An interactive modeling program for DNA

An interactive program for modeling A-, B- and Z-DNA in a schematic and nonatomic representation has been developed for the Evans and Sutherland PS300. The program lets users display several molecules for which parameters determining the three-dimensional structure can be calculated either on the basis of theoretical models or inferred from experimental data. The calculation of the curvature and torsion of the helical axis, by a method based on Frenet's equations, makes it possible to quantify the effects of the parameters on the helical axis.     

Mathematical modeling of laser based potato cutting and peeling

A mathematical model is developed and validated to predict the depth of cut in potato tuber slabs as a function of laser power and travel speed. The model considers laser processing parameters such as input power, spot size and exposure time as well as the properties of the material being cut such as specific heat, thermal conductivity, surface reflectance, etc. The model also considers the phase change of water in potato and the ignition temperature of the solid portion. The composition of the potato tuber is assumed to be of water and solid. The model also assumes that the ablation process is accomplished through ejection of liquid water, debris and water vapour, and combustion of solid. A CO₂ laser operating in c.w. mode was chosen for the experimental work because water absorbs laser energy highly at 10.6 μm, and CO₂ laser units with relatively high output power are available. Slabs of potato tuber were chosen to be laser processed since potato contains high moisture and large amounts of relatively homogeneous tissue. The results of the preliminary calculations and experiments concluded that the model is able to predict the depth of cut in potato tuber parenchyma when subjected to a CO₂ laser beam.     

Mathematical modeling of laser based potato cutting and peeling

A mathematical model is developed and validated to predict the depth of cut in potato tuber slabs as a function of laser power and travel speed. The model considers laser processing parameters such as input power, spot size and exposure time as well as the properties of the material being cut such as specific heat, thermal conductivity, surface reflectance, etc. The model also considers the phase change of water in potato and the ignition temperature of the solid portion. The composition of the potato tuber is assumed to be of water and solid. The model also assumes that the ablation process is accomplished through ejection of liquid water, debris and water vapour, and combustion of solid. A CO₂ laser operating in c.w. mode was chosen for the experimental work because water absorbs laser energy highly at 10.6 μm, and CO₂ laser units with relatively high output power are available. Slabs of potato tuber were chosen to be laser processed since potato contains high moisture and large amounts of relatively homogeneous tissue. The results of the preliminary calculations and experiments concluded that the model is able to predict the depth of cut in potato tuber parenchyma when subjected to a CO₂ laser beam.     

PCDRA: PC interactive molecular representation and modeling system

PCDRA was designed to provide the average biologist with a user-friendly molecular display on a low-cost personal computer. The package is menu driven and is built so that a biologist, with tittle or no computing knowledge, finds it easy to use. The system gives a color representation with depth cueing of a protein whose atomic coordinates are stored as a PDB file. Moreover, the system presents several features similar to HYDRA¹ and therefore is a good introduction to molecular graphics, especially for beginners in protein modeling.     

An affordable approach to interactive desktop molecular modeling

The amazing revolution in computer hardware performance and cost reduction has yet to be carried over to computer software. In fact, application software today is often more expensive and less reliable than the hardware. New enhancements in software development techniques, such as object oriented programming and interactive graphics based user interface design, finally may be having a significant impact on the time-to-market and reliability of these application programs. We discuss our experiences using one such set of software development tools available on the NeXT workstation and describe the effort required to port our MidasPlus molecular modeling package to the NeXT workstation.     

Envelope: interactive software for modeling and fitting complex isotope distributions

Background  

An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope labeling patterns. These patterns can be quite complex, in particular with in vivo metabolic labeling experiments producing fractional atomic labeling or fractional residue labeling of peptides or other macromolecules. In general, it can be difficult to distinguish the contributions of species with different labeling patterns to an experimental spectrum and difficult to calculate a theoretical isotope distribution to fit such data. There is a need for interactive and user-friendly software that can calculate and fit the entire isotope distribution of a complex mixture while comparing these calculations with experimental data and extracting the contributions from the differently labeled species.     

An interactive modeling lesson increases students' understanding of ploidy during meiosis

Chromosome structure is confusing to students at all levels, and chromosome behavior during meiosis is a notoriously difficult topic. Undergraduate biology majors are exposed to the process of meiosis numerous times during their presecondary and postsecondary education, yet understanding of key concepts, such as the point at which haploidy is established, does not improve substantially with repeated exposure. Based on student's drawings, 96% of intermediate-level biology majors have unclear or incorrect ideas about meiosis. Students have difficulty diagramming the process of meiosis starting with three unreplicated pairs of chromosomes, and even when they can produce an accurate diagram, they are unclear how to assign the terms "haploid" and "diploid." We designed an interactive lesson based on constructivist theory to address these issues in a large lecture class. Pretest and posttest scores showed a significant improvement in students' understanding of ploidy compared to a parallel class taught in the traditional way (e.g. using the textbook diagrams). In interviews afterward, those students whose scores improved on exams specifically pointed to the features of the in-class modeling that were deliberately incorporated for that purpose.     

Microscopy images as interactive tools in cell modeling and cell biology education

The advent of genomics, proteomics, and microarray technology has brought much excitement to science, both in teaching and in learning. The public is eager to know about the processes of life. In the present context of the explosive growth of scientific information, a major challenge of modern cell biology is to popularize basic concepts of structures and functions of living cells, to introduce people to the scientific method, to stimulate inquiry, and to analyze and synthesize concepts and paradigms. In this essay we present our experience in mixing science and education in Brazil. For two decades we have developed activities for the science education of teachers and undergraduate students, using microscopy images generated by our work as cell biologists. We describe open-air outreach education activities, games, cell modeling, and other practical and innovative activities presented in public squares and favelas. Especially in developing countries, science education is important, since it may lead to an improvement in quality of life while advancing understanding of traditional scientific ideas. We show that teaching and research can be mutually beneficial rather than competing pursuits in advancing these goals.     

A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings

Residual dipolar couplings (RDC), measured by dissolving proteins in dilute liquid crystal media, or by studying naturally paramagnetic molecules, have rapidly become established as routine measurements in the investigation of the structure of macromolecules by NMR. One of the most obvious applications of the previously inaccessible long-range angular information afforded by RDC is the accurate definition of domain orientation in multi-module macromolecules or complexes. In this paper we describe a novel program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation to construct low-resolution models of macromolecular structure. For multi-domain systems the program determines the relative orientation of individual structured domains, and provides graphical user-driven rigid-body modeling of the different modules relative to the common tensorial frame. Translational freedom in the common frame, and equivalent rotations about the diagonalized (x,y,z) axes are used to position the different modules in the common frame to find a model in best agreement with experimentally measured couplings alone or in combination with additional experimental or covalent information.     

竞争和景观格局相互作用对外来入侵物种传播影响的动态模拟

通过中性景观模型和元胞自动机模型模拟了不同景观格局、不同竞争力和关键种群特征的外来入侵物种的传播动态,模拟结果表明:(1)竞争力强的外来入侵物种,可利用生境面积越大,集聚度越高,越有利于其入侵和传播,而对竞争力弱的外来入侵物种来说,可利用生境面积越小,越分散,越有利于其生存。竞争力强可以有效利用整块的高集聚度的资源,而弱竞争力的外来入侵物种为了逃避土著种的竞争往往趋向于分布在分散的小生境中;(2)可利用生境面积大于50%时,景观格局集聚度越小,竞争力弱的外来入侵物种适应环境的弛豫时间越长;(3)外来入侵物种的传播与种子产量呈正相关关系,与繁殖年龄呈负相关关系,拟合关系因景观格局和竞争而异;(4)平均迁移距离对外来入侵物种传播的影响最大,在管理过程中应根据不同的目标,不同的景观格局、竞争力和种群特征选择合适的管理措施。     

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data

KnowledgeEditor is a graphical workbench for biological experts to model biomolecular network graphs. The modeled network data are represented by SRML, and can be published via the internet with the help of plug-in module 'GSCope'. KnowledgeEditor helps us to model and analyze biological pathways based on microarray data. It is possible to analyze the drawn networks by simulating up-down regulatory cascade in molecular interactions. AVAILABILITY: KnowledgeEditor is available at http://gscope.gsc.riken.go.jp/.     

Use of virtual, interactive, musculoskeletal system (VIMS) in modeling and analysis of shoulder throwing activity

Our purpose in this study was to apply the virtual, interactive, musculoskeletal system (VIMS) software for modeling and biomechanical analysis of the glenohumeral joint during a baseball pitching activity. The skeletal model was from VIMS library and muscle fiber attachment sites were derived from the visible human dataset. The muscular moment arms and function changes are mainly due to the large humeral motion involved during baseball pitching. The graphic animation of the anatomic system using VIMS software is an effective tool to model and visualize the complex anatomical structure of the shoulder for biomechanical analysis.     

Development of a dynamic deformable thorax phantom for the quality management of deformable image registration

The purpose of this study was to develop a novel dynamic deformable thorax phantom for deformable image registration (DIR) quality assurance (QA) and to verify as a tool for commissioning and DIR QA.The phantom consists of a base phantom, an inner phantom, and a motor-derived piston. The base phantom is an acrylic cylinder phantom with a diameter of 180 mm. The inner phantom consists of deformable, 20 mm thick disk-shaped sponges. To evaluate the physical characteristics of the phantom, we evaluated its image quality and deformation. DIR accuracies were evaluated using the three types of commercially DIR software (MIM, RayStation, and Velocity AI) to test the feasibility of this phantom. We used different DIR parameters to test the impact of parameters on DIR accuracy in various phantom settings. To evaluate DIR accuracy, a target registration error (TRE) was calculated using the anatomical landmark points.The three locations (i.e., distal, middle, and proximal positions) had different displacement amounts. This result indicated that the inner phantom was not moved but deformed. In cases with different phantom settings and marker settings, the ranges of the average TRE were 0.63–15.60 mm (MIM). In cases with different DIR parameters settings, the ranges of the average TRE were as follows: 0.73–7.10 mm (MIM), 8.25–8.66 mm (RayStation), and 8.26–8.43 mm (Velocity). These results suggest that our phantom could evaluate the detailed DIR behaviors with TRE. Therefore, this is indicative of the potential usefulness of our phantom in DIR commissioning and QA.     

Volumetric and spectroscopic characterizations of glucose-hexokinase association

The binding of D-glucose to hexokinase PII at 25 degrees C and pH 8.7 has been investigated by a combination of ultrasonic velocimetry, high precision densimetry, and fluorescence spectroscopy. The binding of glucose to the enzyme results in significant dehydration of the two interacting molecules, while the intrinsic coefficient of adiabatic compressibility of hexokinase slightly decreases. Glucose-hexokinase association is an entropy-driven process. The favorable change in entropy results from compensation between two large contributions. The binding-induced increase in hydrational entropy slightly prevails over the decrease in the configurational entropy of the enzyme. Taken together, our results emphasize the crucial role of water in modulating the energetics of protein recognition.     

Volumetric components of seed imbibition

Swelling parameters were determined for 15 seed species; the swelling quotients were found to range from less than 1.1 (castorbean) to 2.8 (mungbean) and swelling coefficients ranged from 0.09 (castorbean) to 0.42 (cowpea). Swelling leads to a lowering of specific gravity of those seeds with high initial specific gravity, and an elevation of those with low initial specific gravity. The extent of swelling bears a linear relationship with moisture content. Redrying to air dryness only partially restores the original volume, but oven drying completely restores it. Temperatures alter both the rate and the extent of swelling. Solutes in the imbibing solution alter the dynamics of the volume increases, indicating several types of influences; these include osmotic effects, salt effects, valence effects, pH effects, and lyotropic effects. It is suggested that deformation resulting from imbibitional swelling may contribute to the stresses experienced by seed tissues during hydration.     

Volumetric and projective bone mineral density

Projectional bone mineral density measurement so far used extensively in radiogrammetry and single and dual source absorptiometry is confronted with a serious limitation for the accurate evaluation of true density artifactually providing higher values along with the increase of body size and bone depth on account of the omission of one dimension. Computed tomography is capable of measuring true volumetric density and also accomplishes a separate measurement of trabecular and cortical bone especially on application to the distal and mid-radius with abundant cortical bone in peripheral computed tomography (pQCT). New lines of information may be obtained by such separate trabecular and cortical bone measurement in decreases of bone density due to various causes, estrogen withdrawal, corticosteroid, diabetes mellitus, renal failure, etc. Dynamic analysis of the result of pQCT may also make it possible to assess bone strength and resistance to fracture.     

Volumetric properties of nucleic acids

Volumetric studies can yield useful new information on a myriad of intra- and intermolecular interactions that stabilize nucleic acid structures. In particular, appropriately designed volumetric measurements can characterize the conformation-dependent hydration properties of nucleic acids as a function of solution conditions, including temperature, pressure, ionic strength, pH, and cosolvent concentration. We have started to accumulate a substantial database on volumetric properties of DNA and RNA, as well as on related low molecular weight model compounds. This database already has provided unique insights into the molecular origins of various nucleic acid recognition processes, including helix-to-coil and helix-to-helix conformational transitions, as well as drug-DNA interactions. In this article, we review recent progress in volumetric investigations of nucleic acids, emphasizing how these data can be used to gain insight into intra-and intermolecular interactions, including hydration properties. Throughout this review, we underscore the importance of volume and compressibility data for characterizing the hydration properties of nucleic acids and their constituents. We also describe how such volumetric data can be interpreted at the molecular level to yield a better understanding of the role that hydration can play in modulating the stability and recognition of nucleic acids.     

Volumetric imaging of fish locomotion

Fishes use multiple flexible fins in order to move and maintain stability in a complex fluid environment. We used a new approach, a volumetric velocimetry imaging system, to provide the first instantaneous three-dimensional views of wake structures as they are produced by freely swimming fishes. This new technology allowed us to demonstrate conclusively the linked ring vortex wake pattern that is produced by the symmetrical (homocercal) tail of fishes, and to visualize for the first time the three-dimensional vortex wake interaction between the dorsal and anal fins and the tail. We found that the dorsal and anal fin wakes were rapidly (within one tail beat) assimilated into the caudal fin vortex wake. These results show that volumetric imaging of biologically generated flow patterns can reveal new features of locomotor dynamics, and provides an avenue for future investigations of the diversity of fish swimming patterns and their hydrodynamic consequences.