in patients and controls. Results. The median CRRT, stratum corneum hydration, and melanin measurements were significantly lower in patients with keratoconus in comparison with healthy controls. Conclusion. There are some alterations of skin biophysical properties in patients with keratoconus. Therefore, the assessment of these skin parameters could provide us some clues to the possible common biophysical variations of cornea and skin tissue in diseases such as keratoconus. PMID:27403376

  5. Institutional Factors Affecting Biophysical Outcomes in Forest Management

    Science.gov (United States)

    Coleman, Eric A.

    2009-01-01

    Although there is considerable interest in the impact of diverse policies affecting the biophysical outcomes in forests, gaining a substantial sample over time of forests under different institutional arrangements has been difficult. This article analyzes data from 46 forests located in six countries over time. In forests where policies have been…

  6. Biophysical Evaluation of Food Decontamination Effects on Tissue and Bacteria

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan;

    2011-01-01

    that there are no contradictions between data obtained by either approach. However, the biophysical methods draw a much more nuanced picture of the effects and efficiency of the investigated decontamination method, revealing, e.g., an exponential dose/response relationship between SonoSteam® treatment time and changes in collagen...

  7. Skin Biophysical Characteristics in Patients with Keratoconus: A Controlled Study

    Directory of Open Access Journals (Sweden)

    Reza M. Robati

    2016-01-01

    Full Text Available Background. Keratoconus is a relatively common corneal disease causing significant visual disability. Individuals with connective tissue disorders that affect the skin such as Marfan’s syndrome and Ehlers-Danlos syndrome or patients with atopic dermatitis show an increased prevalence of keratoconus. It seems that there are some concurrent alterations of skin and cornea in patients with keratoconus. Objective. We plan to compare skin biophysical characteristics in patients with keratoconus and healthy controls. Methods. Forty patients with keratoconus (18 females and 22 males with mean (SD age of 33.32 (9.55 years (range 19–56 and 40 healthy controls were recruited to this study. Skin biophysical characteristics including cutaneous resonance running time (CRRT, stratum corneum hydration, and melanin values were measured in patients and controls. Results. The median CRRT, stratum corneum hydration, and melanin measurements were significantly lower in patients with keratoconus in comparison with healthy controls. Conclusion. There are some alterations of skin biophysical properties in patients with keratoconus. Therefore, the assessment of these skin parameters could provide us some clues to the possible common biophysical variations of cornea and skin tissue in diseases such as keratoconus.

  8. Synthesis and Biophysical Characterization of Chlorambucil Anticancer Ether Lipid Prodrugs

    DEFF Research Database (Denmark)

    Pedersen, Palle Jacob; Christensen, Mikkel Stochkendahl; Ruysschaert, Tristan;

    2009-01-01

    The synthesis and biophysical characterization of four prodrug ether phospholipid conjugates are described. The lipids are prepared from the anticancer drug chlorambucil and have C16 and C18 ether chains with phosphatidylcholine or phosphatidylglycerol headgroups. All four prodrugs have the ability...

  9. Surface-enhanced Raman scattering: a new optical probe in molecular biophysics and biomedicine

    DEFF Research Database (Denmark)

    Kneipp, J.; Wittig, B.; Bohr, Henrik;

    2010-01-01

    Sensitive and detailed molecular structural information plays an increasing role in molecular biophysics and molecular medicine. Therefore, vibrational spectroscopic techniques, such as Raman scattering, which provide high structural information content are of growing interest in biophysical and ...

  10. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    International Nuclear Information System (INIS)

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995

  11. Small-Angle X-ray Scattering Screening Complements Conventional Biophysical Analysis

    DEFF Research Database (Denmark)

    Tian, Xinsheng; Langkilde, Annette Eva; Thorolfsson, Matthias;

    2014-01-01

    introduce small-angle X-ray scattering (SAXS) to characterize antibody solution behavior, which strongly complements conventional biophysical analysis. First, we apply a variety of conventional biophysical techniques for the evaluation of structural, conformational, and colloidal stability and report...

  12. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995.

  13. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Science.gov (United States)

    Mellem, Daniel; Fischer, Frank; Jaspers, Sören; Wenck, Horst; Rübhausen, Michael

    2016-01-01

    Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes. PMID:26771181

  14. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Directory of Open Access Journals (Sweden)

    Daniel Mellem

    Full Text Available Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  15. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Science.gov (United States)

    Mellem, Daniel; Fischer, Frank; Jaspers, Sören; Wenck, Horst; Rübhausen, Michael

    2016-01-01

    Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  16. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model

    Science.gov (United States)

    Mellem, Daniel; Fischer, Frank; Jaspers, Sören; Wenck, Horst; Rübhausen, Michael

    2016-01-01

    Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes. PMID:26771181

  17. Mapping technological and biophysical capacities of watersheds to regulate floods

    Science.gov (United States)

    Mogollon, Beatriz; Villamagna, Amy M.; Frimpong, Emmanuel A.; Angermeier, Paul

    2016-01-01

    Flood regulation is a widely valued and studied service provided by watersheds. Flood regulation benefits people directly by decreasing the socio-economic costs of flooding and indirectly by its positive impacts on cultural (e.g., fishing) and provisioning (e.g., water supply) ecosystem services. Like other regulating ecosystem services (e.g., pollination, water purification), flood regulation is often enhanced or replaced by technology, but the relative efficacy of natural versus technological features in controlling floods has scarcely been examined. In an effort to assess flood regulation capacity for selected urban watersheds in the southeastern United States, we: (1) used long-term flood records to assess relative influence of technological and biophysical indicators on flood magnitude and duration, (2) compared the widely used runoff curve number (RCN) approach for assessing the biophysical capacity to regulate floods to an alternative approach that acknowledges land cover and soil properties separately, and (3) mapped technological and biophysical flood regulation capacities based on indicator importance-values derived for flood magnitude and duration. We found that watersheds with high biophysical (via the alternative approach) and technological capacities lengthened the duration and lowered the peak of floods. We found the RCN approach yielded results opposite that expected, possibly because it confounds soil and land cover processes, particularly in urban landscapes, while our alternative approach coherently separates these processes. Mapping biophysical (via the alternative approach) and technological capacities revealed great differences among watersheds. Our study improves on previous mapping of flood regulation by (1) incorporating technological capacity, (2) providing high spatial resolution (i.e., 10-m pixel) maps of watershed capacities, and (3) deriving importance-values for selected landscape indicators. By accounting for technology that enhances

  18. What's your lab's strategy?

    Science.gov (United States)

    Francis, Peter

    2016-07-01

    Important strategic choices cascade throughout a laboratory. Senior management should create a document that answers each of the five key questions explained on page 60. Once this has been detailed in writing, it remains important to disseminate the basics to all employees so they are singing the same tune. A useful way to accomplish this is through a coherent strategy statement that specifies three components: 1) objectives; 2) scope; and 3) advantages. Commercial and hospital outreach labs should be in business to win. It all starts with a definition of what winning looks like. To "participate" in your market contributes to mediocrity-and it's self-defeating. With no clear strategic direction of where-to-play and how-to-win choices that associate with the aspiration, a mission or vision statement can be frustrating rather than inspiring for employees. Articulate it plainly and concisely for everybody. With a care-fully prepared and designed strategy, you will be on your way to winning in the zero-sum game! PMID:27548928

  19. Biophysical and physiological integration of proper clothing for exercise.

    Science.gov (United States)

    Gonzalez, R R

    1987-01-01

    In this chapter, I have presented a potpourri of examples of proper clothing to wear during various exercise demands in different environments. These examples are not wholly exact for all persons. For example, during the 1984 Olympics in Los Angeles, clothing wear related to the particular environment was totally different. We have already described the aerodynamic necessities of cyclists and runners. At the other extreme, equestrians had to contend with a warm, moderately humid environment, plus a solar load that added to the effective heat stress, while wearing clothing having clo values of nearly 0.8-0.9, plus headgear that limited evaporative heat loss. Obviously, garments with high water vapor permeation and bellows properties were necessary. Runners in the marathon faced equal thermal challenges. In addition, they incurred variable levels of hypovolemia and cardiovascular strain. A. Salazar, for example, was advised to omit shower sprays, and he ran with a prototype high-permeability singlet. The excessive wetting plus time to maneuver to the spray was deemed of no value, since Mr. Salazar chafes easily from wet clothes (L. Armstrong, personnel communication). One interesting response to this advice is to consider the clothed runner as a wet globe thermometer under forced convection. A high-contact fabric, especially one like cotton, does allow evaporative cooling, provided that the skin-ambient vapor pressure gradient is not diminished by high relative humidity. Salts in sweat may reduce the skin's vapor pressure ; however, Woodcock and Breckenridge point out that "secreted sweat (especially with heat acclimation) is so dilute that no appreciable lowering of vapor pressure would occur unless sweat were concentrated many times by evaporation." Thus, the degree of "human" wet bulb depression simulated by a completely wet runner may or may not be an advantage, since all other variables are also constant (i.e., humidity, weight of clothing as in Figure 13, etc

  20. Future{at}Labs.Prosperity Game{trademark}

    Energy Technology Data Exchange (ETDEWEB)

    Beck, D.F.; Boyack, K.W.; Berman, M. [Sandia National Labs., Albuquerque, NM (United States). Innovative Alliances Dept.

    1996-10-01

    Prosperity Games{trademark} are an outgrowth and adaptation of move/countermove and seminar War Games, Prosperity Games{trademark} are simulations that explore complex issues in a variety of areas including economics, politics, sociology, environment, education, and research. These issues can be examined from a variety of perspectives ranging from global, macroeconomic and geopolitical viewpoint down to the details of customer/supplier/market interactions specific industries. All Prosperity Games{trademark} are unique in that both the game format and the player contributions vary from game to game. This report documents the Future{at}Labs.Prosperity Game{trademark} conducted under the sponsorship of the Industry Advisory Boards of the national labs, the national labs, Lockheed Martin Corporation, and the University of California. Players were drawn from all stakeholders involved including government, industry, labs, and academia. The primary objectives of this game were to: (1) explore ways to optimize the role of the multidisciplinary labs in serving national missions and needs; (2) explore ways to increase collaboration and partnerships among government, laboratories, universities, and industry; and (3) create a network of partnership champions to promote findings and policy options. The deliberations and recommendations of these players provided valuable insights as to the views of this diverse group of decision makers concerning the future of the labs.

  1. Metallurgical Laboratory (MET-LAB)

    Data.gov (United States)

    Federal Laboratory Consortium — The MET-LAB can perform materials characterization for all types of metallic components and systems to any industry-specific or military standard. Capabilities: The...

  2. Advanced Active Acoustics Lab (AAAL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Active Acoustics Lab (AAAL) is a state-of-the-art Undersea Warfare (USW) acoustic data analysis facility capable of both active and passive underwater...

  3. Pollution hazard closes neutrino lab

    CERN Multimedia

    Jones, Nicola

    2003-01-01

    "A leading astrophysics laboratory in Italy has closed down all but one of its experiments over concerns that toxic polluants could leak form the underground lab into the local water supply" (0.5 page)

  4. Incorporating Bio-Physical Sciences into a Decision Support Tool for Sustainable Urban Planning

    Directory of Open Access Journals (Sweden)

    Zina Mitraka

    2014-11-01

    Full Text Available Deciding upon optimum planning actions in terms of sustainable urban planning involves the consideration of multiple environmental and socio-economic criteria. The transformation of natural landscapes to urban areas affects energy and material fluxes. An important aspect of the urban environment is the urban metabolism, and changes in such metabolism need to be considered for sustainable planning decisions. A spatial Decision Support System (DSS prototyped within the European FP7-funded project BRIDGE (sustainaBle uRban plannIng Decision support accountinG for urban mEtabolism, enables accounting for the urban metabolism of planning actions, by exploiting the current knowledge and technology of biophysical sciences. The main aim of the BRIDGE project was to bridge the knowledge and communication gap between urban planners and environmental scientists and to illustrate the advantages of considering detailed environmental information in urban planning processes. The developed DSS prototype integrates biophysical observations and simulation techniques with socio-economic aspects in five European cities, selected as case studies for the pilot application of the tool. This paper describes the design and implementation of the BRIDGE DSS prototype, illustrates some examples of use, and highlights the need for further research and development in the field.

  5. A Remote Direct Sequence Spread Spectrum Communications Lab Utilising the Emona DATEx

    Directory of Open Access Journals (Sweden)

    Cosmas Mwikirize

    2012-12-01

    Full Text Available Remote labs have become popular learning aids due to their versatility and considerable ease of utilisation as compared to their physical counterparts. At Makerere University, the remote labs are based on the standard Massachusetts Institute of Technology (MIT iLabs Shared Architecture (ISA - a scalable and generic platform. Presented in this paper is such a lab, addressing the key practical aspects of Direct Sequence Spread Spectrum (DSSS communication. The lab is built on the National Instruments Educational Laboratory Virtual Instrumentation Suite (NI ELVIS with the Emona Digital and Analog Telecommunications Experimenter (DATEx add-on board. It also incorporates switching hardware. The lab facilitates real-time control of the equipment, with users able to set, manipulate and observe signal parameters in both the frequency and the time domains. Simulation and data Acquisition modes of the experiment are supported to provide a richer learning experience.

  6. A Virtual Circuits Lab

    Science.gov (United States)

    Vick, Matthew E.

    2010-01-01

    The University of Colorado's Physics Education Technology (PhET) website offers free, high-quality simulations of many physics experiments that can be used in the classroom. The Circuit Construction Kit, for example, allows students to safely and constructively play with circuit components while learning the mathematics behind many circuit…

  7. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Huaying, E-mail: zhaoh3@mail.nih.gov; Schuck, Peter, E-mail: zhaoh3@mail.nih.gov [National Institutes of Health, Bethesda, MD 20892 (United States)

    2015-01-01

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.

  8. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    International Nuclear Information System (INIS)

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design

  9. Biophysical climate impacts of recent changes in global forest cover.

    Science.gov (United States)

    Alkama, Ramdane; Cescatti, Alessandro

    2016-02-01

    Changes in forest cover affect the local climate by modulating the land-atmosphere fluxes of energy and water. The magnitude of this biophysical effect is still debated in the scientific community and currently ignored in climate treaties. Here we present an observation-driven assessment of the climate impacts of recent forest losses and gains, based on Earth observations of global forest cover and land surface temperatures. Our results show that forest losses amplify the diurnal temperature variation and increase the mean and maximum air temperature, with the largest signal in arid zones, followed by temperate, tropical, and boreal zones. In the decade 2003-2012, variations of forest cover generated a mean biophysical warming on land corresponding to about 18% of the global biogeochemical signal due to CO2 emission from land-use change.

  10. Elucidating diversity of exosomes: biophysical and molecular characterization methods.

    Science.gov (United States)

    Khatun, Zamila; Bhat, Anjali; Sharma, Shivani; Sharma, Aman

    2016-09-01

    Exosomes are cell-secreted nanovesicles present in biological fluids in normal and diseased conditions. Owing to their seminal role in cell-cell communication, emerging evidences suggest that exosomes are fundamental regulators of various diseases. Due to their potential usefulness in disease diagnosis, robust isolation and characterization of exosomes is critical in developing exosome-based assays. In the last few years, different exosome characterization methods, both biophysical and molecular, have been developed to characterize these tiny vesicles. Here, in this review we summarize: first, biophysical techniques based on spectroscopy (e.g., Raman spectroscopy, dynamic light scattering) and other principles, for example, scanning electron microscopy, atomic force microscopy; second, antibody-based molecular techniques including flow cytometry, transmission electron microscopy and third, nanotechnology-dependent exosome characterization methodologies. PMID:27488053

  11. Biophysical climate impacts of recent changes in global forest cover

    Science.gov (United States)

    Alkama, Ramdane; Cescatti, Alessandro

    2016-02-01

    Changes in forest cover affect the local climate by modulating the land-atmosphere fluxes of energy and water. The magnitude of this biophysical effect is still debated in the scientific community and currently ignored in climate treaties. Here we present an observation-driven assessment of the climate impacts of recent forest losses and gains, based on Earth observations of global forest cover and land surface temperatures. Our results show that forest losses amplify the diurnal temperature variation and increase the mean and maximum air temperature, with the largest signal in arid zones, followed by temperate, tropical, and boreal zones. In the decade 2003-2012, variations of forest cover generated a mean biophysical warming on land corresponding to about 18% of the global biogeochemical signal due to CO2 emission from land-use change.

  12. "The Physics of Life," an undergraduate general education biophysics course

    CERN Document Server

    Parthasarathy, Raghuveer

    2014-01-01

    Improving the scientific literacy of non-scientists is an important goal, both because of the ever-increasing impact of science and technology on our lives, and because understanding science enriches our experience of the natural world. One route to improving scientific literacy is via general education undergraduate courses -- i.e. courses intended for students not majoring in the sciences or engineering -- which in many cases provide these students' last formal exposure to science. I describe here a course on biophysics for non-science-major undergraduates recently developed at the University of Oregon (Eugene, OR, USA). Biophysics, I claim, is a particularly useful vehicle for addressing scientific literacy. It involves important and general scientific concepts, demonstrates connections between basic science and tangible, familiar phenomena related to health and disease, and illustrates that scientific insights develop by applying tools and perspectives from disparate fields in creative ways. In addition, ...

  13. The problem of morphogenesis: unscripted biophysical control systems in plants

    OpenAIRE

    Lintilhac, Philip M.

    2013-01-01

    The relative simplicity of plant developmental systems, having evolved within the universal constraints imposed by the plant cell wall, may allow us to outline a consistent developmental narrative that is not currently possible in the animal kingdom. In this article, I discuss three aspects of the development of the mature form in plants, approaching them in terms of the role played by the biophysics and mechanics of the cell wall during growth. First, I discuss axis extension in terms of a l...

  14. Biophysical basis for the geometry of conical stromatolites

    OpenAIRE

    Petroff, Alexander P.; Sim, Min Sub; Maslov, Andrey; Krupenin, Mikhail; Rothman, Daniel H.; Bosak, Tanja

    2010-01-01

    Stromatolites may be Earth’s oldest macroscopic fossils; however, it remains controversial what, if any, biological processes are recorded in their morphology. Although the biological interpretation of many stromatolite morphologies is confounded by the influence of sedimentation, conical stromatolites form in the absence of sedimentation and are, therefore, considered to be the most robust records of biophysical processes. A qualitative similarity between conical stromatolites and some moder...

  15. Biophysics of protein-DNA interactions and chromosome organization

    OpenAIRE

    Marko, John F.

    2015-01-01

    The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.

  16. Population Evacuation: Assessing Biophysical Risk and Social Vulnerability to Floods

    Science.gov (United States)

    Sim, S.; Lee, D. H.

    2014-12-01

    A relatively new topic of environmental hazards research revolves around vulnerability to disasters. These studies focused separately on biophysical and social vulnerability perspectives. Only recently, community-based vulnerability studies have become common because of the recognition that combining social and biophysical components is important and practical (Cutter, et al., 2000; Cutter, et al., 2003; Turner, et al., 2003). Researchers have modeled vulnerability to analyze its spatial variation (Montz, Cross, and Cutter, 2006). This study aimed at developing a technical framework for community-based vulnerability to the specific hazards of floods. Developing a technical framework in this research used a "vulnerability of place" method (Hebb & Mortsch, 2007). The data reduction technique used was Principal Components Analysis (PCA) which allows for each variable to explain part of the vulnerability. The case study was on flooding in the Tennessee River Basin. The initial run with all 46 variables produced 13 components that explained 69.77% of the variance. Because of the relative homogeneity across the county (i.e., land use and soil types most vulnerable to flooding being located away from heavily populated areas) biophysical variables became less important in this region in creating overall risk scores. This is made all the more obvious by the number of social variables (17) compared to the number of biophysical variables (8) in the final components. The lowest risk block groups are located within the cities: central Florence, central, and central Madison. The highest risk block groups are in rural areas covered predominately with pasture and agricultural land or forests. They also lie near or within the 100 year floodplain.

  17. Photodynamic therapy: Biophysical mechanisms and molecular responses

    Science.gov (United States)

    Mitra, Soumya

    In photodynamic therapy (PDT), photochemical reactions induced by optical activation of sensitizer molecules cause destruction of the target tissue. In this thesis we present results of several related studies, which investigated the influence of photophysical properties and photobleaching mechanisms of sensitizers and oxygen-dependent tissue optical properties on PDT treatment efficacy. The bleaching mechanism of the sensitizer meso-tetra hydroxyphenyl chlorin (mTHPC) is examined indirectly using measurements of photochemical oxygen consumption during PDT irradiation of multicell tumor spheroids. Analysis of the results with a theoretical model of oxygen diffusion that incorporates the effects of sensitizer photobleaching shows that mTHPC is degraded via a singlet-oxygen (1O2)-mediated bleaching process. The analysis allows us to extract photophysical parameters of mTHPC which are used to account for its enhanced clinical photodynamic potency in comparison to that of Photofrin. Evaluation of the spatially-resolved fluorescence in confocal optical sections of intact spheroids during PDT irradiation allows for the direct experimental verification of mTHPC's 1O2-mediated bleaching mechanism. The technique is also used to investigate the complex bleaching kinetics of Photofrin. The results allow us to successfully reconcile apparently contradictory experimental observations and to confirm the predictions of a new theoretical model in which both 1O2 and excited triplet sensitizer molecules are allowed to contribute to photobleaching. Based on studies performed in tissue-simulating erythrocyte phantoms and in a murine tumor model in vivo, we present clinically relevant results which indicate that a shift toward increased hemoglobin-oxygen saturation due to improved tissue oxygenation reduces PDT treatment beam attenuation and may allow for more effective treatment of deeper lesions. Finally, we investigate the induction of the stress protein, heat shock protein 70 (HSP

  18. A quantitative overview of biophysical forces impinging on neural function

    International Nuclear Information System (INIS)

    The fundamentals of neuronal membrane excitability are globally described using the Hodgkin-Huxley (HH) model. The HH model, however, does not account for a number of biophysical phenomena associated with action potentials or propagating nerve impulses. Physical mechanisms underlying these processes, such as reversible heat transfer and axonal swelling, have been compartmentalized and separately investigated to reveal neuronal activity is not solely influenced by electrical or biochemical factors. Instead, mechanical forces and thermodynamics also govern neuronal excitability and signaling. To advance our understanding of neuronal function and dysfunction, compartmentalized analyses of electrical, chemical, and mechanical processes need to be revaluated and integrated into more comprehensive theories. The present perspective is intended to provide a broad overview of biophysical forces that can influence neural function, but which have been traditionally underappreciated in neuroscience. Further, several examples where mechanical forces have been shown to exert their actions on nervous system development, signaling, and plasticity are highlighted to underscore their importance in sculpting neural function. By considering the collective actions of biophysical forces influencing neuronal activity, our working models can be expanded and new paradigms can be applied to the investigation and characterization of brain function and dysfunction. (topical review)

  19. Biophysical parameters in a wheat producer region in southern Brazil

    Science.gov (United States)

    Leivas, Janice F.; de C. Teixeira, Antonio Heriberto; Andrade, Ricardo G.; de C. Victoria, Daniel; Bolfe, Edson L.; Cruz, Caroline R.

    2014-10-01

    Wheat (Triticum aestivum) is the second most produced cereal in the world, and has major importance in the global agricultural economy. Brazil is a large producer of wheat, especially the Rio Grande do Sul state, located in the south of the country. The purpose of this study was to analyze the estimation of biophysical parameters - evapotranspiration (ET), biomass (BIO) and water productivity (WP) - from satellite images of the municipalities with large areas planted with wheat in Rio Grande do Sul (RS). The evapotranspiration rate was obtained using the SAFER Model (Simple Algorithm for Retrieving Evapotranspiration) on MODIS (Moderate Resolution Imaging Spectroradiometer) images taken in the agricultural year 2012. In order to obtain biomass and water productivity rates we applied the Monteith model and the ratio between BIO and ET. In the beginning of the cycle (the planting period) we observed low values for ET, BIO and WP. During the development period, we observed an increase in the values of the parameters and decline at the end of the cycle, for the period of the wheat harvest. The SAFER model proved effective for estimating the biophysical parameters evapotranspiration, biomass production and water productivity in areas planted with wheat in Brazilian Southern. The methodology can be used for monitoring the crops' water conditions and biomass using satellite images, assisting in estimates of productivity and crop yield. The results may assist the understanding of biophysical properties of important agro-ecosystems, like wheat crop, and are important to improve the rational use of water resources.

  20. Modelling benthic biophysical drivers of ecosystem structure and biogeochemical response

    Science.gov (United States)

    Stephens, Nicholas; Bruggeman, Jorn; Lessin, Gennadi; Allen, Icarus

    2016-04-01

    The fate of carbon deposited at the sea floor is ultimately decided by biophysical drivers that control the efficiency of remineralisation and timescale of carbon burial in sediments. Specifically, these drivers include bioturbation through ingestion and movement, burrow-flushing and sediment reworking, which enhance vertical particulate transport and solute diffusion. Unfortunately, these processes are rarely satisfactorily resolved in models. To address this, a benthic model that explicitly describes the vertical position of biology (e.g., habitats) and biogeochemical processes is presented that includes biological functionality and biogeochemical response capturing changes in ecosystem structure, benthic-pelagic fluxes and biodiversity on inter-annual timescales. This is demonstrated by the model's ability to reproduce temporal variability in benthic infauna, vertical pore water nutrients and pelagic-benthic solute fluxes compared to in-situ data. A key advance is the replacement of bulk parameterisation of bioturbation by explicit description of the bio-physical processes responsible. This permits direct comparison with observations and determination of key parameters in experiments. Crucially, the model resolves the two-way interaction between sediment biogeochemistry and ecology, allowing exploration of the benthic response to changing environmental conditions, the importance of infaunal functional traits in shaping benthic ecological structure and the feedback the resulting bio-physical processes exert on pore water nutrient profiles. The model is actively being used to understand shelf sea carbon cycling, the response of the benthos to climatic change, food provision and other societal benefits.

  1. Biophysical research requirements for Beaufort Sea hydrocarbon development

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-08-15

    This review identified biophysical research requirements and data gaps for the development of hydrocarbon resources in the Beaufort Sea. The potential major effects of critical activities during each phase of the offshore oil and gas development cycle were identified in order to assess the impacts on local communities and traditional harvesting methods. Baseline environmental conditions were established. Information needs were ranked using 3 criteria: (1) the current understanding of the biophysical component in terms of present status and long-term sustainability, (2) the potential impact of the oil and gas development on the long-term sustainability of the biophysical component, and (3) the timeline for completion of the research relative to the expected development for the Beaufort Sea region. Mitigation and environmental management plans were outlined, and key research, data collection, and data analyses required to address data gaps were identified. Previous gap analyses for the region were reviewed. Data from a series of workshops conducted with various stakeholders were also included in the study. High research priorities include the assessment of the effects of climatic change on the physical oceanography of the region, studies on deepwater plankton, benthos, and fish. It was concluded that studies are needed to determine the effects of development on marine mammals, avifauna, and macroalgae. 207 refs., 49 tabs., 4 figs.

  2. PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

    Science.gov (United States)

    Tao, Nongjian

    2012-04-01

    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

  3. Simulation

    DEFF Research Database (Denmark)

    Gould, Derek A; Chalmers, Nicholas; Johnson, Sheena J;

    2012-01-01

    Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable...... performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used....

  4. The USA-National Phenology Network Biophysical Program

    Science.gov (United States)

    Losleben, M. V.; Crimmins, T. M.; Weltzin, J. F.

    2009-12-01

    On January 1, 2009, the USA National Phenology Network (USA-NPN, www.usanpn.org) launched the USA-NPN Biophysical Program. The overarching goal of the Biophysical Program (BP) is to link phenology, the study of recurring plant and animal life cycle stages, with climate through the integration of phenology observations, meteorological, and spectral remote sensing measurements at sites across a broad a spectrum of environments. Phenology is critical for understanding a changing world. Many of the recurring plant and animal life cycle stages such as leafing and flowering of plants, maturation of agricultural crops, emergence of insects, and migration of birds are sensitive to climatic variation and change, and are simple to observe and record. Such changes can effect, for example, timing mismatches between the emergence of food sources and the arrival of migrating populations, or create new disease and invasive species vectors via increasingly suitable growing seasons relative to the climatic life cycle requirements of hosts or the organisms themselves. New vectors or crashing populations can have major repercussions on entire ecosystems and regional economics. Thus, to track phenology and build a national database, the USA-NPN is providing standard phenology monitoring protocols. Further, the integration of weather stations with phenological data provides an opportunity to understand how a changing climate is altering phenology. Thus, the USA-NPN Biophysical Program is developing an integrative biology-climate site template for widespread dissemination, in collaboration with the Rocky Mountain Biological Laboratory (RMBL, http://rmbl.org/rockymountainbiolab/). This poster presents the USA-NPN Biophysical Program, and the results of the collaboration with RMBL during the summer of 2009, including the installation of an elevational network of climate stations. The National Science Foundation’s Major Research Instrumentation (NSF’s MRI) program provides funding

  5. EUSO@TurLab: An experimental replica of ISS orbits

    Directory of Open Access Journals (Sweden)

    Bertaina M.

    2015-01-01

    Full Text Available The EUSO@TurLab project is an on-going activity aimed to reproduce atmospheric and luminous conditions that JEM-EUSO will encounter on its orbits around the Earth. The use of the TurLab facility, part of the Department of Physics of the University of Torino, allows the simulation of different surface conditions in a very dark and rotating environment in order to test the response of JEM-EUSO's sensors and sensitivity. The experimental setup currently in operation has been used to check the potential of the TurLab facility for the above purposes, and the acquired data will be used to test the concept of JEM-EUSO's trigger system.

  6. Carrier Analysis Lab (CAL) – Aircraft/Weapons/Ship Compatibility Lab

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The Carrier Analysis Lab (CAL) - Aircraft/Weapons/Ship Compatibility Lab located at the Naval Air Warfare Center Aircraft Division, Lakehurst, NJ provides...

  7. Lab-on-fiber technology

    CERN Document Server

    Cusano, Andrea; Crescitelli, Alessio; Ricciardi, Armando

    2014-01-01

    This book focuses on a research field that is rapidly emerging as one of the most promising ones for the global optics and photonics community: the "lab-on-fiber" technology. Inspired by the well-established 'lab on-a-chip' concept, this new technology essentially envisages novel and highly functionalized devices completely integrated into a single optical fiber for both communication and sensing applications.Based on the R&D experience of some of the world's leading authorities in the fields of optics, photonics, nanotechnology, and material science, this book provides a broad and accurate de

  8. Virtual Labs in proteomics: new E-learning tools.

    Science.gov (United States)

    Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva

    2012-05-17

    Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. PMID:22484059

  9. Simulation

    CERN Document Server

    Ross, Sheldon

    2006-01-01

    Ross's Simulation, Fourth Edition introduces aspiring and practicing actuaries, engineers, computer scientists and others to the practical aspects of constructing computerized simulation studies to analyze and interpret real phenomena. Readers learn to apply results of these analyses to problems in a wide variety of fields to obtain effective, accurate solutions and make predictions about future outcomes. This text explains how a computer can be used to generate random numbers, and how to use these random numbers to generate the behavior of a stochastic model over time. It presents the statist

  10. Using biophysical models to manage nitrogen pollution from agricultural sources: Utopic or realistic approach for non-scientist users? Case study of a drinking water catchment area in Lorraine, France.

    Science.gov (United States)

    Bernard, Pierre-Yves; Benoît, Marc; Roger-Estrade, Jean; Plantureux, Sylvain

    2016-12-01

    The objectives of this comparison of two biophysical models of nitrogen losses were to evaluate first whether results were similar and second whether both were equally practical for use by non-scientist users. Results were obtained with the crop model STICS and the environmental model AGRIFLUX based on nitrogen loss simulations across a small groundwater catchment area (challenges for non-scientists such as lack of parameter optimization, which is essential to accurately assessing nitrogen fluxes and indirectly not to limit the diversity of uses of simulated results. Despite current restrictions, with some improvement, biophysical models could become useful environmental assessment tools for non-scientists. PMID:27596940

  11. 基于飞思卡尔单片机和LabVIEW的汽车组合仪表功能模拟系统设计%ON THE SIMULATION SYSTEM DESIGN OF AUTOMOTIVE INSTRUMENT BASED ON THE FREESCALE MICROCONTROLLER AND LABVIEW

    Institute of Scientific and Technical Information of China (English)

    钱峰; 李敏; 庞辉; 胡孝福

    2013-01-01

      At present, the instrument manufacturers or the automobile factory need to carry out the strict test for automobile combined instruments, and the testing method is about testing the system of automobile sensor simulation signal, transmitting through a harness to the instrument and observing the instrument display state. In this paper, based on the signal simulation, the design, based on the LabVIEW software development virtual instrument interface, uses the Freescale xs128 single-chip to achieve the simulation of the automobile instrument tachometer, speedometer, fuel, water temperature signal and switch signal, and the standard of RS-232 in the upper and lower machine communication can also be achieved.%  目前在汽车仪表生产厂和整车厂都需要对汽车组合仪表进行严格测试,测试方法主要是测试系统模拟汽车传感器信号,通过线束传输到仪表上,观察仪表显示状态。模拟系统基于信号模拟思想,使用Lab VIEW平台实现上位机虚拟仪表界面,飞思卡尔XS128单片机作为下位机实现对汽车仪表中的转速、车速、燃油、水温信号以及开关量信号的功能模拟,上、下位机通信标准为RS-232C。

  12. Ntal/Lab/Lat2

    DEFF Research Database (Denmark)

    Iwaki, Shoko; Jensen, Bettina M; Gilfillan, Alasdair M

    2007-01-01

    Non-T cell activation linker (NTAL)/linker for activation of B cells (LAB), now officially termed LAT2 (linker for activation of T cells 2) is a 25-30kDa transmembrane adaptor protein (TRAP) associated with glycolipid-enriched membrane fractions (GEMs; lipid rafts) in specific cell types...

  13. The Telecom Lab is moving

    CERN Multimedia

    IT Department

    2009-01-01

    As of 2nd March 2009, the Telecom Lab will move to Building 58 R-017. The Telecom Lab is the central point for all support questions regarding CERN mobile phone services (provision of SIM cards, requests for modifications of subscriptions, diagnostics for mobile phone problems, etc.). The opening hours as well as the contact details for the Telecom Lab remain unchanged: New location: Building 58 R-017 Opening hours: Every week day, from 11 a.m. to 12 a.m. Phone number: 72480 Email address: labo.telecom@cern.ch This change has no impact on support requests for mobile services. Users can still submit their requests concerning mobile phone subscriptions using the usual EDH form (https://edh.cern.ch/Document/GSM). The automatic message sent to inform users of their SIM card availability will be updated to indicate the new Telecom Lab location. You can find all information related to CERN mobile phone services at the following link: http://cern.ch/gsm CS Section - IT/CS group

  14. Effects of graphene oxide nanosheets on the ultrastructure and biophysical properties of the pulmonary surfactant film

    Science.gov (United States)

    Hu, Qinglin; Jiao, Bao; Shi, Xinghua; Valle, Russell P.; Zuo, Yi Y.; Hu, Guoqing

    2015-10-01

    Graphene oxide (GO) is the most common derivative of graphene and has been used in a large range of biomedical applications. Despite considerable progress in understanding its cytotoxicity, its potential inhalation toxicity is still largely unknown. As the pulmonary surfactant (PS) film is the first line of host defense, interaction with the PS film determines the fate of the inhaled nanomaterials and their potential toxicity. Using a coarse-grained molecular dynamics model, we reported, for the first time, a novel mechanism of toxicity caused by the inhaled GO nanosheets. Upon deposition, the GO nanosheets induce pores in the PS film and thus have adverse effects on the ultrastructure and biophysical properties of the PS film. Notably, the pores induced by GO nanosheets result in increasing the compressibility of the PS film, which is an important indication of surfactant inhibition. In vitro experiments have also been conducted to study the interactions between GO and animal-derived natural PS films, qualitatively confirming the simulation results.Graphene oxide (GO) is the most common derivative of graphene and has been used in a large range of biomedical applications. Despite considerable progress in understanding its cytotoxicity, its potential inhalation toxicity is still largely unknown. As the pulmonary surfactant (PS) film is the first line of host defense, interaction with the PS film determines the fate of the inhaled nanomaterials and their potential toxicity. Using a coarse-grained molecular dynamics model, we reported, for the first time, a novel mechanism of toxicity caused by the inhaled GO nanosheets. Upon deposition, the GO nanosheets induce pores in the PS film and thus have adverse effects on the ultrastructure and biophysical properties of the PS film. Notably, the pores induced by GO nanosheets result in increasing the compressibility of the PS film, which is an important indication of surfactant inhibition. In vitro experiments have also been

  15. Biophysical approach to chronic kidney disease management in older patients

    Directory of Open Access Journals (Sweden)

    Alberto Foletti

    2016-06-01

    Full Text Available Chronic kidney disease (CKD and its clinical progression are a critical issue in an aging population. Therefore, strategies aimed at preventing and managing the decline of renal function are warranted. Recent evidence has provided encouraging results for the improvement of renal function achieved through an integrated biophysical approach, but prospective studies on the clinical efficacy of this strategy are still lacking. This was an open-label prospective pilot study to investigate the effect of electromagnetic information transfer through the aqueous system on kidney function of older patients affected by stage 1 or 2 CKD. Patients received biophysical therapy every 3 months over a 1-year period. Estimated glomerular filtration rate (eGFR values were calculated using the CKD–Epidemiology Collaboration formula, and were recorded at baseline and at the end of treatment. Overall, 58 patients (mean age 74.8 ± 3.7 years were included in the study. At baseline, mean eGFR was 64.6 ± 15.5 mL/min, and it significantly increased to 69.9 ± 15.8 mL/min after 1 year (+5.2 ± 10 mL/min, p<0.0002. The same trend was observed among men (+5.7 ± 10.2 mL/min, p<0.0064 and women (+4.7 ± 9.9 mL/min, p<0.014. When results were analyzed by sex, no difference was found between the 2 groups. Although further and larger prospective studies are needed, our findings suggest that an integrated biophysical approach may be feasible in the management of older patients with early-stage CKD, to reduce and prevent the decline of renal function due to aging or comorbidities.

  16. Spectromicroscopy in Biophysics with MEPHISTO: Instrumentation Aspects and Technical Improvements

    Science.gov (United States)

    de Stasio, Gelsomina; Capozi, Mario; Gilbert, Benjamin; Perfetti, Paolo; Droubay, Tim; Pauli, Brian; Tonner, Giorgio; Margaritondo, Georgio

    1998-03-01

    The synchrotron imaging photoelectron spectromicroscope MEPHISTO recently reached the world record resolution of 50 nm. We will present the design and performance of this novel instrument, which is mainly dedicated to biophysics experiments in neurobiology, but is also used in materials science research. We will also discuss the possibility of using the MEPHISTO in the transmission mode, as opposed to the photoemission mode, and the unique possibility of studying live cells. Elemental analysis of living biological systems in the microscopic domain is not possible with any other instrument to our knowledge.

  17. Plant Sucrose Transporters from a Biophysical Point of View

    Institute of Scientific and Technical Information of China (English)

    Dietmar Geiger

    2011-01-01

    T The majority of higher plants use sucrose as their main mobile carbohydrate. Proton-driven sucrose transporters play a crucial role in cell-to-cell and long-distance distribution of sucrose throughout the plant. A very negative plant membrane potential and the ability of sucrose transporters to accumulate sucrose concentrations of more than 1 M indicate that plants evolved transporters with unique structural and functional features. The knowledge about the transport mechanism and structural/functional domains of these nano-machines is, however, still fragmentary. In this review,the current knowledge about the biophysical properties of plant sucrose transporters is summarized and discussed.

  18. From biophysics to evolutionary genetics: statistical aspects of gene regulation

    Directory of Open Access Journals (Sweden)

    Lässig Michael

    2007-09-01

    Full Text Available Abstract This is an introductory review on how genes interact to produce biological functions. Transcriptional interactions involve the binding of proteins to regulatory DNA. Specific binding sites can be identified by genomic analysis, and these undergo a stochastic evolution process governed by selection, mutations, and genetic drift. We focus on the links between the biophysical function and the evolution of regulatory elements. In particular, we infer fitness landscapes of binding sites from genomic data, leading to a quantitative evolutionary picture of regulation.

  19. A Series of Computational Neuroscience Labs Increases Comfort with MATLAB.

    Science.gov (United States)

    Nichols, David F

    2015-01-01

    Computational simulations allow for a low-cost, reliable means to demonstrate complex and often times inaccessible concepts to undergraduates. However, students without prior computer programming training may find working with code-based simulations to be intimidating and distracting. A series of computational neuroscience labs involving the Hodgkin-Huxley equations, an Integrate-and-Fire model, and a Hopfield Memory network were used in an undergraduate neuroscience laboratory component of an introductory level course. Using short focused surveys before and after each lab, student comfort levels were shown to increase drastically from a majority of students being uncomfortable or with neutral feelings about working in the MATLAB environment to a vast majority of students being comfortable working in the environment. Though change was reported within each lab, a series of labs was necessary in order to establish a lasting high level of comfort. Comfort working with code is important as a first step in acquiring computational skills that are required to address many questions within neuroscience.

  20. Sakshat Labs: India's Virtual Proteomics Initiative

    OpenAIRE

    Sandipan Ray; Nicole R Koshy; Shyam Diwakar; Bipin Nair; Sanjeeva Srivastava

    2012-01-01

    The first Virtual Proteomics Lab of India has been developed at the IIT Bombay as a part of the “Sakshat” Lab Project, established to develop openly accessible, high-quality educational materials on science and technology.

  1. GeoLab Sample Handling System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Develop  a robotic sample handling/ manipulator system for the GeoLab glovebox. This work leverages from earlier GeoLab work and a 2012 collaboration with a...

  2. Flexible HVAC System for Lab or Classroom.

    Science.gov (United States)

    Friedan, Jonathan

    2001-01-01

    Discusses an effort to design a heating, ventilation, and air conditioning system flexible enough to accommodate an easy conversion of classrooms to laboratories and dry labs to wet labs. The design's energy efficiency and operations and maintenance are examined. (GR)

  3. Land Surface Biophysical-Climate Impacts of Tropical Deforestation with Time-dependence: Sensitivity to Deforestation Rates

    Science.gov (United States)

    Castillo, C. G.; Gurney, K. R.

    2010-12-01

    Deforestation perturbs both biophysical and carbon feedbacks on climate. However, biophysical feedbacks operate at more temporally-immediate and spatially-focused scales, and thus may be sensitive to the actual rate at which deforestation occurs rather than just to the total forest cover loss. Most of previous modeling experiments have focused on equilibrium impacts of mass instantaneous replacement of trees; but, anthropogenic deforestation evolves in time and may result in transient climatic changes which holistic assessments of land cover change impacts must be able to characterize for mitigation and adaptation initiatives to be effective. This exploratory work therefore attempts to determine if there exists a time-dependence within biophysical-climate impacts of deforestation; specifically, if indeed the rates of deforestation affect terrestrial biophysics-climate feedbacks during the period of active deforestation as well as the post-deforestation period. Described here is a method for simulating annual tropical deforestation in the fully-coupled Community Climate System Model 3.0 (CCSM3) with the Dynamic Global Vegetation Model (DGVM) for testing biosphere-climate sensitivity to “preservation pathways.” We test two deforestation curves- one with a 10% annual tree population thinning (DFC10-PT10), and one with 1% (DFC1-PT10) - each with a preservation target of 10% tree cover. During the period of active deforestation, surface albedo, net radiation, latent heat flux and climate variables are compared for time-dependence and sensitivity to total tropical tree foliar projective cover across the tropical band, the Amazon Basin, Central Africa and Southeast Asia. The deforestation rates produce characteristic trends in biophysical variables with DFC10-PT10 resulting in rapid increase/decrease during the initial 10-30 years before a slow leveling off, while DFC1-PT10 exhibits more gradual changes. The deforestation rate is also found to have little effect on

  4. Electrophysiological Data and the Biophysical Modelling of Local Cortical Circuits

    Directory of Open Access Journals (Sweden)

    Dimitris Pinotsis

    2014-03-01

    Full Text Available This paper shows how recordings of gamma oscillations – under different experimental conditions or from different subjects – can be combined with a class of population models called neural fields and dynamic causal modeling (DCM to distinguish among alternative hypotheses regarding cortical structure and function. This approach exploits inter-subject variability and trial-specific effects associated with modulations in the peak frequency of gamma oscillations. It draws on the computational power of Bayesian model inversion, when applied to neural field models of cortical dynamics. Bayesian model comparison allows one to adjudicate among different mechanistic hypotheses about cortical excitability, synaptic kinetics and the cardinal topographic features of local cortical circuits. It also provides optimal parameter estimates that quantify neuromodulation and the spatial dispersion of axonal connections or summation of receptive fields in the visual cortex. This paper provides an overview of a family of neural field models that have been recently implemented using the DCM toolbox of the academic freeware Statistical Parametric Mapping (SPM. The SPM software is a popular platform for analyzing neuroimaging data, used by several neuroscience communities worldwide. DCM allows for a formal (Bayesian statistical analysis of cortical network connectivity, based upon realistic biophysical models of brain responses. It is this particular feature of DCM – the unique combination of generative models with optimization techniques based upon (variational Bayesian principles – that furnishes a novel way to characterize functional brain architectures. In particular, it provides answers to questions about how the brain is wired and how it responds to different experimental manipulations. For a review of the general role of neural fields in SPM the reader can consult e.g. see [1]. Neural fields have a long and illustrious history in mathematical

  5. Evaluation of the biophysical limitations on photosynthesis of four varietals of Brassica rapa

    Science.gov (United States)

    Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B.; Weinig, C.

    2014-12-01

    Evaluating performance of agricultural varietals can support the identification of genotypes that will increase yield and can inform management practices. The biophysical limitations of photosynthesis are amongst the key factors that necessitate evaluation. This study evaluated how four biophysical limitations on photosynthesis, stomatal response to vapor pressure deficit, maximum carboxylation rate by Rubisco (Ac), rate of photosynthetic electron transport (Aj) and triose phosphate use (At) vary between four Brassica rapa genotypes. Leaf gas exchange data was used in an ecophysiological process model to conduct this evaluation. The Terrestrial Regional Ecosystem Exchange Simulator (TREES) integrates the carbon uptake and utilization rate limiting factors for plant growth. A Bayesian framework integrated in TREES here used net A as the target to estimate the four limiting factors for each genotype. As a first step the Bayesian framework was used for outlier detection, with data points outside the 95% confidence interval of model estimation eliminated. Next parameter estimation facilitated the evaluation of how the limiting factors on A different between genotypes. Parameters evaluated included maximum carboxylation rate (Vcmax), quantum yield (ϕJ), the ratio between Vc-max and electron transport rate (J), and trios phosphate utilization (TPU). Finally, as trios phosphate utilization has been shown to not play major role in the limiting A in many plants, the inclusion of At in models was evaluated using deviance information criteria (DIC). The outlier detection resulted in a narrowing in the estimated parameter distributions allowing for greater differentiation of genotypes. Results show genotypes vary in the how limitations shape assimilation. The range in Vc-max , a key parameter in Ac, was 203.2 - 223.9 umol m-2 s-1 while the range in ϕJ, a key parameter in AJ, was 0.463 - 0.497 umol m-2 s-1. The added complexity of the TPU limitation did not improve model

  6. Mass spectrometry in structural biology and biophysics architecture, dynamics, and interaction of biomolecules

    CERN Document Server

    Kaltashov, Igor A; Desiderio, Dominic M; Nibbering, Nico M

    2012-01-01

    The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biol

  7. An Approach for WebLabs Analysis

    Directory of Open Access Journals (Sweden)

    Javier García Zubia

    2007-05-01

    Full Text Available The Faculty of Engineering of University of Deusto has a WebLab oriented to Microelectronics available since 2001. The first part of this paper shows several requirements that a WebLab should meet and the following sections present the WebLab-Deusto.

  8. Designing inquiry learning spaces for online labs in the Go-Lab platform

    NARCIS (Netherlands)

    Jong, de Ton; Gillet, Dennis; Sotiriou, Sofoklis; Agogi, Ellinogermaniki; Zacharia, Zacharias

    2015-01-01

    The Go-Lab project (http://www.go-lab-project.eu/) aims to enable the integration of online labs through inquiry-based learning approaches into science classrooms. Through the use of an advanced plug and play technological solution the Go-Lab project opens up remote science laboratories, data archiv

  9. Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations.

    Science.gov (United States)

    Konas, Ryan M; Daristotle, John L; Harbor, Ndubuisi B; Klauda, Jeffery B

    2015-10-15

    Ethanol is widely used as an additive to gasoline, and production of ethanol can come from single-celled organisms such as yeast. We systematically studied the influence of ethanol on common lipids found in yeast plasma membranes, specifically phosphatidylserine (PS), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). Molecular dynamics simulations were used to probe changes to the biophysical properties of membranes with varying equilibrated bulk ethanol concentrations less than 25 mol %. The palmitoyl oleoyl (PO, 18:1/16:0) chain was used for all lipids, and a mixed bilayer of POPE/POPS (7:3 ratio) was also simulated. Ethanol was found to interact strongly with POPC, and thus its surface area per lipid, chain order, and electron density profiles differ the most from the neat bilayer. At 12 mol % ethanol in the bulk, ethanol penetrated into the hydrophobic core for all membranes studied, but POPC had the highest penetration. Although the anionic headgroup of POPS acted as a protectant for membrane structure compared to the zwitterionic lipids, this was not the case for the POPE/POPS mixture that showed more penetration of ethanol into the membrane than the single-component membranes. To fully characterize the impact of ethanol on yeast plasma membranes, our results suggest that experiments and simulations need to consider representative mixtures of lipids that exist in vivo.

  10. Synchrony suppression in complex stimulus responses of a biophysical model of the cochlea.

    Science.gov (United States)

    Shamma, S A; Morrish, K A

    1987-05-01

    A minimal biophysical model of the cochlea is used to investigate the validity of the hypothesis that a single compressive nonlinearity at the hair cell level can explain some of the suppression phenomena in cochlear responses to complex stimuli. The dependencies of the model responses on the amplitudes and frequencies of two-tone stimuli resemble in many respects the behavior of the experimental data, and can be traced to explicit biophysical parameters in the model. Most discrepancies between theory and experiment stem from simplifications in parameters of the minimal model that play no direct role in the hypothesis. The analysis and simulations predict further results which, pending experimental verification, may provide a more direct test of the influence of the compressive nonlinearity on the relative amplitudes of the synchronous response components, and hence of its role in synchrony suppression. For instance, regardless of the overall absolute levels of a two-tone stimulus applied to this type of model, the ratio of the amplitudes at the input and the ratio of the corresponding responses at the output remain approximately constant and equal (the output ratio changes by at most 6 dB in favor of the stronger tone). Other nonlinear responses to multitonal stimuli can also be reproduced, such as "spectral edge enhancement" [Horst et al., Peripheral Auditory Mechanisms (Springer, Berlin, 1985)] and some aspects of three-tone suppression [Javel et al., Mechanisms of Hearing (Monash U.P., Australia, 1983)]. In contrast to the complex behavior of suppression with increasing sound intensity and the drastic influence of the compressive nonlinearity on the absolute response measures on the auditory nerve (e.g., average rate and synchrony profiles), the percepts of complex sounds are relatively stable. This suggests that the invariant relative response measures are more likely used in the encoding and CNS extraction of the spectrum of complex stimuli such as speech.

  11. Quantifying the thermal heat requirement of Brassica in assessing biophysical parameters under semi-arid microenvironments

    Science.gov (United States)

    Adak, Tarun; Chakravarty, N. V. K.

    2010-07-01

    Evaluation of the thermal heat requirement of Brassica spp. across agro-ecological regions is required in order to understand the further effects of climate change. Spatio-temporal changes in hydrothermal regimes are likely to affect the physiological growth pattern of the crop, which in turn will affect economic yields and crop quality. Such information is helpful in developing crop simulation models to describe the differential thermal regimes that prevail at different phenophases of the crop. Thus, the current lack of quantitative information on the thermal heat requirement of Brassica crops under debranched microenvironments prompted the present study, which set out to examine the response of biophysical parameters [leaf area index (LAI), dry biomass production, seed yield and oil content] to modified microenvironments. Following 2 years of field experiments on Typic Ustocrepts soils under semi-arid climatic conditions, it was concluded that the Brassica crop is significantly responsive to microenvironment modification. A highly significant and curvilinear relationship was observed between LAI and dry biomass production with accumulated heat units, with thermal accumulation explaining ≥80% of the variation in LAI and dry biomass production. It was further observed that the economic seed yield and oil content, which are a function of the prevailing weather conditions, were significantly responsive to the heat units accumulated from sowing to 50% physiological maturity. Linear regression analysis showed that growing degree days (GDD) could indicate 60-70% variation in seed yield and oil content, probably because of the significant response to differential thermal microenvironments. The present study illustrates the statistically strong and significant response of biophysical parameters of Brassica spp. to microenvironment modification in semi-arid regions of northern India.

  12. Colloquium: Biophysical principles of undulatory self-propulsion in granular media

    Science.gov (United States)

    Goldman, Daniel I.

    2014-07-01

    Biological locomotion, movement within environments through self-deformation, encompasses a range of time and length scales in an organism. These include the electrophysiology of the nervous system, the dynamics of muscle activation, the mechanics of the skeletal system, and the interaction mechanics of such structures within natural environments like water, air, sand, and mud. Unlike the many studies of cellular and molecular scale biophysical processes, movement of entire organisms (like flies, lizards, and snakes) is less explored. Further, while movement in fluids like air and water is also well studied, little is known in detail of the mechanics that organisms use to move on and within flowable terrestrial materials such as granular media, ensembles of small particles that collectively display solid, fluid, and gaslike behaviors. This Colloquium reviews recent progress to understand principles of biomechanics and granular physics responsible for locomotion of the sandfish, a small desert-dwelling lizard that "swims" within sand using undulation of its body. Kinematic and muscle activity measurements of sand swimming using high speed x-ray imaging and electromyography are discussed. This locomotion problem poses an interesting challenge: namely, that equations that govern the interaction of the lizard with its environment do not yet exist. Therefore, complementary modeling approaches are also described: resistive force theory for granular media, multiparticle simulation modeling, and robotic physical modeling. The models reproduce biomechanical and neuromechanical aspects of sand swimming and give insight into how effective locomotion arises from the coupling of the body movement and flow of the granular medium. The argument is given that biophysical study of movement provides exciting opportunities to investigate emergent aspects of living systems that might not depend sensitively on biological details.

  13. Impacts on the biophysical economy and environment of a transition to 100% renewable electricity in Australia

    International Nuclear Information System (INIS)

    We investigate the impacts on the biophysical economy, employment and environment of a transition scenario to an energy-efficient, 100% renewable electricity (RE) system by 2060, based on wind, solar and biomass technologies, and an introduction of electric vehicles. We employ a CSIRO process-based model of the physical activity of Australia’s economy and environmental resources, the Australian Stocks and Flows Framework. The RE systems are assumed to be manufactured in Australia to identify possible employment benefits. In comparison with the business-as-usual (BAU) scenario, on a national scale, the RE scenario has much lower economy-wide net emissions, remaining below contemporary levels and becoming zero in the electricity sector by 2060. Compared with BAU, the RE scenario also has significantly lower industrial water use, somewhat higher materials use, slightly lower unemployment, lower net foreign debt (relative to a GDP proxy) and, resulting from the growth in electric vehicles, reduced oil imports. The GDP per capita growth, based on the physical stocks of capital and labour, is virtually the same in both scenarios. Hence, from the viewpoint of the biophysical economy, there are no major barriers to implementing policies to facilitate the transition to a 100% renewable electricity system for Australia. - Highlights: ► Simulation of a 100% renewable electricity (RE) system in a process-based model. ► The RE scenario achieves zero GHG emissions in the electricity sector by 2060. ► Consumption of secondary materials is higher and more variable in the RE scenario. ► The RE scenario has lower water use, unemployment, foreign debt and oil imports

  14. Methods of high throughput biophysical characterization in biopharmaceutical development.

    Science.gov (United States)

    Razinkov, Vladimir I; Treuheit, Michael J; Becker, Gerald W

    2013-03-01

    Discovery and successful development of biopharmaceutical products depend on a thorough characterization of the molecule both before and after formulation. Characterization of a formulated biotherapeutic, typically a protein or large peptide, requires a rigorous assessment of the molecule's physical stability. Stability of a biotherapeutic includes not only chemical stability, i.e., degradation of the molecule to form undesired modifications, but also structural stability, including the formation of aggregates. In this review, high throughput biophysical characterization techniques are described according to their specific applications during biopharmaceutical discovery, development and manufacturing. The methods presented here are classified according to these attributes, and include spectroscopic assays based on absorbance, polarization, intrinsic and extrinsic fluorescence, surface plasmon resonance instrumentation, calorimetric methods, dynamic and static light scattering techniques, several visible particle counting and sizing methods, new viscosity assay, based on light scattering and mass spectrometry. Several techniques presented here are already implemented in industry; but, many high throughput biophysical methods are still in the initial stages of implementation or even in the prototype stage. Each technique in this report is judged by the specific application of the method through the biopharmaceutical development process. PMID:22725690

  15. Biophysical Modeling of Alpha Rhythms During Halothane-Induced Unconsciousness.

    Science.gov (United States)

    Vijayan, Sujith; Ching, ShiNung; Purdon, Patrick L; Brown, Emery N; Kopell, Nancy J

    2013-01-01

    During the induction of general anesthesia there is a shift in power from the posterior regions of the brain to the frontal cortices; this shift in power is called anteriorization. For many anesthetics, a prominent feature of anteriorization is a shift specifically in the alpha band (8-13 Hz) from posterior to frontal cortices. Here we present a biophysical computational model that describes thalamocortical circuit-level dynamics underlying anteriorization of the alpha rhythm in the case of halothane. Halothane potentiates GABAA and increases potassium leak conductances. According to our model, an increase in potassium leak conductances hyperpolarizes and silences the high-threshold thalamocortical (HTC) cells, a specialized subset of thalamocortical cells that fire at the alpha frequency at relatively depolarized membrane potentials (>-60 mV) and are thought to be the generators of quiet awake occipital alpha. At the same time the potentiation of GABAA imposes an alpha time scale on both the cortical and the thalamic component of the frontal portion of our model. The alpha activity in the frontal component is further strengthened by reciprocal thalamocortical feedback. Thus, we argue that the dual molecular targets of halothane induce the anteriorization of the alpha rhythm by increasing potassium leak conductances, which abolishes occipital alpha, and by potentiating GABAA, which induces frontal alpha. These results provide a computational modeling formulation for studying highly detailed biophysical mechanisms of anesthetic action in silico.

  16. Voltage-gated sodium channels: biophysics, pharmacology, and related channelopathies

    Directory of Open Access Journals (Sweden)

    Eleonora eSavio Galimberti

    2012-07-01

    Full Text Available Voltage-gated sodium channels (VGSC are multi-molecular protein complexes expressed in both excitable and non-excitable cells. They are primarily formed by a pore-forming multi-spanning integral membrane glycoprotein (α-subunit that can be associated with one or more regulatory β-subunits. The latter are single-span integral membrane proteins that modulate the sodium current (INa and can also function as cell-adhesion molecules (CAMs. In-vitro some of the cell-adhesive functions of the β-subunits may play important physiological roles independently of the α-subunits. Other endogenous regulatory proteins named channel partners or channel interacting proteins (ChiPs like caveolin-3 and calmodulin/calmodulin kinase II (CaMKII can also interact and modulate the expression and/or function of VGSC. In addition to their physiological roles in cell excitability and cell adhesion, VGSC are the site of action of toxins (like tetrodotoxin and saxitoxin, and pharmacologic agents (like antiarrhythmic drugs, local anesthetics, antiepileptic drugs, and newly developed analgesics. Mutations in genes that encode α- and/or β-subunits as well as the ChiPs can affect the structure and biophysical properties of VGSC, leading to the development of diseases termed sodium channelopathies. This review will outline the structure, function and biophysical properties of VGSC as well as their pharmacology and associated channelopathies and highlight some of the recent advances in this field

  17. Biophysical basis for noninvasive skin cancer detection using Raman spectroscopy

    Science.gov (United States)

    Feng, Xu; Moy, Austin J.; Markey, Mia K.; Fox, Matthew C.; Reichenberg, Jason S.; Tunnell, James W.

    2016-03-01

    Raman spectroscopy (RS) is proving to be a valuable tool for real time noninvasive skin cancer detection via optical fiber probe. However, current methods utilizing RS for skin cancer diagnosis rely on statistically based algorithms to provide tissue classification and do not elucidate the underlying biophysical changes of skin tissue. Therefore, we aim to use RS to explore skin biochemical and structural characteristics and then correlate the Raman spectrum of skin tissue with its disease state. We have built a custom confocal micro-Raman spectrometer system with an 830nm laser light. The high resolution capability of the system allows us to measure spectroscopic features from individual tissue components in situ. Raman images were collected from human skin samples from Mohs surgical biopsy, which were then compared with confocal laser scanning, two-photon fluorescence and hematoxylin and eosin-stained images to develop a linear model of skin tissue Raman spectra. In this model, macroscopic tissue spectra obtained from RS fiber probe were fit into a linear combination of individual basis spectra of primary skin constituents. The fit coefficient of the model explains the biophysical changes spanning a range of normal and various disease states. The model allows for determining parameters similar to that a pathologist is familiar reading and will be a significant guidance in developing RS diagnostic decision schemes.

  18. Climate Change Effects on Agriculture: Economic Responses to Biophysical Shocks

    Science.gov (United States)

    Nelson, Gerald C.; Valin, Hugo; Sands, Ronald D.; Havlik, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina

    2014-01-01

    Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change's representative concentration pathway with end-of-century radiative forcing of 8.5 W/m(sup 2). The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

  19. Estimating maize grain yield from crop biophysical parameters using remote sensing

    Science.gov (United States)

    Guindin-Garcia, Noemi

    The overall objective of this investigation was to develop a robust technique to predict maize (Zea mays L.) grain yield that could be applied at a regional level using remote sensing with or without a simple crop growth simulation model. This study evaluated capabilities and limitations of the Moderate Resolution Imaging Spectroradiometer (MODIS) Vegetation Index 250-m and MODIS surface reflectance 500-m products to track and retrieve information over maize fields. Results demonstrated the feasibility of using MODIS data to estimate maize green leaf area index (LAIg). Estimates of maize LAIg obtained from Wide Dynamic Range Vegetation Index using data retrieved from MODIS 250-m products (e.g. MOD13Q1) can be incorporated in crop simulation models to improve LAIg simulations by the Muchow-Sinclair-Bennet (MSB) model reducing the RMSE of LAIg simulations for all years of study under irrigation. However, more accurate estimates of LAIg did not necessarily imply better final yield (FY) predictions in the MSB maize model. The approach of incorporating better LAIg estimates into crop simulation models may not offer a panacea for problem solving; this approach is limited in its ability to simulate other factors influencing crop yields. On the other hand, the approach of relating key crop biophysical parameters at the optimum stage with maize grain final yields is a robust technique to early FY estimation over large areas. Results suggest that estimates of LAI g obtained during the mid-grain filling period can used to detect variability of maize grain yield and this technique offers a rapid and accurate (RMSE products.

  20. Social and Biophysical Predictors of Public Perceptions of Extreme Fires

    Science.gov (United States)

    Hall, T. E.; Kooistra, C. M.; Paveglio, T.; Gress, S.; Smith, A. M.

    2013-12-01

    To date, what constitutes an 'extreme' fire has been approached separately by biophysical and social scientists. Research on the biophysical characteristics of fires has identified potential dimensions of extremity, including fire size and vegetation mortality. On the social side, factors such as the degree of immediate impact to one's life and property or the extent of social disruption in the community contribute to a perception of extremity. However, some biophysical characteristics may also contribute to perceptions of extremity, including number of simultaneous ignitions, rapidity of fire spread, atypical fire behavior, and intensity of smoke. Perceptions of these impacts can vary within and across communities, but no studies to date have investigated such perceptions in a comprehensive way. In this study, we address the question, to what extent is the magnitude of impact of fires on WUI residents' well-being explained by measurable biophysical characteristics of the fire and subjective evaluations of the personal and community-level impacts of the fire? We bring together diverse strands of psychological theory, including landscape perception, mental models, risk perception, and community studies. The majority of social science research on fires has been in the form of qualitative case studies, and our study is methodologically unique by using a nested design (hierarchical modeling) to enable generalizable conclusions across a wide range of fires and human communities. We identified fires that burned in 2011 or 2012 in the northern Rocky Mountain region that were at least 1,000 acres and that intersected (within 15 km) urban clusters or identified Census places. For fires where an adequately large number of households was located in proximity to the fire, we drew random samples of approximately 150 individuals for each fire. We used a hybrid internet (Qualtrics) and mail survey, following the Dillman method, to measure individual perceptions. We developed two

  1. Exclusive processes at Jefferson Lab

    Indian Academy of Sciences (India)

    Haiyan Gao

    2003-11-01

    Mapping the transition from strongly interacting, non-perturbative quantum chromodynamics, where nucleon–meson degrees of freedom are effective to perturbative QCD of quark and gluon degrees of freedom, is one of the most fundamental, challenging tasks in nuclear and particle physics. Exclusive processes such as proton–proton elastic scattering, meson photoproduction, and deuteron photodisintegration have been pursued extensively at many laboratories over the years in the search for such a transition, particularly at Jefferson Lab in recent years, taking the advantage of the high luminosity capability of the CEBAF facility. In this talk, I review recent results from Jefferson Lab on deuteron photodisintegration and photopion production processes and the future 12 GeV program.

  2. LabVIEW 8 student edition

    CERN Document Server

    Bishop, Robert H

    2007-01-01

    For courses in Measurement and Instrumentation, Electrical Engineering lab, and Physics and Chemistry lab. This revised printing has been updated to include new LabVIEW 8.2 Student Edition. National Instruments' LabVIEW is the defacto industry standard for test, measurement, and automation software solutions. With the Student Edition of LabVIEW, students can design graphical programming solutions to their classroom problems and laboratory experiments with software that delivers the graphical programming capabilites of the LabVIEW professional version. . The Student Edition is also compatible with all National Instruments data acquisition and instrument control hardware. Note: The LabVIEW Student Edition is available to students, faculty, and staff for personal educational use only. It is not intended for research, institutional, or commercial use. For more information about these licensing options, please visit the National Instruments website at (http:www.ni.com/academic/)

  3. Lies, Discrimination, and Internalized Racism: Findings from the lab.

    OpenAIRE

    David, Wozniak; Tim, MacNeill

    2015-01-01

    We simulate a job application/hiring market in the lab to examine racial discrimination. We find little evidence of ability differences based on race but we find taste-based racism between groups and statistical racism within groups. When candidates are given the opportunity to lie about their abilities, all groups discriminate against Blacks, suggesting statistical discrimination. But Whites continue to discriminate against Blacks when actual abilities of the candidate are known, suggesting ...

  4. "Supply Chain-Marketing Shark Tank" Experiential Lab Game in Interdisciplinary Business Education: Qualitative and Quantitative Analyses

    Science.gov (United States)

    Arora, A.; Arora, A. Saxena

    2015-01-01

    This article provides educators in business schools with a new interdisciplinary experiential lab game called Supply Chain-Marketing (SC-Mark) Shark Tank game, which can be implemented in both Supply Chain Management (SCM) and Marketing courses. The SC-Mark experiential lab game is a real-life business environment simulation that explores…

  5. Validation of Global EO Biophysical Products at JECAM Test Site in Ukraine

    Science.gov (United States)

    Skakun, Sergii; Kussul, Nataliia; Kravchenko, Oleksiy; Basarab, Ruslan; Ostapenko, Vadym; Yailymov, Bohdan; Shelestov, Andrii; Kolotii, Andrii; Mironov, Andrii

    Efficient global agriculture monitoring requires appropriate validation of Earth observation (EO) products for different regions and cropping system. This problem is addressed within the Joint Experiment of Crop Assessment and Monitoring (JECAM) initiative which aims to develop monitoring and reporting protocols and best practices for a variety of global agricultural systems. Ukraine is actively involved into JECAM, and a JECAM Ukraine test site was officially established in 2011. The following problems are being solved within JECAM Ukraine: (i) crop identification and crop area estimation [1]; (ii) crop yield forecasting [2]; (iii) EO products validation. The following case study regions were selected for these purposes: (i) the whole Kyiv oblast (28,000 sq. km) indented for crop mapping and acreage estimation; (ii) intensive observation sub-site in Pshenichne which is a research farm from the National University of Life and Environmental Sciences of Ukraine and indented for crop biophysical parameters estimation; (iii) Lviv region for rape-seed identification and crop rotation control; (iv) Crimea region for crop damage assessment due to droughts, and illegial field detection. In 2013, Ukrainian JECAM test site was selected as one of the “Champion User” for the ESA Sentinel-2 for Agriculture project. The test site was observed with SPOT-4 and RapidEye satellites every 5 days. The collected images are then used to simulate Sentinel-2 images for agriculture purposes. JECAM Ukraine is responsible for collecting ground observation data for validation purposes, and is involved in providing user requirements for Sentinel-2 agriculture related products. In particular, three field campaigns to characterize the vegetation biophysical parameters at the Pshenichne test site were carried out: First campaign - 14th to 17th of May 2013; second campaign - 12th to 15th of June 2013; third campaign - 14th to 17th of July 2013. Digital Hemispheric Photographs (DHP) images were

  6. BOLTS: a BiOphysical Larval Tracking System for Measuring Dispersal Characteristics and Marine Population Connectivity

    Science.gov (United States)

    Paris, C. B.; Srinivasan, A.; Kourafalou, V.; Sponaugle, S.; Cowen, R. K.

    2008-12-01

    While metapopulation research with hypothetical dispersal matrices has shown how the scales of larval dispersal, transport processes, local recruitment, and temporal and spatial variability in dispersal influence population persistence, the pattern of demographic connectivity produced by larval dispersal is still a key uncertainty. To address this problem, a coupled bio-physical model has been developed that quantifies the degree of connectivity between populations. Such spatially explicit models, forced by dynamic currents coupled to a realistic seascape and life history traits, produce dispersal kernels for a range of scales over which dispersal is practically unquantifiable by current empirical methods. The BiOphysical Larval Tracking System (BOLTS) presented here allows a Lagrangian stochastic individual-based model (IBM) to be coupled via OPENDAP framework to any 3-dimensional fields of circulation models including to domains of various resolutions through 'Lagrangian nesting'. We demonstrate the capabilities of the software in measuring the characteristics of dispersal and evaluating the variability of larval connectivity through two examples at different scales: 1) Caribbean-scale simulations of BOLTS using the large scale (resolution ~7 km) Hybrid Coordinate Ocean Model (HYCOM) from the Global Data Assimilative Experiment (GODAE) provide us with expected connectivity patterns of a reef building coral. By seeding the model with a large number of active particles, it is possible to assemble dispersal kernels and migration matrices from the start (spawning) and the end point (settlement) of individual particle trajectories. Any single run is a stochastic realization of a probabilistic process, thus the full probability density function (pdf) of the kernel requires averaging over many dispersal events. The model output is further corroborated with empirical measures of gene flow among coral colonies around the Caribbean. 2) Coastal-scale simulations of BOLTS

  7. Single File Dynamics Advances with a Focus on Biophysical Relevance

    Science.gov (United States)

    Flomenbom, Ophir

    2014-08-01

    In this review (appearing in the Special Issue on single file dynamics in biophysics and related extensions), three recently treated variants in file dynamics are presented: files with density that is not fixed, files with heterogeneous particles, and files with slow particles. The results in these files include: • In files with a density law that is not fixed, but decays as a power law with an exponent a the distance from the origin, the particle in the origin mean square displacement (MSD) scales like MSD t[1+a]/2, with a Gaussian probability density function (PDF). This extends the scaling, MSD t1/2, seen in a constant density file. • When, in addition, the particles' diffusion coefficients are distributed like a power law with an exponent γ (around the origin), the MSD follows MSD t[1-γ]/[2/(1+a) - γ], with a Gaussian PDF. • In anomalous files that are renewal, namely, when all particles attempt a jump together, yet, with jump times taken from a PDF that decays as a power law with an exponent -1 - ɛ, ψ(t) t-1-ɛ, the MSD scales like the MSD of the corresponding normal file, in the power ɛ. • In anomalous files of independent particles, the MSD is very slow and scales like MSD log2(t). Even more exciting, the particles form clusters, defining a dynamical phase transition: depending on the anomaly power ɛ, the percentage of particles in clusters ξ follows ξ = √ {1-ǎrepsilon3}, yet when ɛ > 1, fluidity rather than clusters is seen. We talk about utilizing these results while focusing on biophysical processes and applications: dynamics in channels, membranes, biosensors, etc. Special Issue Comments: In this article, results about recently suggested variants in single file dynamics appear: heterogeneous files and slow files, yet also, the relevance with biophysical processes. It is related to the Special Issue articles about expansions in files,61 files with force,62 and the zig zag occurrences in files.63

  8. Virtual labs in Leonardo da Vinci 'CELGAS' e-learning project

    International Nuclear Information System (INIS)

    This paper discusses the problem of virtual lab capabilities in the e-learning. Using combination of web conferencing and 'virtual labs' capabilities, a new quality distance learning teaching is now in preparation and will be included in the course teaching to produce interactive, online simulations for the natural gas engineering studies. The activities are designed to enhance the existing curriculum and to include online assessments. A special care is devoted to the security problem between a server and a client computer. Several examples of the virtual labs related to the PVT thermodynamics, fluid flow, the natural gas well-testing, and the gas network flow are prepared and tested. A major challenge for the 'CELGAS' system is in managing the delicate balance between the student collaboration and the isolation. Students may be encouraged to collaborate and work with each other, simulating their exploration of the lab material. (authors)

  9. Biophysics and Thermodynamics: The Scientific Building Blocks of Bio-inspired Drug Delivery Nano Systems.

    Science.gov (United States)

    Demetzos, Costas

    2015-06-01

    Biophysics and thermodynamics are considered as the scientific milestones for investigating the properties of materials. The relationship between the changes of temperature with the biophysical variables of biomaterials is important in the process of the development of drug delivery systems. Biophysics is a challenge sector of physics and should be used complementary with the biochemistry in order to discover new and promising technological platforms (i.e., drug delivery systems) and to disclose the 'silence functionality' of bio-inspired biological and artificial membranes. Thermal analysis and biophysical approaches in pharmaceuticals present reliable and versatile tools for their characterization and for the successful development of pharmaceutical products. The metastable phases of self-assembled nanostructures such as liposomes should be taken into consideration because they represent the thermal events can affect the functionality of advanced drug delivery nano systems. In conclusion, biophysics and thermodynamics are characterized as the building blocks for design and development of bio-inspired drug delivery systems.

  10. Perspective: Quantum mechanical methods in biochemistry and biophysics

    Science.gov (United States)

    Cui, Qiang

    2016-10-01

    In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

  11. Biophysics of selectin-ligand interactions in inflammation and cancer

    Science.gov (United States)

    Siu-Lun Cheung, Luthur; Raman, Phrabha S.; Balzer, Eric M.; Wirtz, Denis; Konstantopoulos, Konstantinos

    2011-02-01

    Selectins (l-, e- and p-selectin) are calcium-dependent transmembrane glycoproteins that are expressed on the surface of circulating leukocytes, activated platelets, and inflamed endothelial cells. Selectins bind predominantly to sialofucosylated glycoproteins and glycolipids (e-selectin only) present on the surface of apposing cells, and mediate transient adhesive interactions pertinent to inflammation and cancer metastasis. The rapid turnover of selectin-ligand bonds, due to their fast on- and off-rates along with their remarkably high tensile strengths, enables them to mediate cell tethering and rolling in shear flow. This paper presents the current body of knowledge regarding the role of selectins in inflammation and cancer metastasis, and discusses experimental methodologies and mathematical models used to resolve the biophysics of selectin-mediated cell adhesion. Understanding the biochemistry and biomechanics of selectin-ligand interactions pertinent to inflammatory disorders and cancer metastasis may provide insights for developing promising therapies and/or diagnostic tools to combat these disorders.

  12. Biophysical and Physiological Basis of Human Cold Acclimatization

    Directory of Open Access Journals (Sweden)

    Bal Krishna

    1968-05-01

    Full Text Available On exposure to cold, the problem is to maintain internal temperature of the human body in the presence of an increased thermal gradient between the core and the external environment. The ability to maintain homeothermy in the cold environment is enhanced in the acclimatized man. Superimposed upon the adaptive responses of the whole body to cold exposure are the adaptive responses of the extermities to avoid severe cold injury. The two major methods of adjustment to cold exposure are metabolic adjustments and peripheral cooling. Metabolic adjustment involve an increase in heat production in response to a cold stress such as shivering and non shivering thermogenesis and voluntary muscular activity. Peripheral cooling reduce the loss of heat from the skin by effectively increasing the thickness of relatively cooler peripheral tissues. The available literature on human cold acclimatization has been surveyed with a view to explain the biophysical and physiological mechanisms involved in the process of acclimatization.

  13. 19th International School of Biophysics "Ettore Majorana"

    CERN Document Server

    Blank, M; Bioelectrochemistry III : Charge Separation across Biomembranes

    1988-01-01

    This book contains aseries of review papers related to the lectures given at the Third Course on Bioelectrochemistry held at Erice in November 1988, in the framework of the International School of Biophysics. The topics covered by this course, "Charge Separation Across Biomembranes, " deal with the electrochemical aspects of some basic phenomena in biological systems, such as transport of ions, ATP synthesis, formation and maintenance of ionic and protonic gradients. In the first part of the course some preliminary lectures introduce the students to the most basic phenomena and technical aspects of membrane bioelectrochemistry. The remaining part of the course is devoted to the description of a selected group of membrane-enzyme systems, capable of promoting, or exploiting, the processes of separation of electrically charged entities (electrons or ions) across the membrane barrier. These systems are systematically discussed both from a structural and functional point of view. The effort of the many dis...

  14. Biophysics and Structure to Counter Threats and Challenges

    CERN Document Server

    Margaris, Manolia

    2013-01-01

    This ASI brought together a diverse group of experts who span virology, biology, biophysics, chemistry, physics and engineering.  Prominent lecturers representing world renowned scientists from nine (9) different countries, and students from around the world representing eighteen (18) countries, participated in the ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU).   The central hypothesis underlying this ASI was that interdisciplinary research, merging principles of physics, chemistry and biology, can drive new discovery in detecting and fighting chemical and bioterrorism agents, lead to cleaner environments and improved energy sources, and help propel development in NATO partner countries.  At the end of the ASI students had an appreciation of how to apply each technique to their own particular research problem and to demonstrate that multifaceted approaches and new technologies are needed to solve the biological challenges of our time.  The course...

  15. Biophysics of filament length regulation by molecular motors

    CERN Document Server

    Kuan, Hui-Shun

    2013-01-01

    Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kines...

  16. TOPICAL REVIEW: The physics, biophysics and technology of photodynamic therapy

    Science.gov (United States)

    Wilson, Brian C.; Patterson, Michael S.

    2008-05-01

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components—light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT.

  17. Lab-on-a-chip devices and micro-total analysis systems a practical guide

    CERN Document Server

    Svendsen, Winnie

    2015-01-01

    This book covers all the steps in order to fabricate a lab-on-a-chip device starting from the idea, the design, simulation, fabrication and final evaluation. Additionally, it includes basic theory on microfluidics essential to understand how fluids behave at such reduced scale. Examples of successful histories of lab-on-a-chip systems that made an impact in fields like biomedicine and life sciences are also provided.

  18. Space Based Ornithology: On the Wings of Migration and Biophysics

    Science.gov (United States)

    Smith, James A.

    2005-01-01

    The study of bird migration on a global scale is one of the compelling and challenging problems of modern biology with major implications for human health and conservation biology. Migration and conservation efforts cross national boundaries and are subject to numerous international agreements and treaties. Space based technology offers new opportunities to shed understanding on the distribution and migration of organisms on the planet and their sensitivity to human disturbances and environmental changes. Migration is an incredibly diverse and complex behavior. A broad outline of space based research must address three fundamental questions: (1) where could birds be, i.e. what is their fundamental niche constrained by their biophysical limits? (2) where do we actually find birds, i.e. what is their realizable niche as modified by local or regional abiotic and biotic factors, and (3) how do they get there (and how do we know?), that is what are their migration patterns and associated mechanisms? Our working hypothesis is that individual organism biophysical models of energy and water balance, driven by satellite measurements of spatio-temporal gradients in climate and habitat, will help us to explain the variability in avian species richness and distribution. Dynamic state variable modeling provides one tool for studying bird migration across multiple scales and can be linked to mechanistic models describing the time and energy budget states of migrating birds. Such models yield an understanding of how a migratory flyway and its component habitats function as a whole and link stop-over ecology with biological conservation and management. Further these models provide an ecological forecasting tool for science and application users to address what are the possible consequences of loss of wetlands, flooding, drought or other natural disasters such as hurricanes on avian biodiversity and bird migration.

  19. Biophysics at the Boundaries: The Next Problem Sets

    Science.gov (United States)

    Skolnick, Malcolm

    2009-03-01

    The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future

  20. Helicopter Landing Gear Dynamic Simulation Based on LMS Vurtual. Lab%基于LMS Virtual . Lab的直升机起落架着陆载荷分析

    Institute of Scientific and Technical Information of China (English)

    史佩; 宋岩; 岳艳丽

    2014-01-01

    Based on the PrinciPle of helicoPter landing gear dynamic and LMS Virtual. Lab,a model for dynamic analysis of helicoPter landing gear is established to search for the effect of the variation of tire Pressure which leaded by the environment temPerature. The results indicate that landing on board increase struts forces by 80% ~90% than on ground. The variation of tire Pressure can not change the Peak value of the struts forces when landing on ground,and it will increase the Peak value of the struts forces by 5 kN if the tire Pressure changes from 0. 6MPa to 0. 8 MPa.%基于直升机起落架着落动力学原理和LMS软件平台,建立了某型直升机起落架着落性能的虚拟仿真模型,研究着陆、着舰情况下由环境温度引起的轮胎压力变化对起落架载荷的影响。结果表明:起落架着舰载荷比着陆载荷提高80%~90%左右;着陆时若因温度变化引起轮胎压力从0.3 MPa上升至0.4 MPa,那么起落架载荷峰值将提高2 kN左右;着舰时若因温度变化引起轮胎压力从0.6 MPa上升至0.8 MPa,那么起落架载荷峰值将提高5 kN左右。

  1. A Probe into Constructing Game-based Virtual Simulated Lab of Computer Assembly and Maintenance%基于游戏模式的计算机组装与维护虚拟仿真实验室建设探究

    Institute of Scientific and Technical Information of China (English)

    王梅亮; 任清褒

    2015-01-01

    With the reform and development of higher in China in recent years, constructing labs that can effectively facilitate the development of students' practical ability and better achieve the objective of experiment teaching has become an urgent task for application-oriented universities. Using virtual reality and 3D game technology, a game-based training system for computer assembly and troubleshooting is developed. The virtual simulated lab can enable students to have fun while learning and mastering the knowledge and operating skills of computer assembly and maintenance by making the process of operation much more interesting, and effectively overcome the limitations of traditional labs in cost of construction and maintenance, timely updates of equipment as well as the limitations on time and space for students'learning.%近年来随着我国高校的改革和发展,建设能够有效培养学生实践能力,更好完成专业实践教学目标的实验室,已经成为广大应用型高校的紧迫任务.利用虚拟现实和三维游戏技术,设计开发出一套基于游戏模式进行虚拟组装和故障处理的训练系统来构建计算机组装与维护虚拟仿真实验室,可以为学生提供一个在寓教于乐中学习和掌握计算机组装与维护知识及操作技能的训练平台与实验场所,弥补传统实验室建设和维护费用高,设备更新不能与时俱进,学生学习实验知识受时间、地点限制,操作过程缺乏兴趣等缺陷.

  2. Double success for neutrino lab

    CERN Multimedia

    2010-01-01

    "The Gran Sasso National Laboratory in Italy is celebrating two key developments in the field of neutrino physics. Number one is the first ever detection, by the OPERA experiement, of possible tau neutrino that has switched its identity from a muon neutrino as it travelled form its origins at CERN in Switzerland to the Italian lab. Number two is the successful start-up of the ICARUS detector, which, like OPERA, is designed to study neutrinos that "oscillate" between types" (0.5 pages)

  3. Laser safety in the lab

    CERN Document Server

    Barat, Ken L

    2012-01-01

    There is no more challenging setting for laser use than a research environment. In almost every other setting the laser controls count on engineering controls, and human exposure is kept to a minimum. In research, however, the user often manipulates the optical layout and thereby places him or herself in peril, but this does not mean that accidents and injury are unavoidable. On the contrary, laser accidents can be avoided by following a number of simple approaches. [i]Laser Safety in the Lab[/i] provides the laser user and laser safety officer with practical guidelines from housekeeping to ey

  4. Digital media labs in libraries

    CERN Document Server

    Goodman, Amanda L

    2014-01-01

    Families share stories with each other and veterans reconnect with their comrades, while teens edit music videos and then upload them to the web: all this and more can happen in the digital media lab (DML), a gathering of equipment with which people create digital content or convert content that is in analog formats. Enabling community members to create digital content was identified by The Edge Initiative, a national coalition of leading library and local government organizations, as a library technology benchmark. Surveying academic and public libraries in a variety of settings and sharing a

  5. Living Labs as Open-Innovation Networks

    Directory of Open Access Journals (Sweden)

    Mika Westerlund

    2012-09-01

    Full Text Available Living labs bring experimentation out of companies’ R&D departments to real-life environments with the participation and co-creation of users, partners, and other parties. This study discusses living labs as four different types of networks characterized by open innovation: utilizer-driven, enabler-driven, provider-driven, and user-driven. The typology is based on interviews with the participants of 26 living labs in Finland, Sweden, Spain, and South Africa. Companies can benefit from knowing the characteristics of each type of living lab; this knowledge will help them to identify which actor drives the innovation, to anticipate likely outcomes, and to decide what kind of role they should play while "living labbing". Living labs are networks that can help them create innovations that have a superior match with user needs and can be upscaled promptly to the global market.

  6. Fields of Applications for Hybrid Online Labs

    OpenAIRE

    Karsten Henke

    2013-01-01

    Based on a grid concept of an interactive hybrid online laboratory we will describe different fields of applications in different learning scenarios. The infrastructure is based on a universal grid concept which guaranties a reliable, flexible as well as robust usage of this online lab. By using the online lab, students are able to design control algorithms with different specification techniques to control electro-mechanical models in the online lab. Additionally, the reconfigurable rapid pr...

  7. Near Space Lab-Rat Experimentation using Stratospheric Balloon

    Science.gov (United States)

    Buduru, Suneel Kumar; Reddy Vizapur, Anmi; Rao Tanneeru, Venkateswara; Trivedi, Dharmesh; Devarajan, Anand; Pandit Manikrao Kulkarni, MR..; Ojha, Devendra; Korra, Sakram; Neerudu, Nagendra; Seng, Lim; Godi, Stalin Peter

    2016-07-01

    First ever balloon borne lab-rat experiment up to near space stratospheric altitude levels carried out at TIFR Balloon Facility, Hydeabad using zero pressure balloons for the purpose of validating the life support system. A series of two balloon experiments conducted under joint collaboration with IN.Genius, Singapore in the year 2015. In these experiments, three lab-rats sent to stratosphere in a pressurized capsule designed to reach an altitude of 30 km by keeping constant pressure, temperature and maintained at a precise rate of oxygen supply inside the capsule. The first experiment conducted on 1 ^{st} February, 2015 with a total suspended weight of 225 kg. During the balloon ascent stage at 18 km altitude, sensors inside the capsule reported drastic drop in internal pressure while oxygen and temperatures maintained at correct levels resulted in premature fligt termination at 20.1 km. All the three lab-rats recovered without life due to the collapse of their lungs caused by the depressurization inside the capsule. The second experiment conducted on 14th March, 2015 using a newly developed capsule with rectification of depressurization fault by using improved sealing gaskets and hermitically sealed connectors for sending lab-rats again to stratosphere comprising a total suspended load of 122.3 kg. The balloon flight was terminated after reaching 29.5 km in 110 minutes and succesfully recovered all the three lab-rats alive. This paper focuses on lessons learnt of the development of the life support system as an integral pressurized vessel, flight control instrumentation, flight simulation tests using thermo-vaccum chamber with pre-flight operations.

  8. Updated version of an interim connection space LabPQR for spectral color reproduction: LabLab.

    Science.gov (United States)

    Cao, Qian; Wan, Xiaoxia; Li, Junfeng; Liang, Jingxing

    2016-09-01

    In this paper, we propose a new interim connection space (ICS) called LabLab, which is an updated version of LabPQR, to overcome the drawback that the last three dimensions of LabPQR have no definite colorimetric meanings. We extended and improved the method by which the first three dimensions of LabPQR are deduced to obtain an ICS consisting of two sets of CIELAB values under different illuminants, and the reconstructed spectra from LabLab were obtained by minimizing colorimetric errors by means of the computational formula of the CIE-XYZ tristimulus values combined with least-squares best fit. The improvement obtained from the proposed method was tested to compress and reconstruct the reflectance spectra of the 1950 Natural Color System color chips and more than 50,000 ISO SOCS color patches as well as six multispectral images acquired by multispectral image acquisition systems using 1600 glossy Munsell color chips as training samples. The performance was evaluated by the mean values of color differences between the original and reconstructed spectra under the CIE 1931 standard colorimetric observer and the CIE standard illuminants D50, D55, D65, D75, F2, F7, F11, and A as well as five multichip white LED light sources. The mean and maximum values of the root mean square errors between the original and reconstructed spectra were also calculated. The experimental results show that the proposed three LabLab interim connection spaces significantly outperform principal component analysis, LabPQR, XYZLMS, Fairman-Brill, and LabRGB in colorimetric reconstruction accuracy at the cost of slight reduction of spectral reconstruction accuracy and illuminant independence of color differences of the suggested LabLab interim connection spaces outperform other interim connection spaces. In addition, the presented LabLab interim connection spaces could be quite compatible with the extensively used colorimetric management system since each dimension has definite colorimetric

  9. Estimating Biophysical Crop Properties by a Machine Learning Model Inversion using Hyperspectral Imagery of Different Resolution

    Science.gov (United States)

    Preidl, S.; Doktor, D.

    2013-12-01

    This study investigates how image resolution and phenology affects the quality of biophysical variable estimation of different crop types. Hence, several hyperspectral at-sensor radiance images (400-2500 nm) of 1, 2 and 3 meter resolution were acquired by an AISA dual airborne system to estimate leaf chlorophyll content and leaf area index (LAI) of different crop types. The study area describes a climatic gradient that ranges from the Magdeburg Börde (130 meter a.s.l.) to the northeast of the Harz Mountain (450 meter a.s.l.), Germany. The 35 kilometer long flight strip is recorded on the same day at all three resolutions. Ground measurements were conducted simultaneously to the flight campaigns on selected crop fields. The SLC model was coupled with the atmospheric model MODTRAN4 to build up a look-up table (LUT) of simulated at-sensor radiances. To support a fast and more accurate inversion process, LUT-spectra were selected for model inversion which location in the PCA space (spanned by the first three principal components) is similar to the one of the measured spectra. A support vector regression (SVR) was trained on the reduced LUT to perform a pixel-based inversion of the hyperspectral images, subsequently. A multi-parameter sensitivity analysis was recently developed to define the most influential parameters for a reasonable model setup in the first place. This completes the development of an automated inversion process chain to estimate leaf and canopy biophysical properties. To achieve reasonable inversion results each pixel should be radiatively independent from its surrounding pixels. Image texture is used to calculate the second-order statistical variance between pixel pairs quantifying spatial heterogeneity throughout the spectral domain. The texture measurement can be employed as an uncertainty assessment of the biophysical variable estimation map. Results show that vegetated areas within the field are representing spectrally homogeneous systems. In

  10. Benchmarking News Recommendations in a Living Lab

    OpenAIRE

    Hopfgartner, Frank; Kille, Benjamin; Lommatzsch, Andreas; Plumbaum, Till; Brodt, Torben; Heintz, Tobias

    2014-01-01

    Most user-centric studies of information access systems in literature suffer from unrealistic settings or limited numbers of users who participate in the study. In order to address this issue, the idea of a living lab has been promoted. Living labs allow us to evaluate research hypotheses using a large number of users who satisfy their information need in a real context. In this paper, we introduce a living lab on news recommendation in real time. The living lab has first been organized as Ne...

  11. Learning from an Ambient Assisted Living Lab

    DEFF Research Database (Denmark)

    Bygholm, Ann; Kanstrup, Anne Marie

    2014-01-01

    This paper presents methodological lessons learned from an Ambient Assisted Living (AAL) lab exploring the use of intelligent beds in a nursing home. The living lab study was conducted over a period of three month. 20 intelligent beds were installed. Data was collected via self...... strengths, weaknesses, opportunities, and threats identified in the living lab of the intelligent bed. The paper concludes by emphasizing the need for mature technology, long-term studies, clarification of role and tasks of different stakeholders, and attention on methods used for living lab evaluations....

  12. MatLab Script and Functional Programming

    Science.gov (United States)

    Shaykhian, Gholam Ali

    2007-01-01

    MatLab Script and Functional Programming: MatLab is one of the most widely used very high level programming languages for scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. The MatLab seminar covers the functional and script programming aspect of MatLab language. Specific expectations are: a) Recognize MatLab commands, script and function. b) Create, and run a MatLab function. c) Read, recognize, and describe MatLab syntax. d) Recognize decisions, loops and matrix operators. e) Evaluate scope among multiple files, and multiple functions within a file. f) Declare, define and use scalar variables, vectors and matrices.

  13. NCL Objective #5 - Nanotechnology Characterization Lab (NCL)

    Science.gov (United States)

    Nanotechnology Characterization Lab (NCL) Objective #5: Engage and Facilitate Academic and Industrial-based Knowledge Sharing of Nanomaterial Performance Data and Behavior Resulting from Pre-Clinical Testing.

  14. Jefferson Lab, a status report

    International Nuclear Information System (INIS)

    Thomas Jefferson National Accelerator Facility (Jefferson Lab; formerly known as CEBAF), operates a 4 GeV, 200 microA continuous wave (CW) electron accelerator that re-circulates the beam five times through two superconducting 400 MeV linacs. Electrons can be extracted from any of the five recirculation passes and beam can be simultaneously delivered to the three experimental halls. As the commissioning stage nears completion, the accelerator is becoming a fully operational machine. Experiments in Hall C have been underway since November 1995 with beam powers of over 300 kW at various energies. Hall A has received beam for spectrometer commissioning, while Hall B is expected to receive its first beam in the fall of 1996. Accelerator availability of greater than 70% during physics runs and excellent beam quality have contributed to making Jefferson Lab a world class laboratory for accelerator-based electromagnetic nuclear physics. With the high performance of the superconducting RF cavities, machine upgrades to 6 GeV, and eventually 8 to 10 GeV are now in the planning stages. Operational and commissioning details concerning all aspects of the machine will be discussed

  15. Building biophysics in mid-century China: the University of Science and Technology of China.

    Science.gov (United States)

    Luk, Yi Lai Christine

    2015-01-01

    Biophysics has been either an independent discipline or an element of another discipline in the United States, but it has always been recognized as a stand-alone discipline in the People's Republic of China (PRC) since 1949. To inquire into this apparent divergence, this paper investigates the formational history of biophysics in China by examining the early institutional history of one of the best-known and prestigious science and technology universities in the PRC, the University of Science and Technology of China (USTC). By showing how the university and its biophysics program co-evolved with national priorities from the school's founding in 1958 to the eve of the Cultural Revolution in 1966, the purpose of this paper is to assess the development of a scientific discipline in the context of national demands and institutional politics. Specific materials for analysis include the school's admission policies, curricula, students' dissertations, and research program. To further contextualize the institutional setting of Chinese biophysics, this paper begins with a general history of proto-biophysical institutions in China during the Nationalist-Communist transitional years. This paper could be of interest to historians wanting to know more about the origin of the biophysics profession in China, and in particular how research areas that constitute biophysics changed in tandem with socio-political contingencies. PMID:25564431

  16. Diagnostic efficacy of biophysical tests and cerebral-umbilical index when assessing fetal oxygenation

    Directory of Open Access Journals (Sweden)

    Čančarević-Đajić Branka

    2013-01-01

    Full Text Available Introduction. Perinatal morbidity and mortality are the ultimate indicators of antenatal care today, whose responsible task is to assess the respiratory function of the placenta, fetal growth and placental maturation in order to provide conditions for the delivery of a living and viable newborn. The diagnostic procedures of antenatal care tested within this study were the biophysical tests of cardiotocography and the fetal biophysical profile, along with the colour doppler evaluation of the cerebral-umbilical ratio. The objective of this study was to determine the most effective diagnostic procedure when assessing fetal oxygenation. Materials and Methods. The prospective study included 119 pregnant women. They all underwent cardiotocography, biophysical profile and colour doppler evaluation of the cerebral-umbilical ratio. The babies’ umbilical artery blood pH was determined in the first minute upon birth, along with the Apgar score. Results. The results were processed statistically and the most effective diagnostic procedure for the evaluation of fetal oxygenation was selected, after which the rates of perinatal morbidity and mortality were calculated. The findings revealed that cardiotocography was the most sensitive antepartal predictor of fetal acidosis, while the fetal biophysical profile proved the most specific. The rates of perinatal morbidity and of perinatal mortality were 24.37% and 1.68%, respectively. Conclusion. The findings analysis revealed a high statistical significance of both biophysical tests and the cerebral-umbilical ratio evaluation as predictors of the fetal distress syndrome. The analysis of the cerebral-umbilical ratio and biophysical tests showed that the cerebral-umbilical ratio evaluation not only was more sensitive as a parameter compared to biophysical tests but it was also more specific than cardiotocography. Cardiotocography is the most sensitive antepartal predictor of fetal acidosis, followed by the cerebral

  17. Soil functional types: surveying the biophysical dimensions of soil security

    Science.gov (United States)

    Cécillon, Lauric; Barré, Pierre

    2015-04-01

    Soil is a natural capital that can deliver key ecosystem services (ES) to humans through the realization of a series of soil processes controlling ecosystem functioning. Soil is also a diverse and endangered natural resource. A huge pedodiversity has been described at all scales, which is strongly altered by global change. The multidimensional concept soil security, encompassing biophysical, economic, social, policy and legal frameworks of soils has recently been proposed, recognizing the role of soils in global environmental sustainability challenges. The biophysical dimensions of soil security focus on the functionality of a given soil that can be viewed as the combination of its capability and its condition [1]. Indeed, all soils are not equal in term of functionality. They show different processes, provide different ES to humans and respond specifically to global change. Knowledge of soil functionality in space and time is thus a crucial step towards the achievement soil security. All soil classification systems incorporate some functional information, but soil taxonomy alone cannot fully describe the functioning, limitations, resistance and resilience of soils. Droogers and Bouma [2] introduced functional variants (phenoforms) for each soil type (genoform) so as to fit more closely to soil functionality. However, different genoforms can have the same functionality. As stated by McBratney and colleagues [1], there is a great need of an agreed methodology for defining the reference state of soil functionality. Here, we propose soil functional types (SFT) as a relevant classification system for the biophysical dimensions of soil security. Following the definition of plant functional types widely used in ecology, we define a soil functional type as "a set of soil taxons or phenoforms sharing similar processes (e.g. soil respiration), similar effects on ecosystem functioning (e.g. primary productivity) and similar responses to global change (land-use, management or

  18. Biophysical Aspects of Radiation Quality. Second Panel Report

    International Nuclear Information System (INIS)

    If a living system is exposed to ionizing radiation a sequence of events follows. It starts with the absorption and dissipation of radiation energy, and continues through various physico-chemical and biochemical reactions up to the final biological end point observed. One of the aims of research in quantitative radiation biology is to understand the mechanism of this sequence of actions and to explore the differences in quality of different kinds of radiations. Because of its complexity, progress in this work requires the combined efforts of physicists, biochemists, biologists and physicians. It should, however, be done in very close collaboration rather than in following isolated lines in any one direction. For this reason, and because of the growing importance of the field for almost all applications of ionizing radiations, it was felt desirable to bring together a group of scientists engaged in research on radiation quality who represented a wide range of interests. The first panel on Biophysical Aspects of Radiation Quality, convened by the International Atomic Energy Agency in Vienna and held from 29 March to 2 April 1965, proved to be a successful beginning, stimulating a useful exchange of ideas and information. By this meeting, and the resulting collection of papers, published in 1966 as No. 58 of the Agency's Technical Reports Series, the importance of research on radiation quality was highlighted and the field itself became more clearly defined. The Agency held a second Panel on the same subject in Vienna from 14 to 18 April 1967. This meeting was attended by 18 experts from 10 countries, and representatives from Euratom and WHO. The Czechoslovak Socialist Republic, France, India and Poland were represented for the first time. Fourteen papers were presented and discussed in some detail. It became evident that much progress had been made since the previous meeting in certain areas such as microdosimetry, the dependence of the oxygen effect on radiation

  19. Italian biophysics and SIBPA speed-up the pace towards the long and winding road of the interdisciplinary science.

    Science.gov (United States)

    Giacomazza, Daniela; Musio, Carlo

    2016-01-01

    This Special Issue of Biophysical Chemistry presents a selection of the contributions presented at the XXII National Congress of the Italian Society of Pure and Applied Biophysics (i.e., SIBPA, Società Italiana di Biofisica Pura ed Applicata) held on September 2014 in Palermo, Italy. Topics cover all biophysical disciplines, from molecular to cellular, to integrative biophysics giving a comprehensive view of the inter- and multi-disciplinary approach of modern biophysics. SIBPA, which turned 40 in 2013, continues to grow and attract interest.

  20. Biophysical mechanism for ras-nanocluster formation and signaling in plasma membrane.

    Directory of Open Access Journals (Sweden)

    Thomas Gurry

    Full Text Available Ras GTPases are lipid-anchored G proteins, which play a fundamental role in cell signaling processes. Electron micrographs of immunogold-labeled Ras have shown that membrane-bound Ras molecules segregate into nanocluster domains. Several models have been developed in attempts to obtain quantitative descriptions of nanocluster formation, but all have relied on assumptions such as a constant, expression-level independent ratio of Ras in clusters to Ras monomers (cluster/monomer ratio. However, this assumption is inconsistent with the law of mass action. Here, we present a biophysical model of Ras clustering based on short-range attraction and long-range repulsion between Ras molecules in the membrane. To test this model, we performed Monte Carlo simulations and compared statistical clustering properties with experimental data. We find that we can recover the experimentally-observed clustering across a range of Ras expression levels, without assuming a constant cluster/monomer ratio or the existence of lipid rafts. In addition, our model makes predictions about the signaling properties of Ras nanoclusters in support of the idea that Ras nanoclusters act as an analog-digital-analog converter for high fidelity signaling.

  1. A simple biophysically plausible model for long time constants in single neurons.

    Science.gov (United States)

    Tiganj, Zoran; Hasselmo, Michael E; Howard, Marc W

    2015-01-01

    Recent work in computational neuroscience and cognitive psychology suggests that a set of cells that decay exponentially could be used to support memory for the time at which events took place. Analytically and through simulations on a biophysical model of an individual neuron, we demonstrate that exponentially decaying firing with a range of time constants up to minutes could be implemented using a simple combination of well-known neural mechanisms. In particular, we consider firing supported by calcium-controlled cation current. When the amount of calcium leaving the cell during an interspike interval is larger than the calcium influx during a spike, the overall decay in calcium concentration can be exponential, resulting in exponential decay of the firing rate. The time constant of the decay can be several orders of magnitude larger than the time constant of calcium clearance, and it could be controlled externally via a variety of biologically plausible ways. The ability to flexibly and rapidly control time constants could enable working memory of temporal history to be generalized to other variables in computing spatial and ordinal representations.

  2. Empirical and biophysical estimations of human cochlea's psychophysical tuning curve sharpness

    Science.gov (United States)

    Chan, Wei Xuan; Kim, Namkeun; Yoon, Yong-Jin

    2016-01-01

    Despite the advances in cochlear research, the estimation of auditory nerve fiber frequency tuning of human cochlea is mostly based on psychophysical measurements. Although efforts had been made to estimate human frequency tuning sharpness from various physiological measurements which are less species dependent such as the compound action potential and stimulus-frequency otoacoustic emission delay, conclusions on the relative frequency tuning sharpness compared with that of other mammals vary. We simulated the biophysical human cochlea's tuning curve based on physiological measurements of human cochlea and compared the human frequency tuning sharpness with results from empirical methods as well as experimental data of other mammalian cochleae. The compound action potential are more accurate at frequencies below 3 kHz while the stimulus frequency-otoacoustic emission delay are more accurate at frequencies above 1 kHz regions. The results from mechanical cochlear models, with support from conclusions of the other two empirical methodologies, suggest that the human frequency tuning sharpness at frequencies below 1 kHz is similar to common laboratory mammals but is exceptionally sharp at higher frequencies.

  3. Effects of graphene oxide nanosheets on the ultrastructure and biophysical properties of the pulmonary surfactant film.

    Science.gov (United States)

    Hu, Qinglin; Jiao, Bao; Shi, Xinghua; Valle, Russell P; Zuo, Yi Y; Hu, Guoqing

    2015-11-21

    Graphene oxide (GO) is the most common derivative of graphene and has been used in a large range of biomedical applications. Despite considerable progress in understanding its cytotoxicity, its potential inhalation toxicity is still largely unknown. As the pulmonary surfactant (PS) film is the first line of host defense, interaction with the PS film determines the fate of the inhaled nanomaterials and their potential toxicity. Using a coarse-grained molecular dynamics model, we reported, for the first time, a novel mechanism of toxicity caused by the inhaled GO nanosheets. Upon deposition, the GO nanosheets induce pores in the PS film and thus have adverse effects on the ultrastructure and biophysical properties of the PS film. Notably, the pores induced by GO nanosheets result in increasing the compressibility of the PS film, which is an important indication of surfactant inhibition. In vitro experiments have also been conducted to study the interactions between GO and animal-derived natural PS films, qualitatively confirming the simulation results.

  4. Integrating Economic Models with Biophysical Models in the Willamette Water 2100 Project

    Science.gov (United States)

    Jaeger, W. K.; Plantinga, A.

    2013-12-01

    This paper highlights the human system modeling components for Willamette Water 2100, a comprehensive, highly integrated study of hydrological, ecological, and human factors affecting water scarcity in the Willamette River Basin (WRB). The project is developing a spatiotemporal simulation model to predict future trajectories of water scarcity, and to evaluate mitigation policies. Economic models of land use and water use are the main human system models in WW2100. Water scarcity depends on both supply and demand for water, and varies greatly across time and space (Jaeger et al., 2013). Thus, the locations of human water use can have enormous influence on where and when water is used, and hence where water scarcity may arise. Modeling the locations of human uses of water (e.g., urban versus agricultural) as well as human values and choices, are the principal quantitative ways that social science can contribute to research of this kind. Our models are empirically-based models of human resource allocation. Each model reflects private behavior (choices by households, farms, firms), institutions (property rights, laws, markets, regulations), public infrastructure (dams, canals, highways), and also 'external drivers' that influence the local economy (migration, population growth, national markets and policies). This paper describes the main model components, emphasizing similarities between human and biophysical components of the overall project, and the model's linkages and feedbacks relevant to our predictions of changes in water scarcity between now and 2100. Results presented include new insights from individual model components as well as available results from the integrated system model. Issues include water scarcity and water quality (temperature) for out-of-stream and instream uses, the impact of urban expansion on water use and potential flood damage. Changes in timing and variability of spring discharge with climate change, as well as changes in human uses of

  5. Biophysical principles predict fitness landscapes of drug resistance.

    Science.gov (United States)

    Rodrigues, João V; Bershtein, Shimon; Li, Anna; Lozovsky, Elena R; Hartl, Daniel L; Shakhnovich, Eugene I

    2016-03-15

    Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational pathways of antibiotic escape. Here, we developed a predictive biophysics-based fitness landscape of trimethoprim (TMP) resistance for Escherichia coli dihydrofolate reductase (DHFR). We investigated the activity, binding, folding stability, and intracellular abundance for a complete set of combinatorial DHFR mutants made out of three key resistance mutations and extended this analysis to DHFR originated from Chlamydia muridarum and Listeria grayi We found that the acquisition of TMP resistance via decreased drug affinity is limited by a trade-off in catalytic efficiency. Protein stability is concurrently affected by the resistant mutants, which precludes a precise description of fitness from a single molecular trait. Application of the kinetic flux theory provided an accurate model to predict resistance phenotypes (IC50) quantitatively from a unique combination of the in vitro protein molecular properties. Further, we found that a controlled modulation of the GroEL/ES chaperonins and Lon protease levels affects the intracellular steady-state concentration of DHFR in a mutation-specific manner, whereas IC50 is changed proportionally, as indeed predicted by the model. This unveils a molecular rationale for the pleiotropic role of the protein quality control machinery on the evolution of antibiotic resistance, which, as we illustrate here, may drastically confound the evolutionary outcome. These results provide a comprehensive quantitative genotype-phenotype map for the essential enzyme that serves as an important target of antibiotic and anticancer therapies.

  6. Unofficial Road Building in the Amazon: Socioeconomic and Biophysical Explanations

    Science.gov (United States)

    Perz, Stephen G.; Caldas, Marcellus M.; Arima, Eugenio; Walker, Robert J.

    2007-01-01

    Roads have manifold social and environmental impacts, including regional development, social conflicts and habitat fragmentation. 'Road ecology' has emerged as an approach to evaluate the various ecological and hydrological impacts of roads. This article aims to complement road ecology by examining the socio-spatial processes of road building itself. Focusing on the Brazilian Amazon, a heavily-studied context due to forest fragmentation by roads, the authors consider non-state social actors who build 'unofficial roads' for the purpose of gaining access to natural resources to support livelihoods and community development. They examine four case studies of roads with distinct histories in order to explain the socio-spatial processes behind road building in terms of profit maximization, land tenure claims, co-operative and conflictive political ecologies, and constraints as well as opportunities afforded by the biophysical environment. The study cases illustrate the need for a multi-pronged theoretical approach to understanding road building, and call for more attention to the role of non-state actors in unofficial road construction.

  7. Biophysical model of prokaryotic diversity in geothermal hot springs.

    Science.gov (United States)

    Klales, Anna; Duncan, James; Nett, Elizabeth Janus; Kane, Suzanne Amador

    2012-02-01

    Recent studies of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than a single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. We present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms.

  8. Biophysical mechanism of transient retinal phototropism in rod photoreceptors

    Science.gov (United States)

    Zhao, Xiaohui; Thapa, Damber; Wang, Benquan; Gai, Shaoyan; Yao, Xincheng

    2016-03-01

    Oblique light stimulation evoked transient retinal phototropism (TRP) has been recently detected in frog and mouse retinas. High resolution microscopy of freshly isolated retinas indicated that the TRP is predominated by rod photoreceptors. Comparative confocal microscopy and optical coherence tomography (OCT) revealed that the TRP predominantly occurred from the photoreceptor outer segment (OS). However, biophysical mechanism of rod OS change is still unknown. In this study, frog retinal slices, which open a cross section of retinal photoreceptor and other functional layers, were used to test the effect of light stimulation on rod OS. Near infrared light microscopy was employed to monitor photoreceptor changes in retinal slices stimulated by a rectangular-shaped visible light flash. Rapid rod OS length change was observed after the stimulation delivery. The magnitude and direction of the rod OS change varied with the position of the rods within the stimulated area. In the center of stimulated region the length of the rod OS shrunk, while in the peripheral region the rod OS tip swung towards center region in the plane perpendicular to the incident stimulus light. Our experimental result and theoretical analysis suggest that the observed TRP may reflect unbalanced disc-shape change due to localized pigment bleaching. Further investigation is required to understand biochemical mechanism of the observed rod OS kinetics. Better study of the TRP may provide a noninvasive biomarker to enable early detection of age-related macular degeneration (AMD) and other diseases that are known to produce retinal photoreceptor dysfunctions.

  9. Alteration of biophysical activity of pulmonary surfactant by aluminosilicate nanoparticles.

    Science.gov (United States)

    Kondej, Dorota; Sosnowski, Tomasz R

    2013-02-01

    The influence of five different types of aluminosilicate nanoparticles (NPs) on the dynamic surface activity of model pulmonary surfactant (PS) (Survanta) was studied experimentally using oscillating bubble tensiometry. Bentonite, halloysite and montmorillonite (MM) NPs, which are used as fillers of polymer composites, were characterized regarding the size distribution, morphology and surface area. Particle doses applied in the studies were estimated based on the inhalation rate and duration, taking into account the expected aerosol concentration and deposition efficiency after penetration of NPs into the alveolar region. The results indicate that aluminosilicate NPs at concentrations in the pulmonary liquid above 0.1 mg cm(-3) are capable of promoting alterations of the original dynamic biophysical activity of the PS. This effect is indicated by deviation of the minimum surface tension, stability index and the size of surface tension hysteresis. Such response is dependent on the type of NPs present in the system and is stronger when particle concentration increases. It is suggested that interactions between NPs and the PS must be related to the surfactant adsorption on the suspended particles, while in the case of surface-modified clay NPs the additional washout of surface-active components may be expected. It is speculated that observed changes in surface properties of the surfactant may be associated with undesired health effects following extensive inhalation of aluminosilicate NPs in the workplace. PMID:23363039

  10. Biophysical and biological meanings of healthspan from C. elegans cohort

    Energy Technology Data Exchange (ETDEWEB)

    Suda, Hitoshi, E-mail: suda@tsc.u-tokai.ac.jp

    2014-09-12

    Highlights: • We focus on a third factor, noise, as well as on genetic and environmental factors. • C. elegans fed a healthy food had an extended healthspan as compared to those fed a conventional diet. • An amplification of ATP noise was clearly evident from around the onset of biodemographic aging. • The extension of timing of noise amplification may contribute to effectively extending the healthspan. • The same mechanism of the mean lifespan extension in C. elegans may be realized in humans. - Abstract: Lifespan among individuals ranges widely in organisms from yeast to mammals, even in an isogenic cohort born in a nearly uniform environment. Needless to say, genetic and environmental factors are essential for aging and lifespan, but in addition, a third factor or the existence of a stochastic element must be reflected in aging and lifespan. An essential point is that lifespan or aging is an unpredictable phenomenon. The present study focuses on elucidating the biophysical and biological meanings of healthspan that latently indwells a stochastic nature. To perform this purpose, the nematode Caenorhabditis elegans served as a model animal. C. elegans fed a healthy food had an extended healthspan as compared to those fed a conventional diet. Then, utilizing this phenomenon, we clarified a mechanism of healthspan extension by measuring the single-worm ATP and estimating the ATP noise (or the variability of the ATP content) among individual worms and by quantitatively analyzing biodemographic data with the lifespan equation that was derived from a fluctuation theory.

  11. Biophysical induction of vascular smooth muscle cell podosomes.

    Directory of Open Access Journals (Sweden)

    Na Young Kim

    Full Text Available Vascular smooth muscle cell (VSMC migration and matrix degradation occurs with intimal hyperplasia associated with atherosclerosis, vascular injury, and restenosis. One proposed mechanism by which VSMCs degrade matrix is through the use of podosomes, transient actin-based structures that are thought to play a role in extracellular matrix degradation by creating localized sites of matrix metalloproteinase (MMP secretion. To date, podosomes in VSMCs have largely been studied by stimulating cells with phorbol esters, such as phorbol 12,13-dibutyrate (PDBu, however little is known about the physiological cues that drive podosome formation. We present the first evidence that physiological, physical stimuli mimicking cues present within the microenvironment of diseased arteries can induce podosome formation in VSMCs. Both microtopographical cues and imposed pressure mimicking stage II hypertension induce podosome formation in A7R5 rat aortic smooth muscle cells. Moreover, wounding using a scratch assay induces podosomes at the leading edge of VSMCs. Notably the effect of each of these biophysical stimuli on podosome stimulation can be inhibited using a Src inhibitor. Together, these data indicate that physical cues can induce podosome formation in VSMCs.

  12. Biophysical principles predict fitness landscapes of drug resistance.

    Science.gov (United States)

    Rodrigues, João V; Bershtein, Shimon; Li, Anna; Lozovsky, Elena R; Hartl, Daniel L; Shakhnovich, Eugene I

    2016-03-15

    Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational pathways of antibiotic escape. Here, we developed a predictive biophysics-based fitness landscape of trimethoprim (TMP) resistance for Escherichia coli dihydrofolate reductase (DHFR). We investigated the activity, binding, folding stability, and intracellular abundance for a complete set of combinatorial DHFR mutants made out of three key resistance mutations and extended this analysis to DHFR originated from Chlamydia muridarum and Listeria grayi We found that the acquisition of TMP resistance via decreased drug affinity is limited by a trade-off in catalytic efficiency. Protein stability is concurrently affected by the resistant mutants, which precludes a precise description of fitness from a single molecular trait. Application of the kinetic flux theory provided an accurate model to predict resistance phenotypes (IC50) quantitatively from a unique combination of the in vitro protein molecular properties. Further, we found that a controlled modulation of the GroEL/ES chaperonins and Lon protease levels affects the intracellular steady-state concentration of DHFR in a mutation-specific manner, whereas IC50 is changed proportionally, as indeed predicted by the model. This unveils a molecular rationale for the pleiotropic role of the protein quality control machinery on the evolution of antibiotic resistance, which, as we illustrate here, may drastically confound the evolutionary outcome. These results provide a comprehensive quantitative genotype-phenotype map for the essential enzyme that serves as an important target of antibiotic and anticancer therapies. PMID:26929328

  13. The biophysical bases of will-less behaviours

    Directory of Open Access Journals (Sweden)

    Jose Luis ePerez Velazquez

    2012-10-01

    Full Text Available Are there distinctions at the neurophysiological level that correlate with voluntary and involuntary actions? Whereas the wide variety of involuntary behaviours (and here mostly the deviant or pathological ones will be considered will necessarily be represented at some biophysical level in nervous system activity, for after all those cellular activity patterns manifest themselves as behaviours and thus there will be a multiplicity of them, there could be some general tendencies to be discerned amongst that assortment. Collecting observations derived from neurophysiological activity associated with several pathological conditions characterised by presenting will-less actions such as Parkinson’s disease, seizures, alien hand syndrome and tics, it is proposed that a general neurophysiologic tendency of brain activity that correlates with involuntary actions is higher than normal synchrony in specific brain cell networks, depending upon the behaviour in question. Wilful, considered normal behaviour, depends on precise coordination of the collective activity in cell ensembles that may be lost, or diminished, when there are tendencies towards more than normal or aberrant synchronization of cellular activity. Hence, rapid fluctuations in synchrony is associated with normal actions and cognition while less variability in brain recordings particularly with regards to synchronization could be a signature of unconscious and deviant behaviours in general.

  14. Ecosystem biophysical memory in the southwestern North America climate system

    International Nuclear Information System (INIS)

    To elucidate the potential role of vegetation to act as a memory source in the southwestern North America climate system, we explore correlation structures of remotely sensed vegetation dynamics with precipitation, temperature and teleconnection indices over 1982–2006 for six ecoregions. We found that lagged correlations between vegetation dynamics and climate variables are modulated by the dominance of monsoonal or Mediterranean regimes and ecosystem-specific physiological processes. Subtropical and tropical ecosystems exhibit a one month lag positive correlation with precipitation, a zero- to one-month lag negative correlation with temperature, and modest negative effects of sea surface temperature (SST). Mountain forests have a zero month lag negative correlation with precipitation, a zero–one month lag negative correlation with temperature, and no significant correlation with SSTs. Deserts show a strong one–four month lag positive correlation with precipitation, a low zero–two month lag negative correlation with temperature, and a high four–eight month lag positive correlation with SSTs. The ecoregion-specific biophysical memories identified offer an opportunity to improve the predictability of land–atmosphere interactions and vegetation feedbacks onto climate. (letter)

  15. A Biophysical Neural Model To Describe Spatial Visual Attention

    Science.gov (United States)

    Hugues, Etienne; José, Jorge V.

    2008-02-01

    Visual scenes have enormous spatial and temporal information that are transduced into neural spike trains. Psychophysical experiments indicate that only a small portion of a spatial image is consciously accessible. Electrophysiological experiments in behaving monkeys have revealed a number of modulations of the neural activity in special visual area known as V4, when the animal is paying attention directly towards a particular stimulus location. The nature of the attentional input to V4, however, remains unknown as well as to the mechanisms responsible for these modulations. We use a biophysical neural network model of V4 to address these issues. We first constrain our model to reproduce the experimental results obtained for different external stimulus configurations and without paying attention. To reproduce the known neuronal response variability, we found that the neurons should receive about equal, or balanced, levels of excitatory and inhibitory inputs and whose levels are high as they are in in vivo conditions. Next we consider attentional inputs that can induce and reproduce the observed spiking modulations. We also elucidate the role played by the neural network to generate these modulations.

  16. Biophysical and biological meanings of healthspan from C. elegans cohort

    International Nuclear Information System (INIS)

    Highlights: • We focus on a third factor, noise, as well as on genetic and environmental factors. • C. elegans fed a healthy food had an extended healthspan as compared to those fed a conventional diet. • An amplification of ATP noise was clearly evident from around the onset of biodemographic aging. • The extension of timing of noise amplification may contribute to effectively extending the healthspan. • The same mechanism of the mean lifespan extension in C. elegans may be realized in humans. - Abstract: Lifespan among individuals ranges widely in organisms from yeast to mammals, even in an isogenic cohort born in a nearly uniform environment. Needless to say, genetic and environmental factors are essential for aging and lifespan, but in addition, a third factor or the existence of a stochastic element must be reflected in aging and lifespan. An essential point is that lifespan or aging is an unpredictable phenomenon. The present study focuses on elucidating the biophysical and biological meanings of healthspan that latently indwells a stochastic nature. To perform this purpose, the nematode Caenorhabditis elegans served as a model animal. C. elegans fed a healthy food had an extended healthspan as compared to those fed a conventional diet. Then, utilizing this phenomenon, we clarified a mechanism of healthspan extension by measuring the single-worm ATP and estimating the ATP noise (or the variability of the ATP content) among individual worms and by quantitatively analyzing biodemographic data with the lifespan equation that was derived from a fluctuation theory

  17. Symposium on Biophysics and Physiology of Biological Transport

    CERN Document Server

    Capraro, V; Porter, K; Robertson, J

    1967-01-01

    The study of cell membranes began to attract increasing interest before the turn of the present century with the observations of 0 verton. Since that time many investigators have become interested in the broad problem of structure and function of the membrane and today we find ourselVes at a stage in which several branches of research, particularly physical chemistry, biochemistry, biophysics, physiology and pharmacology have come together, leading to the possibility of obtaining a better perspective of the overall problems. The purpose of this Symposium was to assemble in an orderly sequence representations of the knowledge of membranes achieved to date in the areas of the various disciplines. It was thought that to bring together many points of view on a problem should allow the conferees to see better what had been accomplished, what has been overlooked and what needs further development. It is to be hoped that efforts of this type have and will fulfill the desired purpose. This volume contains the majorit...

  18. Biophysical characterization of gold nanoparticles-loaded liposomes.

    Science.gov (United States)

    Mady, Mohsen Mahmoud; Fathy, Mohamed Mahmoud; Youssef, Tareq; Khalil, Wafaa Mohamed

    2012-10-01

    Gold nanoparticles were prepared and loaded into the bilayer of dipalmitoylphosphatidylcholine (DPPC) liposomes, named as gold-loaded liposomes. Biophysical characterization of gold-loaded liposomes was studied by transmission electron microscopy (TEM) and Fourier transform infrared (FTIR) spectroscopy as well as turbidity and rheological measurements. FTIR measurements showed that gold nanoparticles made significant changes in the frequency of the CH(2) stretching bands, revealing that gold nanoparticles increased the number of gauche conformers and create a conformational change within the acyl chains of phospholipids. The transmission electron micrographs (TEM) revealed that gold nanoparticles were loaded in the liposomal bilayer. The zeta potential of DPPC liposomes had a more negative value after incorporating of Au NPs into liposomal membranes. Turbidity studies revealed that the loading of gold nanoparticles into DPPC liposomes results in shifting the temperature of the main phase transition to a lower value. The membrane fluidity of DPPC bilayer was increased by loading the gold nanoparticles as shown from rheological measurements. Knowledge gained in this study may open the door to pursuing liposomes as a viable strategy for Au NPs delivery in many diagnostic and therapeutic applications. PMID:22027546

  19. Biophysical interactions between plant and soil: theory and practice

    Science.gov (United States)

    van der Ploeg, Martine

    2016-04-01

    Vegetation plays an essential role in the hydrological cycle, as it regulates the water flux to the atmosphere through evapotranspiration, while it is dependent on adequate water supply. Vegetation shapes the land surface by changing infiltration characteristics as a result of root growth, and controls soil moisture storage, which in turn affect runoff characteristics and groundwater recharge. Vegetation and the underlying geology are in constant interaction, wherein water plays a key role. The resilience of the coupled vegetation-soil system critically depends on its sensitivity to environmental changes. Models are a useful tool to explore interaction and feedbacks between vegetation, soil and landscape. Plants respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may complicate our modelling efforts in for example climate change impacts. Combination of new techniques to assess soil and plant properties facilitates assessment of biophysical interactions. This poster will review these techniques and compare the obtained insights of soil-plant relationships with the current modeling approaches.

  20. Universal buffers for use in biochemistry and biophysical experiments

    Directory of Open Access Journals (Sweden)

    Dewey Brooke

    2015-08-01

    Full Text Available The use of buffers that mimic biological solutions is a foundation of biochemical and biophysical studies. However, buffering agents have both specific and nonspecific interactions with proteins. Buffer molecules can induce changes in conformational equilibria, dynamic behavior, and catalytic properties merely by their presence in solution. This effect is of concern because many of the standard experiments used to investigate protein structure and function involve changing solution conditions such as pH and/or temperature. In experiments in which pH is varied, it is common practice to switch buffering agents so that the pH is within the working range of the weak acid and conjugate base. If multiple buffers are used, it is not always possible to decouple buffer induced change from pH or temperature induced change. We have developed a series of mixed biological buffers for protein analysis that can be used across a broad pH range, are compatible with biologically relevant metal ions, and avoid complications that may arise from changing the small molecule composition of buffers when pH is used as an experimental variable.

  1. Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

    Science.gov (United States)

    Blakaj, Dukagjin M; Fernandez-Fuentes, Narcis; Chen, Zigui; Hegde, Rashmi; Fiser, Andras; Burk, Robert D; Brenowitz, Michael

    2009-01-01

    Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed. PMID:19273107

  2. Biophysical constraints on gross primary production by the terrestrial biosphere

    Directory of Open Access Journals (Sweden)

    H. Wang

    2014-02-01

    Full Text Available Persistent divergences among the predictions of complex carbon cycle models include differences in the sign as well as the magnitude of the response of global terrestrial primary production to climate change. This and other problems with current models indicate an urgent need to re-assess the principles underlying the environmental controls of primary production. The global patterns of annual and maximum monthly terrestrial gross primary production (GPP by C3 plants are explored here using a simple first-principles model based on the light-use efficiency formalism and the Farquhar model for C3 photosynthesis. The model is driven by incident photosynthetically active radiation (PAR and remotely sensed green vegetation cover, with additional constraints imposed by low-temperature inhibition and CO2 limitation. The ratio of leaf-internal to ambient CO2 concentration in the model responds to growing-season mean temperature, atmospheric dryness (indexed by the cumulative water deficit, ΔE and elevation, based on optimality theory. The greatest annual GPP is predicted for tropical moist forests, but the maximum (summer monthly GPP can be as high or higher in boreal or temperate forests. These findings are supported by a new analysis of CO2 flux measurements. The explanation is simply based on the seasonal and latitudinal distribution of PAR combined with the physiology of photosynthesis. By successively imposing biophysical constraints, it is shown that partial vegetation cover – driven primarily by water shortage – represents the largest constraint on global GPP.

  3. Energy efficient neural stimulation: coupling circuit design and membrane biophysics.

    Directory of Open Access Journals (Sweden)

    Thomas J Foutz

    Full Text Available The delivery of therapeutic levels of electrical current to neural tissue is a well-established treatment for numerous indications such as Parkinson's disease and chronic pain. While the neuromodulation medical device industry has experienced steady clinical growth over the last two decades, much of the core technology underlying implanted pulse generators remain unchanged. In this study we propose some new methods for achieving increased energy-efficiency during neural stimulation. The first method exploits the biophysical features of excitable tissue through the use of a centered-triangular stimulation waveform. Neural activation with this waveform is achieved with a statistically significant reduction in energy compared to traditional rectangular waveforms. The second method demonstrates energy savings that could be achieved by advanced circuitry design. We show that the traditional practice of using a fixed compliance voltage for constant-current stimulation results in substantial energy loss. A portion of this energy can be recuperated by adjusting the compliance voltage to real-time requirements. Lastly, we demonstrate the potential impact of axon fiber diameter on defining the energy-optimal pulse-width for stimulation. When designing implantable pulse generators for energy efficiency, we propose that the future combination of a variable compliance system, a centered-triangular stimulus waveform, and an axon diameter specific stimulation pulse-width has great potential to reduce energy consumption and prolong battery life in neuromodulation devices.

  4. A Virtual Lab in Research Methods

    Science.gov (United States)

    Sommer, Barbara A.; Sommer, Robert

    2003-01-01

    A hands-on lab for a lower division research methods course used an online format with Web page, Web forms, an e-mail listproc, and chat room. The virtual section received a higher rating for overall value than did the in-person labs. Students liked its convenience and flexibility. There were no significant differences in examination performance…

  5. Innovation - A view from the Lab

    Science.gov (United States)

    The USDA Ag Lab in Peoria helps bridge the gap between agricultural producers and commercial manufacturers. In 2015, the Ag Lab, officially known as the Agricultural Research Service (ARS) National Center for Agricultural Utilization Research (NCAUR), is celebrating 75 years of research in Peoria. T...

  6. Plan van aanpak project : Social Media Lab

    NARCIS (Netherlands)

    Beer, Erwin; Kox, Corné; Willems, Frank

    2013-01-01

    Dit document beschrijft de projectopdracht voor het project Social Media Lab en geeft de criteria waaraan het project moet voldoen om te slagen. Het bevat tevens het plan van aanpak voor het uitvoeren van het project. Doel van het project is het realiseren van een fysiek Social Media Lab, waar door

  7. Programming Arduino with LabVIEW

    CERN Document Server

    Schwartz, Marco

    2015-01-01

    If you already have some experience with LabVIEW and want to apply your skills to control physical objects and make measurements using the Arduino sensor, this book is for you. Prior knowledge of Arduino and LabVIEW is essential to fully understand the projects detailed in this book.

  8. Hydrogel Beads: The New Slime Lab?

    Science.gov (United States)

    Brockway, Debra; Libera, Matthew; Welner, Heidi

    2011-01-01

    Creating slime fascinates students. Unfortunately, though intrigue is at its peak, the educational aspect of this activity is often minimal. This article describes a chemistry lab that closely relates to the slime lab and allows high school students to explore the concepts of chemical bonding, properties, and replacement reactions. It involves the…

  9. The DVCS program at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Niccolai, Silvia [Institut de Physique Nucleaire, Orsay, France

    2014-06-01

    Recent promising results, obtained at Jefferson Lab, on cross sections and asymmetries for DVCS and their link to the Generalized Parton Distributions are the focus of this paper. The extensive experimental program to measure DVCS with the 12-GeV-upgraded CEBAF in three experimental Halls (A, B, C) of Jefferson Lab, will also be presented.

  10. Jefferson Lab: Present and Future

    Science.gov (United States)

    Rossi, Patrizia

    2016-08-01

    The continuous electron beam accelerator facility and associated experimental equipment at Jefferson Lab comprise a unique facility for nuclear physics research whose upgrade is presently underway, with completion expected in 2017. The upgraded facility will accelerate electron beams to 11 GeV for experiments in the existing Halls A, B and C. In addition, a 12 GeV beam can be provided to a new experimental hall, Hall D, to generate a 9 GeV tagged photon beam. This upgrade will enable a new experimental program with substantial discovery potential to address important topics in hadronic, nuclear, and electroweak physics. Further in the future, it is envisioned that the Laboratory will evolve into an electron-ion colliding beam facility.

  11. Famed lab seeks big grid

    CERN Document Server

    Lillington, K

    2001-01-01

    DUBLIN, Ireland -- CERN, the famed Swiss high-energy particle physics lab, has a problem. It's about to start generating more data than any computer or network anywhere in the world is able to analyze. That prospect has led CERN to drive a major European project to create a vast "grid" research network of computers across Europe. When completed, the 10 million euro, Linux-based endeavor called DataGRID, will become a principal European computing resource for researchers of many disciplines. "I believe grid computing will revolutionize the way we compute, in much the same way as the World Wide Web and Internet changed the way we communicate," said John Ellis, a theoretical physicist and adviser to the director general of CERN.

  12. A dry lab for medical engineers?

    Directory of Open Access Journals (Sweden)

    Olivi Giulia

    2009-07-01

    Full Text Available Abstract Introduction We describe a teaching and training method with objective evaluation to improve medical engineering students' knowledge and analysis skills about Minimally Invasive Surgery (MIS instrumentation and techniques through hands-on experience. Training has been scheduled during a three-month course. Methods Twenty medical engineering students were trained to perform three times on a pelvic trainer a sequence of standardized drills connected with the selected MIS techniques, in order to improve their dexterity. The time required to perform each dexterity drill was recorded in seconds. Then, the participants were divided into groups and asked to write an essay about an instrument they chose, analyzing and criticizing the instrument itself. Results All the trainees showed steady improvement in skill acquisition on the laparoscopic simulator and discussed their essays, making proposals in order to improve the instrument they tested. Conclusion Significant improvement in performance with increasing skillness has been measured; during the course and during their discussion the participants showed deep knowledge of the instrument, ability to analyze and criticize it and ability to make improvement proposals. Dry lab experience for medical engineering students is useful for teaching and improving analysis and management of laparoscopic devices, allowing identification of problems and developing better devices.

  13. Mesenchymal morphogenesis of embryonic stem cells dynamically modulates the biophysical microtissue niche

    Science.gov (United States)

    Kinney, Melissa A.; Saeed, Rabbia; McDevitt, Todd C.

    2014-01-01

    Stem cell fate and function are dynamically modulated by the interdependent relationships between biochemical and biophysical signals constituting the local 3D microenvironment. While approaches to recapitulate the stem cell niche have been explored for directing stem cell differentiation, a quantitative relationship between embryonic stem cell (ESC) morphogenesis and intrinsic biophysical cues within three-dimensional microtissues has not been established. In this study, we demonstrate that mesenchymal embryonic microtissues induced by BMP4 exhibited increased stiffness and viscosity accompanying differentiation, with cytoskeletal tension significantly contributing to multicellular stiffness. Perturbation of the cytoskeleton during ESC differentiation led to modulation of the biomechanical and gene expression profiles, with the resulting cell phenotype and biophysical properties being highly correlated by multivariate analyses. Together, this study elucidates the dynamics of biophysical and biochemical signatures within embryonic microenvironments, with broad implications for monitoring tissue dynamics, modeling pathophysiological and embryonic morphogenesis and directing stem cell patterning and differentiation. PMID:24598818

  14. The extraction of physical quantities of the processor using the LabVIEW software package

    Directory of Open Access Journals (Sweden)

    Stefan Koprda

    2015-11-01

    Full Text Available The article presents the issues of modelling and simulation in the graphic environment LabVIEW from the firm National Instrument. The possibility to simulate real processes offers many advantages to designers and advance designers from various spheres, such as time saving and costs minimization. The paper deal to create a block diagram in the environment LabVIEW which will show the entry about the temperature of the processor and it will be possible to use it, we had to find an appropriate way which will allow it and will be usable for a great number of computer equipments.

  15. The extraction of physical quantities of the processor using the LabVIEW software package

    Directory of Open Access Journals (Sweden)

    Stefan Koprda

    2014-05-01

    Full Text Available he article presents the issues of modelling and simulation in the graphic environment LabVIEW from the firm National Instrument. The possibility to simulate real processes offers many advantages to designers and advance designers from various spheres, such as time saving and costs minimization. The paper deal to create a block diagram in the environment LabVIEW which will show the entry about the temperature of the processor and it will be possible to use it, we had to find an appropriate way wh ich will allow it and will be usable for a great number of computer equipments.

  16. Dlk1 Promotes a Fast Motor Neuron Biophysical Signature Required for Peak Force Execution

    OpenAIRE

    Muller, D.; Cherukuri, P; Henningfeld, K.; Poh, C. H.; Wittler, L; Grote, P.; Schluter, O.; Schmidt, J.; Laborda, J.; Bauer, S R; Brownstone, R M; Marquardt, T

    2014-01-01

    Motor neurons, which relay neural commands to drive skeletal muscle movements, encompass types ranging from "slow" to "fast," whose biophysical properties govern the timing, gradation, and amplitude of muscle force. Here we identify the noncanonical Notch ligand Delta-like homolog 1 (Dlk1) as a determinant of motor neuron functional diversification. Dlk1, expressed by ~30% of motor neurons, is necessary and sufficient to promote a fast biophysical signature in the mouse and chick. Dlk1 suppre...

  17. Mesenchymal morphogenesis of embryonic stem cells dynamically modulates the biophysical microtissue niche

    OpenAIRE

    Kinney, Melissa A.; Rabbia Saeed; McDevitt, Todd C.

    2014-01-01

    Stem cell fate and function are dynamically modulated by the interdependent relationships between biochemical and biophysical signals constituting the local 3D microenvironment. While approaches to recapitulate the stem cell niche have been explored for directing stem cell differentiation, a quantitative relationship between embryonic stem cell (ESC) morphogenesis and intrinsic biophysical cues within three-dimensional microtissues has not been established. In this study, we demonstrate that ...

  18. Extraction of Mangrove Biophysical Parameters Using Airborne LiDAR

    OpenAIRE

    Poonsak Miphokasap; Phisan Santitamnont; Kiyoshi Honda; Wasinee Wannasiri; Masahiko Nagai

    2013-01-01

    Tree parameter determinations using airborne Light Detection and Ranging (LiDAR) have been conducted in many forest types, including coniferous, boreal, and deciduous. However, there are only a few scientific articles discussing the application of LiDAR to mangrove biophysical parameter extraction at an individual tree level. The main objective of this study was to investigate the potential of using LiDAR data to estimate the biophysical parameters of mangrove trees at an individual tree scal...

  19. The problem of the competitiveness of nuclear energy : a biophysical explanation

    OpenAIRE

    Diaz Maurin, François

    2011-01-01

    In this study I try to explain the systemic problem of the low economic competitiveness of nuclear energy for the production of electricity by carrying out a biophysical analysis of its production process. Given the fact that neither econometric approaches nor onedimensional methods of energy analyses are effective, I introduce the concept of biophysical explanation as a quantitative analysis capable of handling the inherent ambiguity associated with the concept of energy. In particular, the...

  20. Diagnostic efficacy of biophysical tests and cerebral-umbilical index when assessing fetal oxygenation

    OpenAIRE

    Čančarević-Đajić Branka; Vilendečić Rade

    2013-01-01

    Introduction. Perinatal morbidity and mortality are the ultimate indicators of antenatal care today, whose responsible task is to assess the respiratory function of the placenta, fetal growth and placental maturation in order to provide conditions for the delivery of a living and viable newborn. The diagnostic procedures of antenatal care tested within this study were the biophysical tests of cardiotocography and the fetal biophysical profile, along with the colour doppler evaluation of...

  1. Biophysical characterization of G-protein coupled receptor-peptide ligand binding

    OpenAIRE

    Langelaan, David N.; Ngweniform, Pascaline; Rainey, Jan K.

    2011-01-01

    G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular response to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GRCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques which have been successfully employed for structural and biophysical characterization of peptide ligands binding to their...

  2. Human Visual System as a Double-Slit Single Photon Interference Sensor: A Comparison between Modellistic and Biophysical Tests.

    Directory of Open Access Journals (Sweden)

    Rita Pizzi

    Full Text Available This paper describes a computational approach to the theoretical problems involved in the Young's single-photon double-slit experiment, focusing on a simulation of this experiment in the absence of measuring devices. Specifically, the human visual system is used in place of a photomultiplier or similar apparatus. Beginning with the assumption that the human eye perceives light in the presence of very few photons, we measure human eye performance as a sensor in a double-slit one-photon-at-a-time experimental setup. To interpret the results, we implement a simulation algorithm and compare its results with those of human subjects under identical experimental conditions. In order to evaluate the perceptive parameters exactly, which vary depending on the light conditions and on the subject's sensitivity, we first review the existing literature on the biophysics of the human eye in the presence of a dim light source, and then use the known values of the experimental variables to set the parameters of the computational simulation. The results of the simulation and their comparison with the experiment involving human subjects are reported and discussed. It is found that, while the computer simulation indicates that the human eye has the capacity to detect the corpuscular nature of photons under these conditions, this was not observed in practice. The possible reasons for the difference between theoretical prediction and experimental results are discussed.

  3. EDITORIAL: Focus on Heavy Ions in Biophysics and Medical Physics FOCUS ON HEAVY IONS IN BIOPHYSICS AND MEDICAL PHYSICS

    Science.gov (United States)

    Durante, Marco

    2008-07-01

    Interest in energetic heavy ions is rapidly increasing in the field of biomedicine. Heavy ions are normally excluded from radiation protection, because they are not normally experienced by humans on Earth. However, knowledge of heavy ion biophysics is necessary in two fields: charged particle cancer therapy (hadrontherapy), and radiation protection in space missions. The possibility to cure tumours using accelerated heavy charged particles was first tested in Berkeley in the sixties, but results were not satisfactory. However, about 15 years ago therapy with carbon ions was resumed first in Japan and then in Europe. Heavy ions are preferable to photons for both physical and biological characteristics: the Bragg peak and limited lateral diffusion ensure a conformal dose distribution, while the high relative biological effectiveness and low oxygen enhancement ration in the Bragg peak region make the beam very effective in treating radioresistant and hypoxic tumours. Recent results coming from the National Institute of Radiological Sciences in Chiba (see the paper by Dr Tsujii and co-workers in this issue) and GSI (Germany) provide strong clinical evidence that heavy ions are indeed an extremely effective weapon in the fight against cancer. However, more research is needed in the field, especially on optimization of the treatment planning and risk of late effects in normal tissue, including secondary cancers. On the other hand, high-energy heavy ions are present in galactic cosmic radiation and, although they are rare as compared to protons, they give a major contribution in terms of equivalent dose to the crews of manned space exploratory-class missions. Exploration of the Solar System is now the main goal of the space program, and the risk caused by exposure to galactic cosmic radiation is considered a serious hindrance toward this goal, because of the high uncertainty on late effects of energetic heavy nuclei, and the lack of effective countermeasures. Risks

  4. Biophysical impacts of climate-smart agriculture in the Midwest United States.

    Science.gov (United States)

    Bagley, Justin E; Miller, Jesse; Bernacchi, Carl J

    2015-09-01

    The potential impacts of climate change in the Midwest United States present unprecedented challenges to regional agriculture. In response to these challenges, a variety of climate-smart agricultural methodologies have been proposed to retain or improve crop yields, reduce agricultural greenhouse gas emissions, retain soil quality and increase climate resilience of agricultural systems. One component that is commonly neglected when assessing the environmental impacts of climate-smart agriculture is the biophysical impacts, where changes in ecosystem fluxes and storage of moisture and energy lead to perturbations in local climate and water availability. Using a combination of observational data and an agroecosystem model, a series of climate-smart agricultural scenarios were assessed to determine the biophysical impacts these techniques have in the Midwest United States. The first scenario extended the growing season for existing crops using future temperature and CO2 concentrations. The second scenario examined the biophysical impacts of no-till agriculture and the impacts of annually retaining crop debris. Finally, the third scenario evaluated the potential impacts that the adoption of perennial cultivars had on biophysical quantities. Each of these scenarios was found to have significant biophysical impacts. However, the timing and magnitude of the biophysical impacts differed between scenarios. PMID:25393245

  5. Transforming Traditional Labs into Virtual Computing Labs for Distance Education

    Directory of Open Access Journals (Sweden)

    Gokhan Gercek

    2008-02-01

    Full Text Available The demand for on-line courses continues to risein academia because (1 on-line courses remove timebarriers that would otherwise restrict a student frompursuing academic endeavors, (2 they remove the distancebarriers for academia in reaching potential students and (3they can to some extent alleviate budgetary and physicalconstraints on the academia in imparting education tostudents. The on-line instruction mode rather easilyaccommodates courses in some disciplines such as history,sociology, and political science. However, it positssignificant adoption challenges for courses that requirehands-on computing experimentation such as computernetworking, system administration, web applicationdevelopment and database administration. Nevertheless,given the demand for on-line courses, there is a need todevise strategies that would allow students to conductcomputing experiments through remote access. This paperpresents an approach to transform traditional computerlabs into a virtual lab environment. Such transformationallows students to remotely conduct experiments thatinvolve software and hardware interaction. Themethodology presented here can be applied to a largenumber of computing courses encountered in ManagementInformation Systems and Computer Sciences disciplines.

  6. Microbial Life in Soil - Linking Biophysical Models with Observations

    Science.gov (United States)

    Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

    2015-04-01

    Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools

  7. The Colorado Plateau II: biophysical, socioeconomic, and cultural research

    Science.gov (United States)

    Mattson, David J.; van Riper, Charles

    2005-01-01

    The publication of The Colorado Plateau: Cultural, Biological, and Physical Research in 2004 marked a timely summation of current research in the Four Corners states. This new volume, derived from the seventh Biennial Conference on the Colorado Plateau in 2003, complements the previous book by focusing on the integration of science into resource management issues. The 32 chapters range in content from measuring human impacts on cultural resources, through grazing and the wildland-urban interface issues, to parameters of climate change on the Plateau. The book also introduces economic perspectives by considering shifting patterns and regional disparities in the Colorado Plateau economy. A series of chapters on mountain lions explores the human-wildland interface. These chapters deal with the entire spectrum of challenges associated with managing this large mammal species in Arizona and on the Colorado Plateau, conveying a wealth of timely information of interest to wildlife managers and enthusiasts. Another provocative set of chapters on biophysical resources explores the management of forest restoration, from the micro scale all the way up to large-scale GIS analyses of ponderosa pine ecosystems on the Colorado Plateau. Given recent concerns for forest health in the wake of fires, severe drought, and bark-beetle infestation, these chapters will prove enlightening for forest service, park service, and land management professionals at both the federal and state level, as well as general readers interested in how forest management practices will ultimately affect their recreation activities. With broad coverage that touches on topics as diverse as movement patterns of rattlesnakes, calculating watersheds, and rescuing looted rockshelters, this volume stands as a compendium of cutting-edge research on the Colorado Plateau that offers a wealth of insights for many scholars.

  8. Structural features underlying raloxifene's biophysical interaction with bone matrix.

    Science.gov (United States)

    Bivi, Nicoletta; Hu, Haitao; Chavali, Balagopalakrishna; Chalmers, Michael J; Reutter, Christopher T; Durst, Gregory L; Riley, Anna; Sato, Masahiko; Allen, Matthew R; Burr, David D; Dodge, Jeffrey A

    2016-02-15

    Raloxifene, a selective estrogen receptor modulator (SERM), reduces fracture risk at least in part by improving the mechanical properties of bone in a cell- and estrogen receptor-independent manner. In this study, we determined that raloxifene directly interacts with the bone tissue. Through the use of multiple and complementary biophysical techniques including nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR), we show that raloxifene interacts specifically with the organic component or the organic/mineral composite, and not with hydroxyapatite. Structure-activity studies reveal that the basic side chain of raloxifene is an instrumental determinant in the interaction with bone. Thus, truncation of portions of the side chain reduces bone binding and also diminishes the increase in mechanical properties. Our results support a model wherein the piperidine interacts with bone matrix through electrostatic interactions with the piperidine nitrogen and through hydrophobic interactions (van der Waals) with the aliphatic groups in the side chain and the benzothiophene core. Furthermore, in silico prediction of the potential binding sites on the surface of collagen revealed the presence of a groove with sufficient space to accommodate raloxifene analogs. The hydroxyl groups on the benzothiophene nucleus, which are necessary for binding of SERMs to the estrogen receptor, are not required for binding to the bone surface, but mediate a more robust binding of the compound to the bone powder. In conclusion, we report herein a novel property of raloxifene analogs that allows them to interact with the bone tissue through potential contacts with the organic matrix and in particular collagen. PMID:26795112

  9. Biophysical Assessment and Predicted Thermophysiologic Effects of Body Armor.

    Directory of Open Access Journals (Sweden)

    Adam W Potter

    Full Text Available Military personnel are often required to wear ballistic protection in order to defend against enemies. However, this added protection increases mass carried and imposes additional thermal burden on the individual. Body armor (BA is known to reduce combat casualties, but the effects of BA mass and insulation on the physical performance of soldiers are less well documented. Until recently, the emphasis has been increasing personal protection, with little consideration of the adverse impacts on human performance.The purpose of this work was to use sweating thermal manikin and mathematical modeling techniques to quantify the tradeoff between increased BA protection, the accompanying mass, and thermal effects on human performance.Using a sweating thermal manikin, total insulation (IT, clo and vapor permeability indexes (im were measured for a baseline clothing ensemble with and without one of seven increasingly protective U.S. Army BA configurations. Using mathematical modeling, predictions were made of thermal impact on humans wearing each configuration while working in hot/dry (desert, hot/humid (jungle, and temperate environmental conditions.In nearly still air (0.4 m/s, IT ranged from 1.57 to 1.63 clo and im from 0.35 to 0.42 for the seven BA conditions, compared to IT and im values of 1.37 clo and 0.45 respectively, for the baseline condition (no BA.Biophysical assessments and predictive modeling show a quantifiable relationship exists among increased protection and increased thermal burden and decreased work capacity. This approach enables quantitative analysis of the tradeoffs between ballistic protection, thermal-work strain, and physical work performance.

  10. Untreatable Pain Resulting from Abdominal Cancer: New Hope from Biophysics?

    Directory of Open Access Journals (Sweden)

    Marineo G

    2003-01-01

    Full Text Available CONTEXT: Visceral pain characterizing pancreatic cancer is the most difficult symptom of the disease to control and can significantly impair the quality of life which remains and increase the demand for euthanasia. AIM: To investigate a possible new method based on biophysical principles (scrambler therapy to be used in the effective treatment of drug-resistant oncological pain of the visceral/neuropathic type. SETTING: Eleven terminal cancer patients (3 pancreas, 4 colon, 4 gastric suffering from elevated drug resistant visceral pain. DESIGN: The trial program was related to the first ten treatment sessions. Subsequently, each patient continued to receive treatment until death. MAIN OUTCOME MEASURES: Pain measures were performed using the visual analogue scale before and after each treatment session and accompanied by diary recordings of the duration of analgesia in the hours following each single application. Any variation in pain-killing drug consumption was also recorded. RESULTS: All patients reacted positively to the treatment throughout the whole reference period. Pain intensity showed a significant decrease (P less than 0.001, accompanied by a gradual rise both in the pain threshold and the duration of analgesia. Nine (81.8% of the patients suspended pain-killers within the first 5 applications, while the remaining two (18.2% considerably reduced the dosage taken prior to scrambler therapy. No undesirable side effects were observed. Compliance was found to be optimal. CONCLUSIONS: The preliminary results obtained using scrambler therapy are extremely encouraging, both in terms of enhanced pain control after each treatment session and in view of the possible maintenance of effectiveness over time.

  11. Biophysical fitness landscapes for transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Allan Haldane

    2014-07-01

    Full Text Available Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions.

  12. Fields of Applications for Hybrid Online Labs

    Directory of Open Access Journals (Sweden)

    Karsten Henke

    2013-04-01

    Full Text Available Based on a grid concept of an interactive hybrid online laboratory we will describe different fields of applications in different learning scenarios. The infrastructure is based on a universal grid concept which guaranties a reliable, flexible as well as robust usage of this online lab. By using the online lab, students are able to design control algorithms with different specification techniques to control electro-mechanical models in the online lab. Additionally, the reconfigurable rapid prototyping platform of the REAL system can be used to test all the taught topics of a given lectures in the field of digital system design. Finally, a special demonstration platform (a ball in a labyrinth on a balance plate can be used to give the students a better feeling about the possibilities and limitations of remote control and observation via Internet and to evaluate these technologies critically. The implemented online lab infrastructure is based on the iLab architecture of the MIT, which allows to interconnect online labs and to exchange remote lab experiments among different universities worldwide.

  13. Designing Viable Business Models for Living Labs

    Directory of Open Access Journals (Sweden)

    Bernhard R. Katzy

    2012-09-01

    Full Text Available Over 300 regions have integrated the concept of living labs into their economic development strategy since 2006, when the former Finnish Prime Minister Esko Aho launched the living lab innovation policy initiative during his term of European presidency. Despite motivating initial results, however, success cases of turning research into usable new products and services remain few and uncertainty remains on what living labs actually do and contribute. This practitioner-oriented article presents a business excellence model that shows processes of idea creation and team mobilization, new product development, user involvement, and entrepreneurship through which living labs deliver high-potential investment opportunities. Customers of living labs are identified as investors such as venture capitalists or industrial firms because living labs can generate revenue from them to create their own sustainable business model. The article concludes that living labs provide extensive support “lab” infrastructure and that it remains a formidable challenge to finance it, which calls for a more intensive debate.

  14. Teachers' Perspectives on Online Virtual Labs vs. Hands-On Labs in High School Science

    Science.gov (United States)

    Bohr, Teresa M.

    This study of online science teachers' opinions addressed the use of virtual labs in online courses. A growing number of schools use virtual labs that must meet mandated laboratory standards to ensure they provide learning experiences comparable to hands-on labs, which are an integral part of science curricula. The purpose of this qualitative case study was to examine teachers' perceptions of the quality and effectiveness of high school virtual labs. The theoretical foundation was constructivism, as labs provide student-centered activities for problem solving, inquiry, and exploration of phenomena. The research questions focused on experienced teachers' perceptions of the quality of virtual vs. hands-on labs. Data were collected through survey questions derived from the lab objectives of The Next Generation Science Standards . Eighteen teachers rated the degree of importance of each objective and also rated how they felt virtual labs met these objectives; these ratings were reported using descriptive statistics. Responses to open-ended questions were few and served to illustrate the numerical results. Many teachers stated that virtual labs are valuable supplements but could not completely replace hands-on experiences. Studies on the quality and effectiveness of high school virtual labs are limited despite widespread use. Comprehensive studies will ensure that online students have equal access to quality labs. School districts need to define lab requirements, and colleges need to specify the lab experience they require. This study has potential to inspire positive social change by assisting science educators, including those in the local school district, in evaluating and selecting courseware designed to promote higher order thinking skills, real-world problem solving, and development of strong inquiry skills, thereby improving science instruction for all high school students.

  15. The BIOMAT facility at FAIR: a new tool for ground-based research in space radiation biophysics

    Science.gov (United States)

    Durante, Marco

    The BIOMAT facility at FAIR: a new tool for ground-based research in space radiation biophysics M.Durante The FAIR accelerator complex at GSI (placeCityDarmstadt, country-regionGermany) will be a unique facility, where heavy ions with energies up to about 45 A GeV can be used for radiation biology experiments. The study of these very high charge and energy (HZE) particles is not only interesting for understanding the mechanisms of radiation action in living system, but also for radiation protection purposes. For space radiobiology, it is generally acknowledged that accelerator-based experiments are preferable to expensive and poorly reproducible flight tests, which are also presently unable to simulate the space radiation field beyond Earth's geomagnetic field. For these very reason, NASA has started the Space Radiation Health Program, building the 34 M NASA Space Radiation Laboratory (NSRL) at the Brookhaven National Laboratory (NY), and funding several research groups for studying biological effects of heavy ions with mass up to 56 (iron) and energy up to metricconverterProductID1 A1 A GeV. FAIR offers a number of unique opportunities in this frame. First, the beamtime available at NSRL is not sufficient to accommodate many non-US research groups, while the research needs are becoming urgent: uncertainty should be reduced to ±50% and effective countermeasures (physical and medical) developed by 2025 if a mission to Mars has to be performed within the first half of the XXI century. FAIR can be used to test a higher energy range (1- metricconverterProductID35 A35 A GeV), which has a low flux in space but is particularly penetrating and consequently impossible to shield. Finally, the raster scanning system used at GSI offers unique opportunities for biological experiments requiring precise exposures of parts of tissue or animal targets. The group of Biophysics at GSI has along experience in the field of space radiation protection, which naturally stems from heavy

  16. e-REAL: Enhanced Reality Lab

    Directory of Open Access Journals (Sweden)

    Fernando Salvetti

    2014-10-01

    Full Text Available e-REAL - enhanced reality lab - is a fully-immersive and multitasking environment, designed to experience challenging situations in a group setting, engaging all participants simultaneously on different levels: with peers, thematic experts and learning facilitators, both on site and remotely. e-REAL is a lab based on visual thinking and knowledge visualization, facilitated by enhanced (or augmented reality tools. It is a highly interactive and face-to-face lab that promotes proactive data and information research (everything is available, but learners have to actively look for it - allowing knowledge sharing with remote teams and integrating training on soft skills with those that are technical and specialized.

  17. Labs not in a lab: A case study of instructor and student perceptions of an online biology lab class

    Science.gov (United States)

    Doiron, Jessica Boyce

    Distance learning is not a new phenomenon but with the advancement in technology, the different ways of delivering an education have increased. Today, many universities and colleges offer their students the option of taking courses online instead of sitting in a classroom on campus. In general students like online classes because they allow for flexibility, the comfort of sitting at home, and the potential to save money. Even though there are advantages to taking online classes, many students and instructors still debate the effectiveness and quality of education in a distant learning environment. Many universities and colleges are receiving pressure from students to offer more and more classes online. Research argues for both the advantages and disadvantages of online classes and stresses the importance of colleges and universities weighing both sides before deciding to adopt an online class. Certain classes may not be suitable for online instruction and not all instructors are suitable to teach online classes. The literature also reveals that there is a need for more research on online biology lab classes. With the lack of information on online biology labs needed by science educators who face the increasing demand for online biology labs, this case study hopes to provide insight into the use of online biology lab classes and the how students and an instructor at a community college in Virginia perceive their online biology lab experience as well as the effectiveness of the online labs.

  18. European labs fight back against cuts

    CERN Multimedia

    König, R

    1997-01-01

    Germany's 1997 budget contains cuts amounting to 3.7% in funding of domestic research programs and in contributions to international labs. Contributions will be cut to the European Space Agency, the European Synchrotron facility and CERN.

  19. Berkeley Lab Laser Accelerator (BELLA) facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Berkeley Lab Laser Accelerator (BELLA) facility (formerly LOASIS) develops advanced accelerators and radiation sources. High gradient (1-100 GV/m) laser-plasma...

  20. Infrared Spectroscopy in the General Chemistry Lab

    Science.gov (United States)

    Hill, Margaret A.

    2001-01-01

    Acquisition of infrared spectrometers for use in general chemistry lab was made possible through the NSF-sponsored Instrumentation and Laboratory Improvement (ILI) program. Three laboratory exercises suitable for first-year students are described in which students learn to interpret infrared spectra for simple structural identification. A polymer identification lab is the first of these with minimal sample preparation. It uses familiar household polymer samples and teaches students how to use infrared spectral data to determine what bond types are present in the polymers. In a second lab, students learn to prepare potassium bromide pellets of fluorene derivatives and identify them by their functional group differences. The final exercise combines IR with several other lab techniques to identify an organic acid from a field of fourteen possibilities.

  1. Photonics and Fiber Optics Processor Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Photonics and Fiber Optics Processor Lab develops, tests and evaluates high speed fiber optic network components as well as network protocols. In addition, this...

  2. NCL Objective #3 - Nanotechnology Characterization Lab (NCL)

    Science.gov (United States)

    The Nanotechnology Characterization Lab (NCL) Objective #3: Identify and Characterize Critical Parameters Related to Nanomaterials' Absorption, Distribution, Metabolism, Excretion, and Acute Toxicity (ADME/Tox) Profile in Animal Models.

  3. NCL Objective #4 - Nanotechnology Characterization Lab (NCL)

    Science.gov (United States)

    The Nanotechnology Characterization Lab (NCL) Objective #4: Examine the Biological and Functional Characteristics of MultiComponent/Combinatorial Aspects of Nanoscaled Therapeutic, Molecular and Clinical Diagnostics, and Detection Platforms.

  4. Airborne Low-Frequency Sonar (ALFS) Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The ALFS lab is dedicated to support acoustic data analysis and processing software support to the AN/AQS-22 dipping sonar system. It includes stand-alone Software...

  5. Engineering and Scientific Applications: Using MatLab(Registered Trademark) for Data Processing and Visualization

    Science.gov (United States)

    Sen, Syamal K.; Shaykhian, Gholam Ali

    2011-01-01

    MatLab(TradeMark)(MATrix LABoratory) is a numerical computation and simulation tool that is used by thousands Scientists and Engineers in many countries. MatLab does purely numerical calculations, which can be used as a glorified calculator or interpreter programming language; its real strength is in matrix manipulations. Computer algebra functionalities are achieved within the MatLab environment using "symbolic" toolbox. This feature is similar to computer algebra programs, provided by Maple or Mathematica to calculate with mathematical equations using symbolic operations. MatLab in its interpreter programming language form (command interface) is similar with well known programming languages such as C/C++, support data structures and cell arrays to define classes in object oriented programming. As such, MatLab is equipped with most of the essential constructs of a higher programming language. MatLab is packaged with an editor and debugging functionality useful to perform analysis of large MatLab programs and find errors. We believe there are many ways to approach real-world problems; prescribed methods to ensure foregoing solutions are incorporated in design and analysis of data processing and visualization can benefit engineers and scientist in gaining wider insight in actual implementation of their perspective experiments. This presentation will focus on data processing and visualizations aspects of engineering and scientific applications. Specifically, it will discuss methods and techniques to perform intermediate-level data processing covering engineering and scientific problems. MatLab programming techniques including reading various data files formats to produce customized publication-quality graphics, importing engineering and/or scientific data, organizing data in tabular format, exporting data to be used by other software programs such as Microsoft Excel, data presentation and visualization will be discussed.

  6. Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages

    Science.gov (United States)

    Djordjevic, Marko

    2005-11-01

    Due to rapid accumulation of biological data, bioinformatics has become a very important branch of biological research. In this thesis, we develop novel bioinformatic approaches and aid design of biological experiments by using ideas and methods from statistical physics. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of the regulatory circuits that control expression of genes. We propose a novel, biophysics based algorithm, for the supervised detection of transcription factor (TF) binding sites. The method classifies potential binding sites by explicitly estimating the sequence-specific binding energy and the chemical potential of a given TF. In contrast with the widely used information theory based weight matrix method, our approach correctly incorporates saturation in the transcription factor/DNA binding probability. This results in a significant reduction in the number of expected false positives, and in the explicit appearance---and determination---of a binding threshold. The new method was used to identify likely genomic binding sites for the Escherichia coli TFs, and to examine the relationship between TF binding specificity and degree of pleiotropy (number of regulatory targets). We next address how parameters of protein-DNA interactions can be obtained from data on protein binding to random oligos under controlled conditions (SELEX experiment data). We show that 'robust' generation of an appropriate data set is achieved by a suitable modification of the standard SELEX procedure, and propose a novel bioinformatic algorithm for analysis of such data. Finally, we use quantitative data analysis, bioinformatic methods and kinetic modeling to analyze gene expression strategies of bacterial viruses. We study bacteriophage Xp10 that infects rice pathogen Xanthomonas oryzae. Xp10 is an unusual bacteriophage, which has morphology and genome organization that most closely

  7. Energy return on investment: Theory and application to biophysical economics

    Science.gov (United States)

    Murphy, David J.

    This dissertation is comprised of an introduction and five manuscripts split into two main sections: theory and application. Manuscripts one and four have been published, manuscript three has been accepted for publication, and manuscripts two and five are currently in review for publication. The theory sections contains the first two manuscripts. The first manuscript is a review of the literature on Energy Return on Investment (EROI) analysis. I cover five areas in this manuscript, including: (1) EROI and corn ethanol, (2) EROI for most major fuels, (3) alternative EROI applications, (4) EROI and the economy, and (5) the minimum EROI for society. The second manuscript provides a methodological framework for performing EROI analysis. I cover the following areas in this manuscript: (1) boundaries of analysis, (2) energy quality corrections, (3) energy intensity values, and lastly (4) alternative EROI statistics. The applications section contains manuscripts three through five. The third manuscript provides a biophysical model of economic growth indicating that the feedback mechanisms between oil supply and oil price have created a growth paradox: maintaining business as usual economic growth will require the production of new sources of oil, yet the only sources of oil remaining require high oil prices, thus hampering economic growth. The fourth manuscript is a study on the geographic variability of corn ethanol production. The main conclusions of this study were: (1) the statistical error associated with calculating the EROI of corn ethanol was enough to cast doubt as to whether corn ethanol yields net energy, and (2) failure to account for the geographic variation in corn yields and fertilizer inputs artificially inflated previous estimates of the EROI or corn ethanol. In the fifth manuscript I measure the impact of the Urban Heat Island within the metropolitan area of San Juan, Puerto Rico, on the electricity demand within the city. I calculated that the UHI

  8. The Multistream Self: Biophysical, Mental, Social, and Existential

    Directory of Open Access Journals (Sweden)

    Vinod D. Deshmukh

    2008-01-01

    Full Text Available Self is difficult to define because of its multiple, constitutive streams of functional existence. A more comprehensive and expanded definition of self is proposed. The standard bio-psycho-social model of psyche is expanded to biophysical-mental-social and existential self. The total human experience is better understood and explained by adding the existential component. Existential refers to lived human experience, which is firmly rooted in reality. Existential living is the capacity to live fully in the present, and respond freely and flexibly to new experience without fear. Four common fears of isolation, insecurity, insignificance, and death can be overcome by developing a lifestyle of whole-hearted engagement in the present reality, creative problem solving, self-actualization, and altruism. Such integrative living creates a sense of presence with self-awareness, understanding, and existential well-being. Well-being is defined as a life of happiness, contentment, low distress, and good health with positive outlook. Self is a complex, integrative process of living organisms. It organizes, coordinates, and integrates energy-information within and around itself, spontaneously, unconsciously, and consciously. Self-process is understood in terms of synergetics, coordination dynamics, and energy-information–directed self-organization. It is dynamic, composite, ever renewing, and enduring. It can be convergent or divergent, and can function as the source or target of its own behavior-mentation. The experience of self is continuously generated by spontaneous activation of neural networks in the cerebral neocortex by the brainstem-diencephalic arousal system. The multiple constitutive behavioral-mental streams develop concurrently into a unique experience of self, specific for a person at his/her developmental stage. The chronological neuro-behavioral-mental development of self is described in detail from embryonic stage to old age. Self can be

  9. The multistream self: biophysical, mental, social, and existential.

    Science.gov (United States)

    Deshmukh, Vinod D

    2008-03-25

    Self is difficult to define because of its multiple, constitutive streams of functional existence. A more comprehensive and expanded definition of self is proposed. The standard bio-psycho-social model of psyche is expanded to biophysical-mental-social and existential self. The total human experience is better understood and explained by adding the existential component. Existential refers to lived human experience, which is firmly rooted in reality. Existential living is the capacity to live fully in the present, and respond freely and flexibly to new experience without fear. Four common fears of isolation, insecurity, insignificance, and death can be overcome by developing a lifestyle of whole-hearted engagement in the present reality, creative problem solving, self-actualization, and altruism. Such integrative living creates a sense of presence with self-awareness, understanding, and existential well-being. Well-being is defined as a life of happiness, contentment, low distress, and good health with positive outlook. Self is a complex, integrative process of living organisms. It organizes, coordinates, and integrates energy-information within and around itself, spontaneously, unconsciously, and consciously. Self-process is understood in terms of synergetics, coordination dynamics, and energy-information-directed self-organization. It is dynamic, composite, ever renewing, and enduring. It can be convergent or divergent, and can function as the source or target of its own behavior-mentation. The experience of self is continuously generated by spontaneous activation of neural networks in the cerebral neocortex by the brainstem-diencephalic arousal system. The multiple constitutive behavioral-mental streams develop concurrently into a unique experience of self, specific for a person at his/her developmental stage. The chronological neuro-behavioral-mental development of self is described in detail from embryonic stage to old age. Self can be behaviorally

  10. Fifteen years experience: Egyptian metabolic lab

    Directory of Open Access Journals (Sweden)

    Ekram M. Fateen

    2014-10-01

    Conclusion: This study illustrates the experience of the reference metabolic lab in Egypt over 15 years. The lab began metabolic disorder screening by using simple diagnostic techniques like thin layer chromatography and colored tests in urine which by time updated and upgraded the methods to diagnose a wide range of disorders. This study shows the most common diagnosed inherited inborn errors of metabolism among the Egyptian population.

  11. e-lab Remote Laboratory Demonstration

    Directory of Open Access Journals (Sweden)

    R. B. Neto

    2013-01-01

    Full Text Available e-lab is a remote laboratory infrastructure, powered by a software framework designed for distributed data collection, that allows to perform experiments and retrieve data from a remote apparatus. In this demonstration we will present the e-lab interface properties and its modus operandi, giving as well some topics of complimentary software use for data interpretation and analysis. An overview of e-lab’s technical specifications will also be presented.

  12. German lab wins linear collider contest

    CERN Multimedia

    Cartlidge, Edwin

    2004-01-01

    Particle physicists have chosen to base the proposed International Linear Collider on superconducting technology developed by an international collaboration centred on the DESY lab in Germany. The superconducting approach was chosen by an internatinal panel ahead of a rival technology developed at Stanford in the US and the KEK lab in Japan. The eagerly-awaited decision was announced at the International Conference on High Energy Physics in Beijing today (½ page)

  13. Using Virtual Security Lab in Teaching Cryptography

    Directory of Open Access Journals (Sweden)

    Salma M. Gaffer

    2012-02-01

    Full Text Available Teaching Information Security for undergraduate students requires a safe hand-on environment for practicing. This paper focuses on using a virtual lab for two modules in cryptography concepts. At the end, a survey was conducted on a group of students atthe Information Systems Department at the King Abdulaziz University to measure the performance of the students' outcomes in the lab comparing with other students from aprevious semester. The result of the survey shows a significant feedback on the system.

  14. ScalaLab and GroovyLab: Comparing Scala and Groovy for Scientific Computing

    OpenAIRE

    2015-01-01

    ScalaLab and GroovyLab are both MATLAB-like environments for the Java Virtual Machine. ScalaLab is based on the Scala programming language and GroovyLab is based on the Groovy programming language. They present similar user interfaces and functionality to the user. They also share the same set of Java scientific libraries and of native code libraries. From the programmer's point of view though, they have significant differences. This paper compares some aspects of the two environments and hig...

  15. LabVIEW Support at CERN

    CERN Multimedia

    HR Department

    2010-01-01

    Since the beginning of 2009, due to the CERN restructuring, LabVIEW support moved from the IT to the EN department, joining the Industrial Controls and Electronics Group (ICE). LabVIEW support has been merged with the Measurement, Test and Analysis (MTA) section which, using LabVIEW, has developed most of the measurement systems to qualify the LHC magnets and components over the past 10 years. The post mortem analysis for the LHC hardware commissioning has also been fully implemented using LabVIEW, customised into a framework, called RADE, for CERN needs. The MTA section has started with a proactive approach sharing its tools and experience with the CERN LabVIEW community. Its framework (RADE) for CERN integrated application development has been made available to the users. Courses on RADE have been integrated into the standard National Instruments training program at CERN. RADE and LabVIEW support were merged together in 2010 on a single email address:labview.support@cern.ch For more information please...

  16. Comparison of biophysical factors influencing on emphysema quantification with low-dose CT

    Science.gov (United States)

    Heo, Chang Yong; Kim, Jong Hyo

    2014-03-01

    Emphysema Index(EI) measurements in MDCT is known to be influenced by various biophysical factors such as total lung volume, and body size. We investigated the association of the four biophysical factors with emphysema index in low-dose MDCT. In particular, we attempted to identify a potentially stronger biophysical factor than total lung volume. A total of 400 low-dose MDCT volumes taken at 120kVp, 40mAs, 1mm thickness, and B30f reconstruction kernel were used. The lungs, airways, and pulmonary vessels were automatically segmented, and two Emphysema Indices, relative area below -950HU(RA950) and 15th percentile(Perc15), were extracted from the segmented lungs. The biophysical factors such as total lung volume(TLV), mode of lung attenuation(ModLA), effective body diameter(EBD), and the water equivalent body diameter(WBD) were estimated from the segmented lung and body area. The association of biophysical factors with emphysema indices were evaluated by correlation coefficients. The mean emphysema indices were 8.3±5.5(%) in RA950, and -930±18(HU) in Perc15. The estimates of biophysical factors were 4.7±1.0(L) in TLV, -901±21(HU) in ModLA, 26.9±2.2(cm) in EBD, and 25.9±2.6(cm) in WBD. The correlation coefficients of biophysical factors with RA950 were 0.73 in TLV, 0.94 in ModLA, 0.31 in EBD, and 0.18 WBD, the ones with Perc15 were 0.74 in TLV, 0.98 in ModLA, 0.29 in EBD, and 0.15 WBD. Study results revealed that two biophysical factors, TLV and ModLA, mostly affects the emphysema indices. In particular, the ModLA exhibited strongest correlation of 0.98 with Perc15, which indicating the ModLA is the most significant confounding biophysical factor in emphysema indices measurement.

  17. Assessing Usage and Maximizing Finance Lab Impact: A Case Exploration

    Science.gov (United States)

    Noguera, Magdy; Budden, Michael Craig; Silva, Alberto

    2011-01-01

    This paper reports the results of a survey conducted to assess students' usage and perceptions of a finance lab. Finance labs differ from simple computer labs as they typically contain data boards, streaming market quotes, terminals and software that allow for real-time financial analyses. Despite the fact that such labs represent significant and…

  18. Experimental Labs for Start-Ups: The Role of the "Venture-Sitter"

    Science.gov (United States)

    Matricano, Diego; Pietrobon, Alberto

    2010-01-01

    Curley and Formica's (2008, 2010) studies of high-expectation entrepreneurship focus on the role of "experimental laboratories" in promoting the start-up and successful development of high-expectation firms. Although it is not difficult to understand the potential usefulness of these experimental labs--business simulators in which skilled partners…

  19. Determination of Enantiomeric Excess of Glutamic Acids by Lab-made Capillary Array Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Jun WANG; Kai Ying LIU; Li WANG; Ji Ling BAI

    2006-01-01

    Simulated enantiomeric excess of glutamic acid was determined by a lab-made sixteen-channel capillary array electrophoresis with confocal fluorescent rotary scanner. The experimental results indicated that the capillary array electrophoresis method can accurately determine the enantiomeric excess of glutamic acid and can be used for high-throughput screening system for combinatorial asymmetric catalysis.

  20. A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

    Science.gov (United States)

    Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

    2010-01-01

    As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

  1. GeneLab: A Systems Biology Platform for Spaceflight Omics Data

    Science.gov (United States)

    Reinsch, Sigrid S.; Lai, San-Huei; Chen, Rick; Thompson, Terri; Berrios, Daniel; Fogle, Homer; Marcu, Oana; Timucin, Linda; Chakravarty, Kaushik; Coughlan, Joseph

    2015-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and

  2. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.

    Science.gov (United States)

    Sikosek, Tobias; Krobath, Heinrich; Chan, Hue Sun

    2016-06-01

    Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein's folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the GA all-α and GB α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between GA and GB. In agreement with experiment, we observe conformational switching from GA to GB upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp GA/GB switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches. PMID:27253392

  3. Biophysical Mechanisms Underlying Hearing Loss Associated with a Shortened Tectorial Membrane

    Science.gov (United States)

    Oghalai, John S.; Xia, Anping; Liu, Christopher C.; Gao, Simon S.; Applegate, Brian E.; Puria, Sunil; Rousso, Itay; Steele, Charles

    2011-11-01

    The tectorial membrane (TM) connects to the stereociliary bundles of outer hair cells (OHCs). Herein, we summarize key experimental data and modeling analyses that describe how biophysical alterations to these connections underlie hearing loss. The heterozygous C1509G mutation in alpha tectorin produces partial congenital hearing loss that progresses in humans. We engineered this mutation in mice, and histology revealed that the TM was shortened. DIC imaging of freshly-dissected cochlea as well as imaging with optical coherence tomography indicated that the TM is malformed and only stimulates the first row of OHCs. Noise exposure produced acute threshold shifts that fully recovered in Tecta+/+ mice although there was some OHC loss within all three rows at the cochlear base. In contrast, threshold shifts only partially recovered in TectaC1509G/+ mice. This was associated with OHC loss more apically and nearly entirely within the first row. Young's modulus of the TM, measured using atomic force microscopy, was substantially reduced at the middle and basal regions. Both the wild-type and heterozygous conditions were simulated in a computational model. This demonstrated that the normalized stress distribution levels between the TM and the tall cilia were significantly elevated in the middle region of the heterozygous cochlea. Another feature of the TectaC1509G/+ mutation is higher prestin expression within all three rows of OHCs. This increased electricallyevoked movements of the reticular lamina and otoacoustic emissions. Furthermore, electrical stimulation was associated with an increased risk of OHC death as measured by vital dye staining. Together, these findings indicate that uncoupling of the TM from some OHCs not only leads to partial hearing loss, but also puts the OHCs that remain coupled at higher risk. Both the mechanics of the malformed TM and increased electromotility contribute to this higher risk profile.

  4. The Design:Lab as platform in participatory design research

    DEFF Research Database (Denmark)

    Binder, Thomas; Brandt, Eva

    2008-01-01

    . Influenced by these currents we use the expression 'Design:Lab' as a shorthand description of open collaborations between many stakeholders sharing a mutual interest in design research in a particular field. Many have reacted to the term 'laboratory' or 'lab' as foreign and awkward to design, and we as well...... as others have frequently used other metaphors like workshop, studio or atelier in design research. In this article we will argue that the laboratory metaphor is particularly suitable and useful for the design:lab, and we will give examples of how we have worked with the design:lab as a platform......The notion of laboratory or simply 'lab' has become popular in recent years in areas outside science and technology development. Learning Labs, Innovation Labs, Usability Labs, Media and Communication Labs and even Art Labs designate institutions or fora dedicated to change and experimentation...

  5. Are Virtual Labs as Effective as Hands-on Labs for Undergraduate Physics? A Comparative Study at Two Major Universities

    Science.gov (United States)

    Darrah, Marjorie; Humbert, Roxann; Finstein, Jeanne; Simon, Marllin; Hopkins, John

    2014-01-01

    Most physics professors would agree that the lab experiences students have in introductory physics are central to the learning of the concepts in the course. It is also true that these physics labs require time and money for upkeep, not to mention the hours spent setting up and taking down labs. Virtual physics lab experiences can provide an…

  6. Innovative Educational Practice: Using Virtual Labs in the Secondary Classroom.

    OpenAIRE

    Marcel Satsky Kerr; Kimberly Rynearson; Marcus C. Kerr

    2004-01-01

    Two studies investigated the effectiveness of teaching science labs online to secondary students. Study 1 compared achievement among students instructed using hands-on Chemistry labs versus those instructed using virtual Chemistry labs (eLabs). Study 2 compared the same groups of students again while both teachers instructed using hands-on Chemistry labs to determine whether teacher or student characteristics may have affected Study 1’s findings. Participants were high school Chemistry studen...

  7. Modifying a Cow-Calf Biophysical Simulation Model for Analyses of Alternative Enterprises

    Science.gov (United States)

    Lutes, Jennifer L.

    Cow-calf producers in the United States, tasked with providing beef calves for the beef industry, have had a multitude of difficulties to overcome in recent years. Producers in northwest Arkansas were negatively impacted by high hay prices coupled with low beef cattle market prices due to severe drought experienced in portions of 2010, 2011, and 2012. During this time they also faced high grain prices, due to a record low harvest, combined with portions of the corn harvest diverted from human and animal feed to ethanol production. Tight lending policies of this time, reminiscent of the housing market crash in 2008, along with the negative public attention associated with high levels of greenhouse gas emissions associated with beef production, lead to a tough situation for cattle producers faced with increasing input costs, decreased revenue, and lack of access to loans. With these issues in mind, this research aimed to determine if incorporating switchgrass (Panicum virgatum) production on a cow-calf farm could serve to increase net returns, decrease income volatility, lower net greenhouse gas (GHG) emissions without decreasing beef output, and provide a viable source of feedstock for a potential bio-refinery. The study determined that switchgrass is a potential solution to these problems and thus aimed to discover differences in switchgrass supply under different government policies in four northwestern counties in Arkansas to an as-yet, non-existent bio-refinery. It was determined that growing switchgrass on pastureland, once devoted to cow-calf production, is a viable enterprise diversification tool that under the right conditions could be used to improve producer financial and environmental outcomes. However, bioenergy production is slow to gain traction in the US due to adverse market conditions from low fossil fuel prices. Thus, in the US, there are only a few bio-refineries currently online and accepting lignocellulosic biomass, however none of them are close enough to northwest Arkansas to incentivize biomass production in this region. With this in mind, the results from an individual farm with switchgrass were extrapolated to a four county region to determine potential biomass supply for a hypothetical biorefinery. In conjunction with this analysis, two potential policies aimed at increasing biomass supply and lowering carbon emissions, were analyzed for their implications on the financial and environmental wellbeing of farms. It turns out, each of the two policies, the Biomass Crop Assistance Program (BCAP) and a Carbon Offset Program (CO), encourage the production of switchgrass and policy outcomes are most favorable when land of adequate quality is chosen to support higher switchgrass yield. At lower yield levels, the inclusion of switchgrass on pastures leads to less positive environmental outcomes and increased producer income variance.

  8. Reengineering the Cardiac Catheterization Lab Processes: A Lean Approach

    Directory of Open Access Journals (Sweden)

    Venkatesh Raghavan

    2010-01-01

    Full Text Available This paper presents a cross-functional effort in a US community hospital for an overall process improvement in its Cardiac Catheterization Lab (CCL. One of the key system performance metrics identified was the patient turnaround time. The objective of this study was to identify the sources of delays in the system that lead to prolonged patient turnaround time using a structured lean approach. A set of qualitative recommendations were proposed and implemented. Quantification of some of these recommendations and certain additional ‘what-if’ scenarios were evaluated using Discrete Event Simulation (DES. The simulation results showed that significant reduction in patient turnaround time could be achieved if the proposed recommendations were implemented. This study demonstrated the benefits of adopting the lean philosophy in the continuous process improvement journey in the healthcare delivery arena.

  9. Introducing interdisciplinary science to second year undergraduates in a Current Topics in Biophysics course

    CERN Document Server

    Jerzak, Stanislaw

    2015-01-01

    We offer second year students the opportunity to explore Current Topics in Biophysics in a course co-taught by a physicist and a biologist. The interdisciplinary course allows university students to engage in analytical thinking that integrates physics and biology. The students are either biophysics majors (50%) or from a diversity of science majors (about 30% life sciences). All will have taken first year courses in biology, physics and mathematics. The course is divided into: 1) The application of physical approaches to biological problems using case studies (how high can a tree grow? and biological pumps are two examples); 2) An introduction to physics concepts for which potential applications are explored (biophotonics and its application in fluorescence microscopy and photodynamic therapy is one example); and 3) Presentations from industry and university researchers who describe careers, research and clinical applications of biophysics. Over the six years the course has been offered, students have achiev...

  10. Materials science and biophysics applications at the ISOLDE radioactive ion beam facility

    CERN Document Server

    Wahl, U

    2011-01-01

    The ISOLDE isotope separator facility at CERN provides a variety of radioactive ion beams, currently more than 800 different isotopes from ~65 chemical elements. The radioisotopes are produced on-line by nuclear reactions from a 1.4 GeV proton beam with various types of targets, outdiffusion of the reaction products and, if possible, chemically selective ionisation, followed by 60 kV acceleration and mass separation. While ISOLDE is mainly used for nuclear and atomic physics studies, applications in materials science and biophysics account for a significant part (currently ~15%) of the delivered beam time, requested by 18 different experiments. The ISOLDE materials science and biophysics community currently consists of ~80 scientists from more than 40 participating institutes and 21 countries. In the field of materials science, investigations focus on the study of semiconductors and oxides, with the recent additions of nanoparticles and metals, while the biophysics studies address the toxicity of metal ions i...

  11. Biophysical interactions in the Cabo Frio upwelling system, southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Sergio Augusto Coelho-Souza

    2012-09-01

    Full Text Available The rising of cold water from deeper levels characterizes coastal upwelling systems. This flow makes nutrients available in the euphotic layer, which enhances phytoplankton production and growth. On the Brazilian coast, upwelling is most intense in the Cabo Frio region (RJ. The basic knowledge of this system was reviewed in accordance with concepts of biophysical interactions. The high frequency and amplitude of the prevailing winds are the main factor promoting the rise of South Atlantic Central Water, but meanders and eddies in the Brazil Current as well as local topography and coast line are also important. Upwelling events are common during spring/summer seasons. Primary biomass is exported by virtue of the water circulation and is also controlled by rapid zooplankton predation. Small pelagic fish regulate plankton growth and in their turn are preyed on by predatory fish. Sardine furnishes an important regional fish stock. Shoreline irregularities define the embayment formation of the Marine Extractive Reserve of Arraial do Cabo making it an area with evident different intensities of upwelled water that harbors high species diversity. Consequently, on a small spatial scale there are environments with tropical and subtropical features, a point to be explored as a particularity of this ecosystem.Os sistemas costeiros de ressurgência são caracterizados pela ascensão de águas frias que tornam os nutrientes disponíveis na camada eufótica para o crescimento e aumento da produção fitoplanctônica. No Brasil, a região do Cabo Frio (RJ é o principal sistema de ressurgência costeira. O objetivo desse artigo foi revisar o atual conhecimento desse sistema através dos conceitos sobre interações biofísicas. A ascensão da Água Central do Atlântico Sul ocorre devido à alta frequência e amplitude dos ventos, à presença de meandros e vórtices na Corrente do Brasil, além da topografia local e da linha de costa. Os eventos de ressurg

  12. Novel Acoustic Wave Microsystems for Biophysical Studies of Cells

    Science.gov (United States)

    Senveli, Sukru Ufuk

    biocompatible polymer, for dispensing cells into microcavities. A high frequency PCB including a matching circuit was designed for the SAW devices. 3D printed housing was also prepared for demonstrating the integration capability. Experimental results were collected first for analysis of high glycerin content in deionized water. Furthermore, polystyrene microbeads were counted with the system, and their sizes were differentiated experimentally to demonstrate the operation with solid media. Ultimately, biological cells were sensed and characterized. After tumor cells in media were transported to and trapped in microcavities, the proposed platform used SAW interaction between the substrate and the cells to extract their mechanical stiffness based on the ultrasound velocity. Measurements showed that output phase information is an indicator of the stiffness modulus of the trapped cells. Small populations of various types of cells such as MCF7, MDA-MB-231, SKBR3, and JJ012 were characterized and characteristic moduli were estimated for each cell population. In conclusion, the results indicate that high frequency stiffness modulus is a possible biomarker for aggressiveness of the tumor and that microcavity coupled SAW devices are a good candidate for non-invasive interrogation and high frequency biophysical studies of single cells. The proposed system is a successfully miniaturized ultrasonic biosensor and can be integrated with microchannels to obtain higher throughput upon refinement of the design as evidenced by the initial results with microfluidics. Improvement in performance and signal strength is also shown to be possible through matching circuits as demonstrated.

  13. A VISIR Lab Server for the iLab Shared Architecture

    Directory of Open Access Journals (Sweden)

    Danilo Garbi Zutin

    2011-09-01

    Full Text Available This paper describes the work done at the Carinthia University of Applied Sciences towards integrating VISIR-based labs on the iLab architecture. The Virtual Systems in Reality (VISIR project is carried out by the Blekinge Institute of Technology, Sweden and features a platform for performing experiments in different domains.

  14. eLabEL: technology-supported living labs in primary care.

    NARCIS (Netherlands)

    Vermeulen, J.; Huygens, M.W.J.; Swinkels, I.; Oude Nijeweme-d'Hollosy, W.; Velsen, L. van; Jansen, Y.; Witte, L.P. de

    2015-01-01

    Abstract— Telecare technologies and eHealth applications can support patients and care professionals. However, these technologies are currently not being implemented in primary care. The eLabEL project aims to contribute to a solution for this problem by establishing Living Labs in which patients, h

  15. Do Online Labs Work? An Assessment of an Online Lab on Cell Division

    Science.gov (United States)

    Gilman, Sharon L.

    2006-01-01

    Some studies show students successfully learning science through online courses. This study compared students doing an online and in-class lab exercise on cell division. Online students performed slightly but significantly better on a follow-up content quiz, however, about half those expressed a strong preference for in-class lab work.

  16. Multiscale Simulations: From Enzyme Kinetics to Fluctuating Hydrodynamics

    OpenAIRE

    Shang, Barry Zhongqi

    2013-01-01

    The development of multiscale methods for computational simulation of biophysical systems represents a significant challenge. Effective computational models that bridge physical insights obtained from atomistic simulations and experimental findings are lacking. An accurate passing of information between these scales would enable: (1) an improved physical understanding of structure-function relationships, and (2) enhanced rational strategies for molecular engineering and materials design. Two ...

  17. Beam Line Commissioning of a UV/VUV FEL at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Benson, Stephen; Blackburn, Keith; Bullard, Daniel; Clavero Perez, Cesar; Coleman, James; Dickover, Cody; Douglas, David; Ellingsworth, Forrest; Evtushenko, Pavel; Hernandez-Garcia, Carlos; Gould, Christopher; Gubeli, Joseph; Hardy, David; Jordan, Kevin; Klopf, John; James, Kortze; Legg, Robert; Marchlik, Matthew; Moore, Steven; Neil, George; Powers, Thomas; Sexton, Daniel; Shinn, Michelle D; Tennant, Christopher; Walker, Richard; Williams, Gwyn; Wilson, Frederick

    2011-08-01

    Many novel applications in photon sciences require very high brightness and/or short pulses in the vacuum ultra-violet (VUV). Jefferson Lab has commissioned a UV oscillator with high gain and has transported the third harmonic of the UV to a user lab. The experimental performance of the UV FEL is much better than simulated performance in both gain and efficiency. This success is important for efforts to push towards higher gain FELs at short wavelengths where mirrors absorb strongly. We will report on efforts to characterize the UV laser and the VUV coherent harmonics as well as designs to lase directly in the VUV wavelength range.

  18. Statistical Inference for Big Data Problems in Molecular Biophysics

    Energy Technology Data Exchange (ETDEWEB)

    Ramanathan, Arvind [ORNL; Savol, Andrej [University of Pittsburgh School of Medicine, Pittsburgh PA; Burger, Virginia [University of Pittsburgh School of Medicine, Pittsburgh PA; Quinn, Shannon [University of Pittsburgh School of Medicine, Pittsburgh PA; Agarwal, Pratul K [ORNL; Chennubhotla, Chakra [University of Pittsburgh School of Medicine, Pittsburgh PA

    2012-01-01

    We highlight the role of statistical inference techniques in providing biological insights from analyzing long time-scale molecular simulation data. Technologi- cal and algorithmic improvements in computation have brought molecular simu- lations to the forefront of techniques applied to investigating the basis of living systems. While these longer simulations, increasingly complex reaching petabyte scales presently, promise a detailed view into microscopic behavior, teasing out the important information has now become a true challenge on its own. Mining this data for important patterns is critical to automating therapeutic intervention discovery, improving protein design, and fundamentally understanding the mech- anistic basis of cellular homeostasis.

  19. Measurement of bio-physical signals for posture movement on the transformation system

    OpenAIRE

    Kim, Jeong-lae; Kim, Kyu-dong

    2014-01-01

    A signal transformation system of posture movement for the stable state was designed in order to measure the bio-physical signal. To estimate the subject in a stable state on the basis of the bio-physical signal in the posture movement, the conditions of vision, vestibular, somatosensory apparatus and the central nervous system (CNS) were detected. Based on the vision condition, there was a greater average variation (Vi-αAVG-MAX and Vi-αAVG-MIN) in position with eyes closed and eyes opened (P...

  20. ESA SnowLab project

    Science.gov (United States)

    Wiesmann, Andreas; Caduff, Rafael; Frey, Othmar; Werner, Charles

    2016-04-01

    Retrieval of the snow water equivalaent (SWE) from passive microwave observations dates back over three decades to initial studies made using the first operational radiometers in space. However, coarse spatial resolution (25 km) is an acknowledged limitation for the application of passive microwave measurements. The natural variability of snow cover itself is also notable; properties such as stratigraphy and snow microstructure change both spatially and over time, affecting the microwave signature. To overcome this deficit, the satellite mission COld REgions Hydrology High-resolution Observatory (CoReH2O) was proposed to the European Space Agency (ESA) in 2005 in response to the call for Earth Explorer 7 candidate missions. CoReH2O was a dual frequency (X- and Ku-band) SAR mission aimed to provide maps of SWE over land and snow accumulation on glaciers at a spatial resolution of 200 to 500 meters with an unprecedented accuracy. Within the frame of preparatory studies for CoReH2O Phase A, ESA undertook several research initiatives from 2009 to 2013 to study the mission concept and capabilities of the proposed sensor. These studies provided a wealth of information on emission and backscattering signatures of natural snow cover, which can be exploited to study new potential mission concepts for retrieval of snow cover properties and other elements of the cryosphere. Currently data related to multi-frequency, multi-polarisation, multitemporal of active and passive microwave measurements are still not available. In addition, new methods related to e.g. tomography are currently under development and need to be tested with real data. Also, the potential of interferometric and polarimetric measurements of the snow cover and its possible impact for novel mission/retrieval concepts must be assessed. . The objective of the SnowLab activity is to fill this gap and complement these datasets from earlier campaigns by acquiring a comprehensive multi-frequency, multi

  1. Collaborative Creation of a Lab Rubric

    Directory of Open Access Journals (Sweden)

    Carrie Miller-DeBoer

    2011-03-01

    Full Text Available While there are a number of tested rubrics in circulation, our task was to intervene in a particular situation: the lead professor was concerned because her graduate teaching assistants held negative views about student performance on the lab reports. GTAs found poor products frustrating, and admitted that their grading was thus superficial and provided no feedback to students. Specifically, GTAs did not feel equipped to evaluate writing and, as a result, simply graded on steps completed in the lab process.We have a rubric now for an Introduction to Zoology lab that could be submitted here as a pretty darn good rubric for other instructors to use. But the intent of our “Tips and Tools” is to describe the actual creation of the rubric. We believe the active “real time” development of the rubric carried as much or more value than the finished product.

  2. A Moodle extension to book online labs

    Directory of Open Access Journals (Sweden)

    Antonio C. Cardoso

    2005-11-01

    Full Text Available The social constructivist philosophy of Moodle makes it an excellent choice to deliver e-learning contents that require collaborative activities, such as those that are associated with online labs. In the case of online labs that enable web access to real devices (remote workbenches, access time should be reserved beforehand. A booking tool will avoid access conflicts and at the same time will help the students to organise their time and activities. This paper presents a Moodle extension that was developed within the Leonardo da Vinci MARVEL project, with the objective of meeting this requirement. The booking tool presented enables resource sharing in general and may be used to organise access to any type of scarce resources, such as to online labs and to the videoconferencing rooms that are needed to support collaborative activities.

  3. Application of Monte Carlo methods in tomotherapy and radiation biophysics

    Science.gov (United States)

    Hsiao, Ya-Yun

    Helical tomotherapy is an attractive treatment for cancer therapy because highly conformal dose distributions can be achieved while the on-board megavoltage CT provides simultaneous images for accurate patient positioning. The convolution/superposition (C/S) dose calculation methods typically used for Tomotherapy treatment planning may overestimate skin (superficial) doses by 3-13%. Although more accurate than C/S methods, Monte Carlo (MC) simulations are too slow for routine clinical treatment planning. However, the computational requirements of MC can be reduced by developing a source model for the parts of the accelerator that do not change from patient to patient. This source model then becomes the starting point for additional simulations of the penetration of radiation through patient. In the first section of this dissertation, a source model for a helical tomotherapy is constructed by condensing information from MC simulations into series of analytical formulas. The MC calculated percentage depth dose and beam profiles computed using the source model agree within 2% of measurements for a wide range of field sizes, which suggests that the proposed source model provides an adequate representation of the tomotherapy head for dose calculations. Monte Carlo methods are a versatile technique for simulating many physical, chemical and biological processes. In the second major of this thesis, a new methodology is developed to simulate of the induction of DNA damage by low-energy photons. First, the PENELOPE Monte Carlo radiation transport code is used to estimate the spectrum of initial electrons produced by photons. The initial spectrum of electrons are then combined with DNA damage yields for monoenergetic electrons from the fast Monte Carlo damage simulation (MCDS) developed earlier by Semenenko and Stewart (Purdue University). Single- and double-strand break yields predicted by the proposed methodology are in good agreement (1%) with the results of published

  4. Digital Design with KP-Lab

    Directory of Open Access Journals (Sweden)

    D. Ponta

    2007-08-01

    Full Text Available KP-Lab is an EU Integrated Project envisioning a learning system that facilitates innovative practices of sharing, creating and working with knowledge in education and workplaces. The project exploits a novel pedagogical view, the knowledge-creation metaphor of learning. According to such “trialogical” approach, cognition arises through collaborative work in systematically developing shared “knowledge artefacts”, such as concepts, plans, material products, or social practices. The paper presents the plan of a pilot course to test the KP-Lab methodologies and tools in the field of Digital Design.

  5. [Semiotic Studies Lab for Patient Care Interactions].

    Science.gov (United States)

    Nunes, Dulce Maria; Portella, Jean Cristtus; Bianchi e Silva, Laura

    2011-12-01

    The aim of this experience report is to present the Semiotic Studies Lab for Patient Care Interactions (Laboratório de Estudos Semióticos nas Interações de Cuidado - LESIC). The lab was set up at the Nursing School of the Federal University of Rio Grande do Sul (UFRGS), Brazil in 2010. It has the purpose of providing didactic and pedagogical updates, based on the Theory developed by the Paris School of Semiotics, that enable the increase of knowledge and interactive/observational skills regarding the nature and mastery of human care.

  6. LabVIEW A Developer's Guide to Real World Integration

    CERN Document Server

    Fairweather, Ian

    2011-01-01

    LabVIEW(t) has become one of the preeminent platforms for the development of data acquisition and data analysis programs. LabVIEW(t): A Developer's Guide to Real World Integration explains how to integrate LabVIEW into real-life applications. Written by experienced LabVIEW developers and engineers, the book describes how LabVIEW has been pivotal in solving real-world challenges. Each chapter is self-contained and demonstrates the power and simplicity of LabVIEW in various applications, from image processing to solar tracking systems. Many of the chapters explore how exciting new technologies c

  7. Utah Virtual Lab: JAVA interactivity for teaching science and statistics on line.

    Science.gov (United States)

    Malloy, T E; Jensen, G C

    2001-05-01

    The Utah on-line Virtual Lab is a JAVA program run dynamically off a database. It is embedded in StatCenter (www.psych.utah.edu/learn/statsampler.html), an on-line collection of tools and text for teaching and learning statistics. Instructors author a statistical virtual reality that simulates theories and data in a specific research focus area by defining independent, predictor, and dependent variables and the relations among them. Students work in an on-line virtual environment to discover the principles of this simulated reality: They go to a library, read theoretical overviews and scientific puzzles, and then go to a lab, design a study, collect and analyze data, and write a report. Each student's design and data analysis decisions are computer-graded and recorded in a database; the written research report can be read by the instructor or by other students in peer groups simulating scientific conventions.

  8. Learning from Our Evolving Understanding of Biophysical Interactions to Improve River Restoration Practice.

    Science.gov (United States)

    Sear, D. A.

    2014-12-01

    Restoration of riverine habitats has largely proceeded on the assumption that by improving physical habitat, and more latterly processes, biophysical interactions will reassemble to a state similar to that prior to the disturbance event. Whilst there had been little monitoring to support this view, there is increasing evidence that the complexity of ecological systems demands a greater understanding of these biophysical interactions before we can state that a restoration has succeeded. In this paper I will draw on two examples to demonstrate the importance of understanding the spatial as well as the temporal scale of biophysical interactions. In the first example, field and modelling was used to demonstrate how different location of large wood and forest restoration can result in different hydrological outcomes. Similarly, as the forest matures it is possible to see change in restoration outcomes, extending beyond the lifetime of the project. In the second example I demonstrate how climate and land use drive the biophysical interactions within spawning salmonid habitats, research that questions accepted models used in the restoration of salmonid spawning habitat. Finally the paper reflects on the problems of restoring complex ecosystems; and points towards the need for improvements in how we research and communicate with stakeholders who ultimately live by the streams we restore.

  9. Biophysical properties of membrane lipids of anammox bacteria : I. Ladderane phospholipids form highly organized fluid membranes

    NARCIS (Netherlands)

    Boumann, Henry A.; Longo, Marjorie L.; Stroeve, Pieter; Poolman, Bert; Hopmans, Ellen C.; Stuart, Marc C. A.; Damste, Jaap S. Sinninghe; Schouten, Stefan

    2009-01-01

    Anammox bacteria that are capable of anaerobically oxidizing ammonium (anammox) with nitrite to nitrogen gas produce unique membrane phospholipids that comprise hydrocarbon chains with three or five linearly condensed cyclobutane rings. To gain insight into the biophysical properties of these 'ladde

  10. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Pittroff, Connie; Strasser, Susan Barr [lead editors

    1999-08-03

    This STI product consists of the Program/Abstracts book that was prepared for the participants in the Sixth International Conference on Biophysics and Synchrotron Radiation that was held August 4-8, 1998, at the Advanced Photon Source, Argonne National Laboratory. This book contains the full conference program and abstracts of the scientific presentations.

  11. Study of the Peculiarities of Color Vision in the Course of "Biophysics" in a Pedagogical University

    Science.gov (United States)

    Petrova, Elena Borisovna; Sabirova, Fairuza Musovna

    2016-01-01

    The article substantiates the necessity of studying the peculiarities of color vision of human in the course "Biophysics" that have been integrated into many types of higher education institutions. It describes the experience of teaching this discipline in a pedagogical higher education institution. The article presents a brief review of…

  12. From global change to a butterfly flapping: biophysics and behaviour affect tropical climate change impacts.

    Science.gov (United States)

    Bonebrake, Timothy C; Boggs, Carol L; Stamberger, Jeannie A; Deutsch, Curtis A; Ehrlich, Paul R

    2014-10-22

    Difficulty in characterizing the relationship between climatic variability and climate change vulnerability arises when we consider the multiple scales at which this variation occurs, be it temporal (from minute to annual) or spatial (from centimetres to kilometres). We studied populations of a single widely distributed butterfly species, Chlosyne lacinia, to examine the physiological, morphological, thermoregulatory and biophysical underpinnings of adaptation to tropical and temperate climates. Microclimatic and morphological data along with a biophysical model documented the importance of solar radiation in predicting butterfly body temperature. We also integrated the biophysics with a physiologically based insect fitness model to quantify the influence of solar radiation, morphology and behaviour on warming impact projections. While warming is projected to have some detrimental impacts on tropical ectotherms, fitness impacts in this study are not as negative as models that assume body and air temperature equivalence would suggest. We additionally show that behavioural thermoregulation can diminish direct warming impacts, though indirect thermoregulatory consequences could further complicate predictions. With these results, at multiple spatial and temporal scales, we show the importance of biophysics and behaviour for studying biodiversity consequences of global climate change, and stress that tropical climate change impacts are likely to be context-dependent.

  13. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    International Nuclear Information System (INIS)

    This STI product consists of the Program/Abstracts book that was prepared for the participants in the Sixth International Conference on Biophysics and Synchrotron Radiation that was held August 4-8, 1998, at the Advanced Photon Source, Argonne National Laboratory. This book contains the full conference program and abstracts of the scientific presentations

  14. Absorption and Scattering Coefficients: A Biophysical-Chemistry Experiment Using Reflectance Spectroscopy

    Science.gov (United States)

    Cordon, Gabriela B.; Lagorio, M. Gabriela

    2007-01-01

    A biophysical-chemistry experiment, based on the reflectance spectroscopy for calculating the absorption and scattering coefficients of leaves is described. The results show that different plants species exhibit different values for both the coefficients because of their different pigment composition.

  15. Biophysical and human factors determine the distribution of poached elephants in Tsavo East National Park, Kenya

    NARCIS (Netherlands)

    Kyale, D.M.; Ngene, S.M.; Maingi, J.

    2011-01-01

    This study investigates the distribution of poached elephants as well as the biophysical and anthropogenic factors that determine the distribution of the poached elephants in Tsavo East National Park (TENP), Kenya. Data on the distribution of poached elephants, from 1990 to 2005, were acquired from

  16. Summaries of fiscal year 1994 projects in medical applications and biophysical research

    International Nuclear Information System (INIS)

    This report provides information on the research supported in Fiscal Year 1994 by the Medical Applications and Biophysical Research Division of the Office of Health and Environmental Research. A brief statement of the scope of the following areas is presented: dosimetry; measurement science; radiological and chemical physics; structural biology; human genome; and medical applications. Summaries of the research projects in these categories are presented

  17. Biophysical inhibition of synthetic vs. naturally-derived pulmonary surfactant preparations by polymeric nanoparticles.

    Science.gov (United States)

    Beck-Broichsitter, Moritz; Ruppert, Clemens; Schmehl, Thomas; Günther, Andreas; Seeger, Werner

    2014-01-01

    Reasonable suspicion has accumulated that inhaled nano-scale particulate matter influences the biophysical function of the pulmonary surfactant system. Hence, it is evident to provide novel insights into the extent and mechanisms of nanoparticle-surfactant interactions in order to facilitate the fabrication of safe nanomedicines suitable for pulmonary applications. Negatively- and positively-charged poly(styrene) nanoparticles (diameters of ~100nm) served as model carriers. Nanoparticles were incubated with several synthetic and naturally-derived pulmonary surfactants to characterize the sensitivity of each preparation to biophysical inactivation. Changes in surface properties (i.e. adsorption and dynamic surface tension behavior) were monitored in a pulsating bubble surfactometer. Both nanoparticle formulations revealed a dose-dependent influence on the biophysical behavior of all investigated pulmonary surfactants. However, the surfactant sensitivity towards inhibition depended on both the carrier type, where negatively-charged nanoparticles showed increased inactivation potency compared to their positively-charged counterparts, and surfactant composition. Among the surfactants tested, synthetic mixtures (i.e. phospholipids, phospholipids supplemented with surfactant protein B, and Venticute®) were more susceptible to surface-activity inhibition as the more complex naturally-derived preparations (i.e. Alveofact® and large surfactant aggregates isolated from rabbit bronchoalveolar lavage fluid). Overall, nanoparticle characteristics and surfactant constitution both influence the extent of biophysical inhibition of pulmonary surfactants.

  18. Biophysical inhibition of pulmonary surfactant function by polymeric nanoparticles: role of surfactant protein B and C.

    Science.gov (United States)

    Beck-Broichsitter, Moritz; Ruppert, Clemens; Schmehl, Thomas; Günther, Andreas; Seeger, Werner

    2014-11-01

    The current study investigated the mechanisms involved in the process of biophysical inhibition of pulmonary surfactant by polymeric nanoparticles (NP). The minimal surface tension of diverse synthetic surfactants was monitored in the presence of bare and surface-decorated (i.e. poloxamer 407) sub-100 nm poly(lactide) NP. Moreover, the influence of NP on surfactant composition (i.e. surfactant protein (SP) content) was studied. Dose-elevations of SP advanced the biophysical activity of the tested surfactant preparation. Surfactant-associated protein C supplemented phospholipid mixtures (PLM-C) were shown to be more susceptible to biophysical inactivation by bare NP than phospholipid mixture supplemented with surfactant protein B (PLM-B) and PLM-B/C. Surfactant function was hindered owing to a drastic depletion of the SP content upon contact with bare NP. By contrast, surface-modified NP were capable of circumventing unwanted surfactant inhibition. Surfactant constitution influences the extent of biophysical inhibition by polymeric NP. Steric shielding of the NP surface minimizes unwanted NP-surfactant interactions, which represents an option for the development of surfactant-compatible nanomedicines.

  19. X-ray structure and biophysical properties of rabbit fibroblast growth factor 1

    International Nuclear Information System (INIS)

    This report shows that the tertiary structure of rabbit FGF-1 is essentially identical to that of human FGF-1, with four surface mutations (140-amino-acid form). Biophysical data indicate that rabbit FGF-1 is less thermostable than human FGF-1 and has a slower association rate with the FGF-1 receptor. Mitogenic assays indicate that rabbit FGF-1 is tenfold less potent than human FGF-1; however, rabbit FGF-1 exhibits greater heparin stimulation such that its mitogenic activity in the presence of heparin is essentially indistinguishable from that of human FGF-1. The rabbit is an important and de facto animal model in the study of ischemic disease and angiogenic therapy. Additionally, fibroblast growth factor 1 (FGF-1) is emerging as one of the most important growth factors for novel pro-angiogenic and pro-arteriogenic therapy. However, despite its significance, the fundamental biophysical properties of rabbit FGF-1, including its X-ray structure, have never been reported. Here, the cloning, crystallization, X-ray structure and determination of the biophysical properties of rabbit FGF-1 are described. The X-ray structure shows that the amino-acid differences between human and rabbit FGF-1 are solvent-exposed and therefore potentially immunogenic, while the biophysical studies identify differences in thermostability and receptor-binding affinity that distinguish rabbit FGF-1 from human FGF-1

  20. Curved spacetimes in the lab

    CERN Document Server

    Szpak, Nikodem

    2014-01-01

    We present some new ideas on how to design analogue models of quantum fields living in curved spacetimes using ultra-cold atoms in optical lattices. We discuss various types of static and dynamical curved spacetimes achievable by simple manipulations of the optical setup. Examples presented here contain two-dimensional spaces of positive and negative curvature as well as homogeneous cosmological models and metric waves. Most of them are extendable to three spatial dimensions. We mention some interesting phenomena of quantum field theory in curved spacetimes which might be simulated in such optical lattices loaded with bosonic or fermionic ultra-cold atoms. We also argue that methods of differential geometry can be used, as an alternative mathematical approach, for dealing with realistic inhomogeneous optical lattices.

  1. The Portuguese Contribution for lab2go - pt.lab2go

    Directory of Open Access Journals (Sweden)

    Maria Teresa Restivo

    2013-01-01

    Full Text Available Online experimentation provides innovative and valuable tools for use in academy, in high schools, in industry and in medical areas. It has also become a precious tool for educational and training purposes in any of those areas. Looking at online experimentation as a pure distance learning tool it represents a very efficient way of sharing hands-on capabilities, for example with developing countries. In Portugal a new consortium of online experimentation was created for fostering the national potential, using the Portuguese version of lab2go web platform, pt.lab2go. The authors pretend to demonstrate some of capabilities of the consortium in sharing online labs.

  2. Improving the Quality of Lab Reports by Using Them as Lab Instructions

    Science.gov (United States)

    Haagen-Schuetzenhoefer, Claudia

    2012-10-01

    Lab exercises are quite popular in teaching science. Teachers have numerous goals in mind when teaching science laboratories. Nevertheless, empirical research draws a heterogeneous picture of the benefits of lab work. Research has shown that it does not necessarily contribute to the enhancement of practical abilities or content knowledge. Lab activities are frequently based on recipe-like, step-by-step instructions ("cookbook style"), which do not motivate students to engage cognitively. Consequently, students put the emphasis on "task completion" or "manipulating equipment."2

  3. Go-Lab Report on Development of the Virtual Go-Lab User Community -V1

    OpenAIRE

    Doran, Rosa; Sotiriou, Sofoklis

    2015-01-01

    The focus of this document is to perform an analysis into the type and intensity of Go-Lab engagement, exhibited by its users, mainly teachers in the current period. The emphasis is still on measuring and interpreting the way the community of users has grown, as well as on the type and degree of involvement and experience sharing in the Go-Lab infrastructure. In the framework of Go-Lab, Community Building is considered as a professional development activity. In this framework apart from the d...

  4. Awakening interest in the natural sciences - BASF's Kids' Labs.

    Science.gov (United States)

    Lang, Cinthia

    2012-01-01

    At BASF's Ludwigshafen headquarters, kids and young adults in grades 1-13 can learn about chemistry in the Kids' Labs. Different programs exist for different levels of knowledge. In the two 'Hands-on Lab H(2)O & Co.' Kids' Labs, students from grades 1-6 explore the secrets of chemistry. BASF Kids' Labs have now been set up in over 30 countries. In Switzerland alone, almost 2,000 students have taken part in the 'Water Loves Chemistry' Kids' Lab since it was started in 2011. In Alsace, 600 students have participated to date. In the Teens' Lab 'Xplore Middle School', middle school students explore five different programs with the themes 'substance labyrinth', 'nutrition', 'coffee, caffeine & co.', 'cosmetics' and 'energy'. Biotechnological methods are the focus of the Teens' Lab 'Xplore Biotech' for students taking basic and advanced biology courses. In the 'Xplore High School' Teens' Lab, chemistry teachers present their own experimental lab instruction for students in basic and advanced chemistry courses. The Virtual Lab has been expanding the offerings of the BASF Kids' Labs since 2011. The online lab was developed by the company for the International Year Of Chemistry and gives kids and young adults the opportunity to do interactive experiments outside of the lab. PMID:23394237

  5. Structures and functions in the crowded nucleus: new biophysical insights

    Directory of Open Access Journals (Sweden)

    Ronald eHancock

    2014-09-01

    Full Text Available Concepts and methods from the physical sciences have catalysed remarkable progress in understanding the cell nucleus in recent years. To share this excitement with physicists and encourage their interest in this field, this review offers an overview of how the physics which underlies structures and functions in the nucleus is becoming more clear thanks to methods which have been developed to simulate and study macromolecules, polymers, and colloids. The environment in the nucleus is very crowded with macromolecules, making entropic (depletion forces major determinants of interactions. Simulation and experiments are consistent with their key role in forming membraneless compartments such as nucleoli, PML and Cajal bodies, and discrete territories for chromosomes. The chromosomes, giant linear polyelectrolyte polymers, exist in vivo in a state like a polymer melt. Looped conformations are predicted in crowded conditions, and have been confirmed experimentally and are central to the regulation of gene expression. Polymer theory has revealed how the chromosomes are so highly compacted in the nucleus, forming a crumpled globule with fractal properties which avoids knots and entanglements in DNA while allowing facile accessibility for its replication and transcription. Entropic repulsion between looped polymers can explain the confinement of each chromosome to a discrete region of the nucleus. Crowding and looping are predicted to facilitate finding the specific targets of factors which modulate activities of DNA. Simulation shows that entropic effects contribute to finding and repairing potentially lethal double-strand breaks in DNA by increasing the mobility of the broken ends, favouring their juxtaposition for repair. Signaling pathways are strongly influenced by crowding, which favours a processive mode of response (consecutive reactions without releasing substrates. This new information contributes to understanding the sometimes counter

  6. Past and present biophysical redundancy of countries as a buffer to changes in food supply

    Science.gov (United States)

    Fader, Marianela; Rulli, Maria Cristina; Carr, Joel; Dell'Angelo, Jampel; D'Odorico, Paolo; Gephart, Jessica A.; Kummu, Matti; Magliocca, Nicholas; Porkka, Miina; Prell, Christina; Puma, Michael J.; Ratajczak, Zak; Seekell, David A.; Suweis, Samir; Tavoni, Alessandro

    2016-05-01

    Spatially diverse trends in population growth, climate change, industrialization, urbanization and economic development are expected to change future food supply and demand. These changes may affect the suitability of land for food production, implying elevated risks especially for resource-constrained, food-importing countries. We present the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Biophysical redundancy, defined as unused biotic and abiotic environmental resources, is represented by the potential food production of ‘spare land’, available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. In 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as ‘Low Income Economies (LIEs)’ since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

  7. An ethnographic study: Becoming a physics expert in a biophysics research group

    Science.gov (United States)

    Rodriguez, Idaykis

    Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the common practices of graduate students in their biophysics weekly research group meetings. I recorded notes on observations and conduct interviews with all participants of the biophysics research group for a period of eight months. I apply the theoretical framework of Communities of Practice to distinguish the cultural norms of the group that cultivate physics expert practices. Results indicate that physics expertise is specific to a topic or subfield and it is established through effectively publishing research in the larger biophysics research community. The participant biophysics research group follows a learning trajectory for its students to contribute to research and learn to communicate their research in the larger biophysics community. In this learning trajectory students develop expert member competencies to learn to communicate their research and to learn the standards and trends of research in the larger research community. Findings from this dissertation expand the model of physics expertise beyond the cognitive realm and add the social and cultural nature of physics expertise development. This research also addresses ways to increase physics graduate student success towards their PhD. and decrease the 48% attrition rate of physics graduate students. Cultivating effective research

  8. Past and Present Biophysical Redundancy of Countries as a Buffer to Changes in Food Supply

    Science.gov (United States)

    Fader, Marianela; Rulli, Maria Cristina; Carr, Joel; Dell' Angelo, Jampel; D' Odorico, Paolo; Gephart, Jessica A.; Kummu, Matti; Magliocca, Nicholas; Porkka, Miina; Prell, Christina; Puma, Michael J.

    2016-01-01

    Spatially diverse trends in population growth, climate change, industrialization, urbanization and economic development are expected to change future food supply and demand. These changes may affect the suitability of land for food production, implying elevated risks especially for resource constrained, food-importing countries. We present the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Biophysical redundancy, defined as unused biotic and abiotic environmental resources, is represented by the potential food production of 'spare land', available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. In 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as 'Low Income Economies (LIEs)' since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

  9. A Hardware Lab Anywhere At Any Time

    Directory of Open Access Journals (Sweden)

    Tobias Schubert

    2004-12-01

    Full Text Available Scientific technical courses are an important component in any student's education. These courses are usually characterised by the fact that the students execute experiments in special laboratories. This leads to extremely high costs and a reduction in the maximum number of possible participants. From this traditional point of view, it doesn't seem possible to realise the concepts of a Virtual University in the context of sophisticated technical courses since the students must be "on the spot". In this paper we introduce the so-called Mobile Hardware Lab which makes student participation possible at any time and from any place. This lab nevertheless transfers a feeling of being present in a laboratory. This is accomplished with a special Learning Management System in combination with hardware components which correspond to a fully equipped laboratory workstation that are lent out to the students for the duration of the lab. The experiments are performed and solved at home, then handed in electronically. Judging and marking are also both performed electronically. Since 2003 the Mobile Hardware Lab is now offered in a completely web based form.

  10. Displacing Media: LCD LAB Artistic Residency

    Directory of Open Access Journals (Sweden)

    Filipe Pais

    2012-12-01

    Full Text Available This review refers to an artistic residency which took place at LCD LAB -  CAAA at Guimarães, in March, exploring a strategy for media art called Media Displacement. The text introduces the strategy very briefly and describes the residency's organization, structure, processses and the results produced.

  11. Information at a Cost: A Lab Experiment

    NARCIS (Netherlands)

    P. Robalo (Pedro); R.S. Sayag (Rei)

    2012-01-01

    textabstractThe supposed irrelevance of historical costs for rational decision making has been the subject of much interest in the economic literature. In this paper we explore whether individual decision making under risk is affected by the cost of the supplied information. Outside of the lab, it i

  12. FameLab - Swiss Semi Finals

    CERN Multimedia

    Corinne Pralavorio

    2012-01-01

    Twenty-two young scientists participated in the FameLab semi-final at CERN's Globe of Science and Innovation on 4 February, supported by a large audience and by more than 100 fans following via webcast. A panel of judges chose Lemmer and four other candidates to join five other semi-finalists at the national finals in Zurich on 30 March.

  13. Computer Labs Report to the Holodeck

    Science.gov (United States)

    Raths, David

    2011-01-01

    In many ways, specialized computer labs are the black holes of IT organizations. Budgets, equipment, employees--even space itself--are sucked in. Given a choice, many IT shops would engage warp drive and escape their gravitational pull forever. While Captain Kirk might have looked to Scotty for a fix to the problem, colleges and universities are…

  14. Surfactant Adsorption: A Revised Physical Chemistry Lab

    Science.gov (United States)

    Bresler, Marc R.; Hagen, John P.

    2008-01-01

    Many physical chemistry lab courses include an experiment in which students measure surface tension as a function of surfactant concentration. In the traditional experiment, the data are fit to the Gibbs isotherm to determine the molar area for the surfactant, and the critical micelle concentration is used to calculate the Gibbs energy of micelle…

  15. Carleton to oversee $40 million lab grant

    CERN Multimedia

    Singer, Zev

    2003-01-01

    "Carleton University got a major gift yesterday, as the federal government announced the university will oversee a $40-million grant to run the world's deepest underground lab at the Sudbury Neutrino Observatory. Five other universities are partners in the project" (1/2 page).

  16. Lab. X - projektrapport udarbejdet maj 2015

    DEFF Research Database (Denmark)

    Bangshaab, Jette

    2015-01-01

    Nærværende projektrapport for Lab. X projektet (ERDFN-13-0129) fremstiller og vurderer udviklingen af projektforløbet, og hvorledes projektets hovedaktiviteter er gennemført, og i hvilket omfang milepælene er nået. Desuden præsenteres det, hvilke konkrete resultater projektet har nået og, hvordan...

  17. Volkswagen Sets up Central Lab in BRICI

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ On June 2, Volkswagen Corp of Germany settled its Chinese central laboratory in Sinopec Beijing Research Institute of Chemical Industry (BRICI). This is the top-level lab of Volkswagen in Asia - Pacific region and it marks another close cooperation between Volkswagen Corp of Germany and Sinopec Corp.

  18. Design Lab 2005 : pilk steriilsesse elektrotulevikku

    Index Scriptorium Estoniae

    2005-01-01

    Design Lab kutsub disainereid ja üliõpilasi üle terve maailma tegelema kaugemale tulevikku suunatud visioonidega. 2005. a. konkurss otsis nutikaid ja säästlikke lahendusi, mis võiksid 2020. a. kodudes olla juba juurdunud, keskenduti kodutehnikale

  19. Biophysical constraints on lateral inhibition in the olfactory bulb.

    Science.gov (United States)

    McIntyre, Alexa B R; Cleland, Thomas A

    2016-06-01

    The mitral cells (MCs) of the mammalian olfactory bulb (OB) constitute one of two populations of principal neurons (along with middle/deep tufted cells) that integrate afferent olfactory information with top-down inputs and intrinsic learning and deliver output to downstream olfactory areas. MC activity is regulated in part by inhibition from granule cells, which form reciprocal synapses with MCs along the extents of their lateral dendrites. However, with MC lateral dendrites reaching over 1.5 mm in length in rats, the roles of distal inhibitory synapses pose a quandary. Here, we systematically vary the properties of a MC model to assess the capacity of inhibitory synaptic inputs on lateral dendrites to influence afferent information flow through MCs. Simulations using passivized models with varying dendritic morphologies and synaptic properties demonstrated that, even with unrealistically favorable parameters, passive propagation fails to convey effective inhibitory signals to the soma from distal sources. Additional simulations using an active model exhibiting action potentials, subthreshold oscillations, and a dendritic morphology closely matched to experimental values further confirmed that distal synaptic inputs along the lateral dendrite could not exert physiologically relevant effects on MC spike timing at the soma. Larger synaptic conductances representative of multiple simultaneous inputs were not sufficient to compensate for the decline in signal with distance. Reciprocal synapses on distal MC lateral dendrites may instead serve to maintain a common fast oscillatory clock across the OB by delaying spike propagation within the lateral dendrites themselves. PMID:27009162

  20. Hydrogen-rich gas production via fast pyrolysis of biophysical dried sludge: Effect of particle size and moisture content on product yields and syngas composition.

    Science.gov (United States)

    Han, Rong; Liu, Jinwen; Zhao, Chenxi; Li, Yuliang; Chen, Aixia

    2016-06-01

    After biophysical drying, a novel biophysical dried sludge particle was obtained. This work aims to investigate the function and effects of particle sizes and moisture contents on the fast pyrolysis of biophysical dried sludge particles. The results showed that large particles (>4 mm) favoured the oil generation with a maximum value of 19.0%, and small particles (pyrolysis. PMID:27118735