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Journal articles on the topic 'DNA motion modeling'
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1
Johnson, David A. "DNA in Motion." American Biology Teacher 83, no. 7 (September 1, 2021): 458–63. http://dx.doi.org/10.1525/abt.2021.83.7.458.
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Students often struggle to understand the full implications of some basic chemical concepts of DNA structure and function, especially how DNA’s directionality and antiparallel nature determine key functional features of replication and molecular recombination. Visualizing the complexities of these processes requires a working knowledge of how DNA’s nucleotides are assembled and how these components interact. This article describes a simple activity that can be used to visualize how nucleotides join together, how base pairs form, and, most importantly, how the active processes of replication and recombination are related to DNA chemistry. In this activity, students model DNA structure, with each student representing a single nucleotide, then join together to form a polynucleotide with 5′ to 3′ directionality. Two chains then pair to form the antiparallel DNA duplex. The activity not only illustrates the basic chemistry of DNA but also allows students to participate in active modeling of leading-strand and lagging-strand replication and in the formation of the Holliday junction molecule, the basic intermediate of recombination events including crossing over and gene conversion. The demonstrations can be videotaped from above to make a permanent copy of these events for teaching and study purposes. Example illustrations and links to videos are included.
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Rapino, Stefania, and Francesco Zerbetto. "Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface." Langmuir 21, no. 6 (March 2005): 2512–18. http://dx.doi.org/10.1021/la047091o.
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Якушевич, Л. В., and L. V. Yakushevich. "On the DNA Kink Motion Under the Action of Constant Torque." Mathematical Biology and Bioinformatics 11, no. 1 (April 18, 2016): 81–90. http://dx.doi.org/10.17537/2016.11.81.
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The influence of the torsion moment on the DNA kink motion is studied by the methods of mathematical modeling. Time dependence of the kink coordinate, velocity, size, and energy on the different values of the parameters of the external torsion moment have been found. It has been shown that by changing the parameters, by switching on and off of the external action, one could regulate the velocity and the direction of the kink movement. Estimation of the torque value necessary for the kink (open state) movement with the velocity comparable to the transcription velocity, has been made.
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Huang, Chao-Min, Anjelica Kucinic, Jenny V. Le, Carlos E. Castro, and Hai-Jun Su. "Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis." Nanoscale 11, no. 4 (2019): 1647–60. http://dx.doi.org/10.1039/c8nr06377j.
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We report a hybrid computational framework combining coarse-grained modeling with kinematic variance analysis for predicting uncertainties in the motion pathway of a multi-component DNA origami mechanism.
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Zakirianov, F. K., V. Yu Melnikov, G. T. Zakirianova, G. K. Galina, and L. F. Zakirianova. "MODELING OF MOTION OF CONFORMATIONAL PERTURBATIONS IN DNA MOLECULE WITH ACCOUNT OF RNA POLYMERASE." Vestnik Bashkirskogo universiteta 7, no. 1 (2018): 14. http://dx.doi.org/10.33184/bulletin-bsu-2018.1.3.
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Blatt, Simon, and Philipp Reiter. "Modeling repulsive forces on fibres via knot energies." Computational and Mathematical Biophysics 2, no. 1 (January 1, 2014): 56–72. http://dx.doi.org/10.2478/mlbmb-2014-0004.
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Abstract Modeling of repulsive forces is essential to the understanding of certain bio-physical processes, especially for the motion of DNA molecules. These kinds of phenomena seem to be driven by some sort of “energy” which especially prevents the molecules from strongly bending and forming self-intersections. Inspired by a physical toy model, numerous functionals have been defined during the past twenty-five years that aim at modeling self-avoidance. The general idea is to produce “detangled” curves having particularly large distances between distant strands. In this survey we present several families of these so-called knot energies. It turns out that they are quite similar from an analytical viewpoint. We focus on proving self-avoidance and existence of minimizers in every knot class. For a suitable subfamily of these energies we show how to prove that these minimizers are even infinitely differentiable.
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Faraji, Elham, Roberto Franzosi, Stefano Mancini, and Marco Pettini. "Transition between Random and Periodic Electron Currents on a DNA Chain." International Journal of Molecular Sciences 22, no. 14 (July 8, 2021): 7361. http://dx.doi.org/10.3390/ijms22147361.
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By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields.
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Chen, Y. H., X. J. Li, X. F. Zhou, Jia Lin Sun, W. H. Huang, and J. Hu. "Determining the Radial Modulus of DNA Measured by VPSFM." Key Engineering Materials 295-296 (October 2005): 83–88. http://dx.doi.org/10.4028/www.scientific.net/kem.295-296.83.
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Mechanical properties of DNA, for example the elastic modulus, are of vital importance for its biological function. Previously, the modulus is mainly obtained by bending, stretching and twisting DNA using various techniques and tools. By applying vibrating mode scanning polarization force microscopy (VPSFM), deformations of DNA under ultra-small indentation forces can be measured and so the radial modulus can be computed. In this paper, modeling of the VPSFM measuring system is presented. The system is modeled as a spring-mass-damper oscillator under various force fields, such as van der Waals force, attractive electrical force and repulsive interactions between the tip and sample. The electrical polarization force is described by using uniformly charged line model and the DNA is considered to be a simple elastic rod. By numerically integrating the equation of tip motion, the contact force and the radial modulus of DNA under different deformation can be calculated. We found that in measuring radial modulus of DNA, the existence of substrate cannot be neglected, especially when the relative large deformation is reached.
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Fialko, Nadezhda, Maxim Olshevets, and Victor Lakhno. "Charge Transfer in Dimer with Dissipation." EPJ Web of Conferences 224 (2019): 03006. http://dx.doi.org/10.1051/epjconf/201922403006.
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The study of the charge transfer processes in biomacromolecules such as DNA is essential for the development of nanobioelectronics, design and construction of DNA-based nanowires, memory devices, logical elements, etc. Mathematical and computer modeling of charge transfer in biopolymer chains is an important part of these investigations. Some properties of charge transfer can be demonstrated by modeling of two-site chain. Based on the semi-classical Holstein model we consider a system of two sites and charged particle (electron or hole) in which the oscillations of the first site are not related to the charge motion, and the parameters of the second site correspond to a small-radius polaron. The system steady states depending on the electron energy H at the second site are studied numerically. The dynamics of the charge initially localized at the first site is modeled. Various modes depending on H are demonstrated: charge tunneling, resonant transfer, and lack of transfer.
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Socol, Marius, Renjie Wang, Daniel Jost, Pascal Carrivain, Cédric Vaillant, Eric Le Cam, Vincent Dahirel, et al. "Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes." Nucleic Acids Research 47, no. 12 (May 22, 2019): 6195–207. http://dx.doi.org/10.1093/nar/gkz374.
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Abstract DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of –0.3 to –0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in ‘theta’ conditions, in which they are poised for compartmentalization and phase separation.
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Li, Yunlang, and Tamar Schlick. "Modeling DNA Polymerase μ Motions: Subtle Transitions before Chemistry." Biophysical Journal 99, no. 10 (November 2010): 3463–72. http://dx.doi.org/10.1016/j.bpj.2010.09.056.
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Yekti, Bharoto. "Studi Efektivitas Praktik Modeling Dalam Produksi Asset Animasi Stop Motion Menggunakan 3D Printing." ULTIMART Jurnal Komunikasi Visual 7, no. 2 (November 12, 2016): 36–46. http://dx.doi.org/10.31937/ultimart.v7i2.384.
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Teknologi 3D printing sudah mulai banyak digunakan di industri animasi terutama animasi stop motion. Penggunaan 3D printer untuk animasi stop motion paling banyak digunakan pada teknik replacement animation. Perangkat lunak yang digunakan untuk membuat aset animasi stop motion tidak terbatas pada jenis perangkat lunak untuk animasi 3 Dimensi (3D) saja, Teknik 3D digital sculpting juga dapat digunakan untuk membentuk 3D model yang kemudian bisa diproses menjadi aset untuk animasi stop motion dengan 3D printer. Penelitian ini membandingkan pembuatan model 3Dimensi yang menggunakan metode polygon modeling (memakai perangkat lunak Softimage) dengan pembuatan 3D model yang menggunakan metode digital sculpting (memakai perangkat lunak Zbrush). Penelitian ini bertujuan untuk mengetahui kelemahan serta kelebihan metode poly modeling dan digital sculpting untuk membuat 3D model, dari proses modeling awal sampai ke tahap converting file perangkat lunak native menjadi file .stl yang siap diproses dengan 3D printer.
Key words : 3d modeling, 3d printing, Stop motion, animationEngine.
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Ragosta, M., C. Serio, M. T. Lanfredi, and M. Macchiato. "Dynamical Degrees of Freedom of DNA Sequences by Local and Global Short-Range Prediction." Fractals 05, no. 01 (March 1997): 1–10. http://dx.doi.org/10.1142/s0218348x97000024.
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The dynamical properties of DNA sequence samples have been analyzed on the basis of a procedure able to distinguish chaos from randomness. The procedure relies on the concept of short-term (range) predictability of low-dimensional chaotic motions and can distinguish merely linear stochastic processes, e.g. fractional Brownian motion, from truly nonlinear deterministic systems. The method consists in obtaining forecasts on the basis of past events in the sequence. Two forecasting strategies are used. The local strategy views the sequence as the outcome of a nonlinear process, whereas the global approach considers the series as the outcome of a linear stochastic process. For both approaches, the predictive skill is computed and their inter-comparison allows us to get insight into and an understanding of the structure of DNA sequences. Nucleotidic sequences belonging to different taxonomic and functional groups have been analyzed. Different behaviors have been detected according to the existence of finite correlation dimension for specific groups of sequences.
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Munadi, Munadi, Ismoyo Haryanto, and Toni Prahasto. "ANALISA KINEMATIK, DINAMIK DAN METODE GERAK KAKI MODEL SNOOPER HEXAPOD ROBOT." ROTASI 17, no. 3 (July 1, 2015): 137. http://dx.doi.org/10.14710/rotasi.17.3.137-144.
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This article presents how to make a model of snooper hexapod robot as a legged robot which is inspired by the spider. This model robot is used for monitoring systems of an industrial area. We design an hexapod robot that consists of 18 dof, which it used acrylic as a base material, servomotor as a driver and an ATmega 128 as microcontroller. We start to make a mechanical design of a snooper hexapod robot construction. Furthermore, kinematics and dynamics analysis of hexapod robot is discussed using Matlab from the control point of view. The objective of kinematic analysis is to determine the kinematic quatities such as displacements, velocities, and accelerations of the elements of model robot when the input motion is given. It establishes the relationship between the motions of various components of the link. The dynamics analysis will inform a torque at the joint ankle hexapod robot using modeling Matlab Simmechanics. The model of hexapod robot is used for monitoring systems so called snooper hexapod will be designed and manufactured so have the required capabilities as a surveillance robot that is able to reach the difficult area and can transmit visual information to the operators who control it. Analysis is done on the robot motion algorithm on three kinds of methods of walk (one wave, two wave, and tripod) with few parameters specified
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Brzeski, J., T. Grycuk, A. W. Lipkowski, W. Rudnicki, B. Lesyng, and A. Jerzmanowski. "Binding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies." Acta Biochimica Polonica 45, no. 1 (March 31, 1998): 221–31. http://dx.doi.org/10.18388/abp.1998_4304.
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The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK-type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.
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Craig, Jonathan M., Andrew H. Laszlo, Ian C. Nova, and Jens H. Gundlach. "Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT)." Essays in Biochemistry 65, no. 1 (April 2021): 109–27. http://dx.doi.org/10.1042/ebc20200027.
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Abstract Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT’s spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT’s ability to discern an enzyme’s nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
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Stormo, Gary D. "Maximally Efficient Modeling of DNA Sequence Motifs at All Levels of Complexity." Genetics 187, no. 4 (February 7, 2011): 1219–24. http://dx.doi.org/10.1534/genetics.110.126052.
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Piechowiak, Tadeusz. "Modelling of various railway brakes types in the individual vehicles for the simulation of train motion." Rail Vehicles, no. 4 (November 2, 2016): 24–32. http://dx.doi.org/10.53502/rail-138748.
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Artykuł prezentuje rozszerzenie opracowanej przez autora metody modelowania układu hamulca pneumatycznego całego pociągu. Model składa się z różnych części składowych spojonych modelem ciągłym układu przewodu głównego. Rozszerzenie polega na możliwości występowania w symulowanym pociągu różnych komponentów hamulcowych na poszczególnych wagonach. Przedstawiono warianty metody, przykłady wyników i praktyczne znaczenie tych rozszerzeń.
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Kim, Young-Joo, and Do-Nyun Kim. "Sensitivity Analysis for the Mechanical Properties of DNA Bundles." Journal of Nanomaterials 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/6287937.
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In structural DNA nanotechnology, programming a three-dimensional shape into DNA bundles has been a primary design objective. However, the mechanical properties of these DNA bundle structures are another important factor to be considered in the design process. While the mechanics of the individual DNA double helix has been explored extensively and hence its properties are well known, the mechanical properties of structural motifs such as DNA junctions and strand breaks important to bundle mechanics have not been well characterized due to experimental limitations, rendering it difficult to predict the mechanical properties of DNA bundles. Here, we investigate the effect of these structural motifs on the global bundle rigidities by performing sensitivity analysis on a six-helix DNA bundle structure using the finite element modeling approach. Results reveal the primary structural features and their parametric values required to reproduce the experimental bundle rigidities.
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Meng, Max Q.-H., and Hong Zhang. "Perspectives of Computational Intelligence in Robotics and Automation." Journal of Advanced Computational Intelligence and Intelligent Informatics 8, no. 3 (May 20, 2004): 235–36. http://dx.doi.org/10.20965/jaciii.2004.p0235.
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As people attempt to build biomimetic robots and realize automation processes through artificial intelligence, computational intelligence plays a very important role in robotics and automation. This special issue contains several important papers that address various aspects of computational intelligence in robotics and automation. While acknowledging its limited coverage, this special issue offers a range of interesting contributions such as intelligent trajectory planning for flying and land mobile robots, fuzzy decision making, control of rigid and teleoperated robots, modeling of human sensations, and intelligent sensor fusion techniques. Let us scan through these contributions of this special issue. The first paper, "Planar Spline Trajectory Following for an Autonomous Helicopter," by Harbick et al., proposes a technique for planar trajectory following for an autonomous aerial robot. A trajectory is modeled as a planar spline. A behavior-based control system stabilizes the robot and enforces trajectory following of an autonomous helicopter with a reasonable trajectory tracking error on the order of the size of the helicopter (1.8m). In the second paper, "A Biologically Inspired Approach to Collision-Free Path Planning and Tracking Control of a Mobile Robot," by Yang et al., a novel biologically inspired neural network approach is proposed for dynamic collision-free path planning and stable tracking control of a nonholonomic mobile robot in a non-stationary environment, based on shunting equations derived from Hodgkin and Huxley's biological membrane equation. The third paper, "Composite Fuzzy Measure and Its Application to Decision Making," by Kaino and Kaoru, builds a composite fuzzy measure from fuzzy measures defined on fuzzy measurable spaces using composite fuzzy weights by the authors, with a successful application to an automobile factory capital investment decision making problem. In "Intelligent Control of a Miniature Climbing Robot," by Xiao et al., a fuzzy logic based intelligent optimal control system for a miniature climbing robot to achieve precision motion control, minimized power consumption, and versatile behaviors is presented with validation via experimental studies. The fifth paper, "Incorporating Motivation in a Hybrid Robot Architecture," by Stoytchev and Arkin, describes a hybrid mobile robot architecture capable of deliberative planning, reactive control, and motivational drives, which addresses three main challenges for robots living in human-inhabited environments: operating in dynamic and unpredictable environment, dealing with high-level human commands, and engaging human users. Experimental results for a fax delivery mission in a normal office environment are included. In the next paper, "Intelligent Scaling Control for Internet-based Teleoperation," by Liu et al., an adaptive scaling control scheme, with a neural network based time-delay prediction algorithm trained using the maximum entropy principle, is proposed with successful experimental studies on an Internet mobile robot platform. The next paper, "Feature Extraction of Robot Sensor Data Using Factor Analysis for Behavior Learning," by Fung and Liu, discusses important knowledge extraction of sensor data for robot behavior learning using a new approach based on the inter-correlation of sensor data via factor analysis and construction of logical perceptual space by hypothetical latent factors. Experimental results are included to demonstrate the process of logical perceptual space extraction from ultrasonic range data for robot behavior learning. "Trajectory Planning of Mobile Robots Using DNA Computing," by Kiguchi et al., presents an optimal trajectory planning method for mobile robots using Watson-Crick pairing to find the shortest trajectory in the robot working area with the DNA sequences representing the locations of the obstacles removed during the process. The proposed algorithm is especially suitable for computing on a DNA molecular computer. In the ninth paper, "Computational Intelligence for Modeling Human Sensations in Virtual Environments," by Lee and Xu, cascade neural networks with node-decoupled extended Kalman filter training for modeling human sensations in virtual environments are proposed, with a stochastic similarity measure based on hidden Markov models to calculate the relative similarity between model-generated sensations and actual human sensations. A new input selection technique, based on independent component analysis capable of reducing the data size and selecting the stimulus information, is developed and reported. The next paper, "Intelligent Sensor Fusion in Robotic Prosthetic Eye System," by Gu et al., is concerned with the design, sensing and control of a robotic prosthetic eye that moves horizontally in synchronization with the movement of the natural eye. It discusses issues on sensor failure detection and recovery and sensor data fusion techniques using statistical methods and artificial neural network based methods. Simulation and experimental results are included to demonstrate the effectiveness of the results. The final contribution in our collection is a paper by Sun et al., entitled "A Position Control of Direct-Drive Robot Manipulators with PMAC Motors Using Enhanced Fuzzy PD Control." It presents a simple and easy-to-implement position control scheme for direct-drive robot manipulators based on enhanced fuzzy PD control, incorporating two nonlinear tracking differentiators into a conventional PD controller. Experiments on a single-link manipulator directly driven by a permanent magnet AC (PMAC) motor demonstrate the validity of the proposed approach. The Guest Editors would like to thank the contributors and reviewers of this special issue for their time and effort in making this special issue possible. They would also like to express their sincere appreciation to the JACIII editorial board, especially Profs. Kaoru and Fukuda, Editors-in-Chief and Kenta Uchino, Managing Editor, for the opportunity and help they provided for us to put together this special issue.
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Waspada, Heri Priya, Ismanto Ismanto, and Firman Hidayah. "Penggunaan Hasil Motion Capture (Data Bvh) Untuk Menganimasikan Model Karakter 3d Agar Menghasilkan Animasi Yang Humanoid." JAMI: Jurnal Ahli Muda Indonesia 1, no. 2 (December 31, 2020): 94–102. http://dx.doi.org/10.46510/jami.v1i2.34.
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Abstrak
Objektif. Proses pemodelan karakter 3D memegang peranan penting dalam menghasilkan model karakter 3D yang baik. Proses ini merupakan proses awal yang harus dilalui oleh seorang desainer dalam membuat sebuah model karakter 3D. Setelah proses pemodelan dikerjakan dengan baik agar karakter tersebut bisa dibuat bergerak maka diperlukan proses rigging. Dengan proses pemodelan dan rigging tersebut model karakter 3D bisa digunakan untuk menghasilkan animasi sesuai dengan keinginan animator. Tentunya seorang animator akan memerlukan kerja keras untuk membuat suatu adegan gerakan apabila animasi yang dibuat masih manual. Untuk itu dengan memanfaatkan data BVH, animator akan lebih ringan dalam membuat adegan animasinya. Hasil animasi karakter di tunjukkan kepada 40 responden untuk menilai dan menghasilkan rata-rata tingkat humanoid animasi karakter bernilai 65%.
Material and Metode. Menganimasikan model karakter 3D memanfaatkan hasil motion capture (.bvh)
Hasil. Animasi karakter 3D dengan menggunakan hasil motion capture menghasilkan animasi yang humanoid.
Kesimpulan. Hasil motion capture merupakan susunan tulang yang sudah dilengkapi dengan hasil perekaman gerakan sehingga untuk memproduksi animasi model karakter 3D akan lebih mudah karena animator tidak perlu menggambar tiap gerakan yang diinginkan.
Abstrack
Objective. The process of modeling 3D characters plays an important role in producing good 3D character models. This process is the initial process that must be passed by a designer in creating a 3D character model. After the modeling process is done well so that the character can be moved, a rigging process is needed. With the modeling and rigging process, 3D character models can be used to produce animations in accordance with the wishes of the animator. Of course, an animator will need to work hard to create a motion scene if the animation created is still manual. For this reason, by utilizing BVH data, animators will be lighter in making their animated scenes. The results of the character animation were shown to 40 respondents to rate and produce an average humanoid character animation level of 65%.
Materials and Methods. Menganimasikan model karakter 3D memanfaatkan hasil motion capture (.bvh)
Results. 3D character animation using the results of motion capture produces humanoid animation.
Conclusion. The result of motion capture is the arrangement of bones that has been equipped with the results of recording the motion so that to produce animated 3D character models will be easier because the animator does not need to draw every desired movement.
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Sayatman, Sayatman, Nugrahardi R, Anjrah H, Rabendra Y, and Kartika Kartika. "DESAIN MODEL KARAKTER CLAY UNTUK MENDUKUNG PROMOSI ANIMASI STOP MOTION." Jurnal Dimensi Seni Rupa dan Desain 11, no. 2 (September 1, 2014): 197. http://dx.doi.org/10.25105/dim.v11i2.104.
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<p><strong>Abstract</strong><br />The animated film is one of the assets of the national creative industries, which has great potential to be developed into economic creative sectors. Animation products not only featured in the film industry but also widely used for the videography products, advertising and multimedia gaming applications. In<br />addition to the strength of the story, one of the important aspects in the production of the animated film is the character design. The success of delivering the message is heavily influenced by the strength of characters that play the part. This study will discuss the topic of clay based design modelling<br />where it would be useful as an alternate method in designing a clay based animated character and can make a positive contribution to the development of creative industries Indonesia.</p><p> </p><p><strong>Abstrak</strong><br />Film animasi merupakan salah satu aset industri kreatif nasional yang potensial untuk terus dikembangkan menjadi sektor ekonomi kreatif. Produk-produk animasi kini tidak saja digunakan dalam industri film layar lebar, namun juga banyak dimanfaatkan untuk produksi videografi, iklan maupun aplikasi game multimedia. Selain kekuatan cerita, salah satu aspek penting dalam film animasi adalah desain karakter/figur. Karena sebagian besar keberhasilan penyampaian pesan cerita sebuah film termasuk animasi banyak dipengaruhi oleh kekuatan<br />desain karakter/figure yang memerankannya. Penelitian ini akan membahasnya dalam topik rancang bangun karakter modeling berbasis clay. Semoga dapat bermanfaat sebagai alternatif metode dalam desain model karakter animasi berbasis clay dan dapat memberikan kontribusi positif untuk perkembangan industri kreatif di Indonesia.<br /><br /></p>
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Kholil, Moch d., Ismanto Ismanto, and M. Nur Fu’ad. "REKONTRUKSI MODEL 3D DARI BANYAK GAMBAR MENGGUNAKAN ALGORITMA STRUCTURE FROM MOTION (SFM) DAN MULTI VIEW STEREO (MVS) BERBASIS COMPUTER VISION." Jurnal RESISTOR (Rekayasa Sistem Komputer) 3, no. 2 (November 6, 2020): 108–13. http://dx.doi.org/10.31598/jurnalresistor.v3i2.655.
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With the development of the field of Information and Computer Technology (ICT), three-dimensional technology (3D) is also growing rapidly. Currently, the need to visualize 3D objects is widely used in animation and graphics applications, architecture, education, cultural recognition and virtual reality. 3D modeling of historical buildings has become a concern in recent years. 3D reconstruction is a documentation effort for reconstruction or restoration if the building is destroyed. By using a 3D model reconstruction approach based on multiple images using the Structure From Motion (SFM) and Multi View Stereo (MVS) algorithm, it is hoped that the 3D modeling results can be used as an effort to preserve 3D objects in the cultural heritage area of Penataran Temple. This research was conducted by taking an object in the form of photos as many as 61 pictures in the area of the Blitar Penataran Temple. The resulting photos are reconstructed into a 3D model using the Structure From Motion algorithm in the meshroom. In this study, a test was carried out on the original image with the compressed image for reconstruction to be compared to the 3D reconstruction process from the two input data. From 61 images processed using the Structure Form Motion algorithm, 33 camera pose and 3D point data were obtained, both original and compressed images. For the number of iterations the compressed image is 1.4% less than the original image and takes 43.53% faster than the original image.
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Halpern, David, Hélène Chiapello, Sophie Schbath, Stéphane Robin, Christelle Hennequet-Antier, Alexandra Gruss, and Meriem El Karoui. "Identification of DNA Motifs Implicated in Maintenance of Bacterial Core Genomes by Predictive Modeling." PLoS Genetics 3, no. 9 (September 14, 2007): e153. http://dx.doi.org/10.1371/journal.pgen.0030153.
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López, Yosvany, Alexis Vandenbon, Akinao Nose, and Kenta Nakai. "Modeling thecis-regulatory modules of genes expressed in developmental stages ofDrosophila melanogaster." PeerJ 5 (May 30, 2017): e3389. http://dx.doi.org/10.7717/peerj.3389.
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Because transcription is the first step in the regulation of gene expression, understanding how transcription factors bind to their DNA binding motifs has become absolutely necessary. It has been shown that the promoters of genes with similar expression profiles share common structural patterns. This paper presents an extensive study of the regulatory regions of genes expressed in 24 developmental stages ofDrosophila melanogaster. It proposes the use of a combination of structural features, such as positioning of individual motifs relative to the transcription start site, orientation, pairwise distance between motifs, and presence of motifs anywhere in the promoter for predicting gene expression from structural features of promoter sequences. RNA-sequencing data was utilized to create and validate the 24 models. When genes with high-scoring promoters were compared to those identified by RNA-seq samples, 19 (79.2%) statistically significant models, a number that exceeds previous studies, were obtained. Each model yielded a set of highly informative features, which were used to search for genes with similar biological functions.
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Zhao, Xiaoyue, Haiyan Huang, and Terence P. Speed. "Finding Short DNA Motifs Using Permuted Markov Models." Journal of Computational Biology 12, no. 6 (July 2005): 894–906. http://dx.doi.org/10.1089/cmb.2005.12.894.
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Roux-Rouquie, M. "Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter." Nucleic Acids Research 28, no. 18 (September 15, 2000): 3433–41. http://dx.doi.org/10.1093/nar/28.18.3433.
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Kot, Witold, Nikoline S. Olsen, Tue K. Nielsen, Geoffrey Hutinet, Valérie de Crécy-Lagard, Liang Cui, Peter C. Dedon, et al. "Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs." Nucleic Acids Research 48, no. 18 (September 17, 2020): 10383–96. http://dx.doi.org/10.1093/nar/gkaa735.
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Abstract In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.
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Corander, Jukka, Magnus Ekdahl, and Timo Koski. "Bayesian Unsupervised Learning of DNA Regulatory Binding Regions." Advances in Artificial Intelligence 2009 (August 11, 2009): 1–11. http://dx.doi.org/10.1155/2009/219743.
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Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either scan for previously known motif types or to attempt de novo identification of a fixed number (typically one) of putative motifs. Most approaches assume the existence of reliable biodatabase information to build probabilistic a priori description of the motif classes. Examples of attempts to do probabilistic unsupervised learning about the number of putative de novo motif types and their positions within a set of DNA sequences are very rare in the literature. Here we show how such a learning problem can be formulated using a Bayesian model that targets to simultaneously maximize the marginal likelihood of sequence data arising under multiple motif types as well as under the background DNA model, which equals a variable length Markov chain. It is demonstrated how the adopted Bayesian modelling strategy combined with recently introduced nonstandard stochastic computation tools yields a more tractable learning procedure than is possible with the standard Monte Carlo approaches. Improvements and extensions of the proposed approach are also discussed.
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Toivonen, Jarkko, Pratyush K. Das, Jussi Taipale, and Esko Ukkonen. "MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs." Bioinformatics 36, no. 9 (January 30, 2020): 2690–96. http://dx.doi.org/10.1093/bioinformatics/btaa045.
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Abstract Motivation Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better performance of higher order models such as Markov models of order one, also called adjacent dinucleotide matrices (ADMs). ADMs can model dependencies between adjacent nucleotides, unlike PPMs. A modeling technique and software tool that would estimate such models simultaneously both for monomers and their dimers have been missing. Results We present an ADM-based mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algorithm MODER2 for learning such models from training data and seeds. The model is a mixture that includes monomers and dimers, built from the monomers, with a description of the dimeric structure (spacing, orientation). The technique is modular, meaning that the co-operative effect of dimerization is made explicit by evaluating the difference between expected and observed models. The model is validated using HT-SELEX and generated datasets, and by comparing to some earlier PPM and ADM techniques. The ADM models explain data slightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (bHLH, bZIP, ETS and Homeodomain), the ADM mixture models by MODER2 being the best on average. Availability and implementation Software implementation is available from https://github.com/jttoivon/moder2. Supplementary information Supplementary data are available at Bioinformatics online.
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Hawkins-Hooker, Alex, Henry Kenlay, and John E. Reid. "Projection layers improve deep learning models of regulatory DNA function." F1000Research 8 (February 5, 2019): 151. http://dx.doi.org/10.12688/f1000research.17125.1.
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With the increasing application of deep learning methods to the modelling of regulatory DNA sequences has come an interest in exploring what types of architecture are best suited to the domain. Networks designed to predict many functional characteristics of noncoding DNA in a multitask framework have to recognise a large number of motifs and as a result benefit from large numbers of convolutional filters in the first layer. The use of large first layers in turn motivates an exploration of strategies for addressing the sparsity of output and possibility for overfitting that result. To this end we propose the use of a dimensionality-reducing linear projection layer after the initial motif-recognising convolutions. In experiments with a reduced version of the DeepSEA dataset we find that inserting this layer in combination with dropout into convolutional and convolutional-recurrent architectures can improve predictive performance across a range of first layer sizes. We further validate our approach by incorporating the projection layer into a new convolutional-recurrent architecture which achieves state of the art performance on the full DeepSEA dataset. Analysis of the learned projection weights shows that the inclusion of this layer simplifies the network’s internal representation of the occurrence of motifs, notably by projecting features representing forward and reverse-complement motifs to similar positions in the lower dimensional feature space output by the layer.
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de With, G., and A. E. Holdø. "The Use of Solution Adaptive Grid for Modeling Small Scale Turbulent Structures." Journal of Fluids Engineering 127, no. 5 (May 12, 2005): 936–44. http://dx.doi.org/10.1115/1.1989359.
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The use of large eddy simulation (LES) is computationally intensive and various studies demonstrated the considerable range of vortex scales to be resolved in an LES type of simulation. The purpose of this study is to investigate the use of a dynamic grid adaptation (DGA) algorithm. Despite many developments related to adaptive methods and adaptive grid strategies, the use of DGA in the context of turbulence modeling is still not well understood, and various profound problems with DGA in relation to turbulence modeling are still present. The work presented in this paper focuses on the numerical modeling of flow around a circular cylinder in the sub-critical flow regime at a Reynolds number of 3.9∙103. LES simulations with conventional mesh and DGA have been performed with various mesh sizes, refinement criteria and re-meshing frequency, to investigate the effects of re-meshing on the flow field prediction. The results indicate that the turbulent flow field is sensitive to modifications in the mesh and re-meshing frequency, and it is suggested that the re-meshing in the unsteady flow region is affecting the onset of small scale flow motions in the free shear layer.
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Wang, Xun, Ying Miao, and Minquan Cheng. "Finding Motifs in DNA Sequences Using Low-Dispersion Sequences." Journal of Computational Biology 21, no. 4 (April 2014): 320–29. http://dx.doi.org/10.1089/cmb.2013.0054.
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Khoukhi, Amar. "Neural based RSPN multi-agent strategy for biped motion control." Robotica 19, no. 6 (September 2001): 611–17. http://dx.doi.org/10.1017/s0263574701003344.
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In this paper fhe problem of motion control of a biped is considered. We develop a new method based on multi-agent associated Neural AIGLS (On-line Augmented Integration of Gradient and Last Sguare method) – RSPN (Recursive Stochastic Petri Nets) strategy. This method deals with organization and coordination aspects in an intelligent modeling of human motion. We propose a cooperative multi-agent model. Based on this model, we develop a control kernel named IMCOK (Intelligent Motion COntrol Kernel) which consists of a controller, a coordinator and an executor of different cycles of the motion of the biped. When walking, IMCOK receives messages and sends offers. A Decision Making of Actions (DMA) is developed at the supervisor level. The articulator agents partially planify the motion of the associated non-articulator agents. The system is hybrid and distributed functionally. The learning of the biped is performed using an On-line Augmented Integration of Gradient and Last Sguare Neural Networks based algorithm. In the conflictual situations of sending or receiving messages by the managers of MABS we apply a new strategy: Recursive Stochastic Petri Nets (RSPN). This module is fundamental in the On-line information processing between agents. It allows particularly the Recursive strategy concept. Cognitive agents communicate with reactive (non-articulator) agents in order to generate the motion.
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Amir, Shahizat, N. S. Mohamed, Siti Aishah Hashim Ali, and Shahrul Amir. "Simulation Model of Multiple Cluster Fractals Cultured in Nanocomposite Polymer Electrolyte Film." Materials Science Forum 864 (August 2016): 163–68. http://dx.doi.org/10.4028/www.scientific.net/msf.864.163.
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This work contributes to the melioration of the modeling and simulation of laboratory cultured fractals using poly (vinylidene fluoride-co-hexafluoropropylene)/poly (ethyl methacrylate)-ammonium trifluorome-thanesulfonate nanocomposite polymer electrolyte films as the media of growth. Main focus is given to fractals and fractal growth models particularly DLA (Diffusion Limited Aggregation). The DLA cluster formed through DLA is formed by particles moving in Brownian motion (diffusion) which meet and stick together randomly (aggregation) to form the cluster. The simulation of multiple cluster fractals is done using DLA methods incorporating different parameters such as its sticking coefficient, lattice geometry and number of particles. To compare the simulation with the real patterns obtained, one vital aspect would be the calculation of their fractal dimension values. The computer program developed is able to calculate the fractal dimension value of each of the simulated fractal patterns. Suitable fractal dimension calculation method is employed according to its usefulness and efficiency. Fractal growth modeling and simulation such as done here can contribute to the understanding of other related studies concerning fractal growth found in areas including medical (nervous systems, cancer growth and more).
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Majid, Abdul, Raden Sumiharto, and Setyawan Bekti Wibisono. "Identifikasi Model dari Pesawat Udara Tanpa Awak Sayap Tetap Jenis Bixler." IJEIS (Indonesian Journal of Electronics and Instrumentation Systems) 5, no. 1 (May 1, 2015): 43. http://dx.doi.org/10.22146/ijeis.7152.
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AbstrakModel terbang merupakan bagian penting dalam pembangunan sistem kontrol suatu pesawat udara tanpa awak sayap tetap, terutama dalam pembangunan sistem kendali mandiri atau autopilot pesawat. Dengan model terbang, gerak terbang pesawat dapat direpresentasikan dan disimulasikan. Pada penelitian ini, model terbang dihasilkan melalui identifikasi sistem atau pemodelan pesawat udara tanpa awak sayap tetap jenis Bixler. Identifikasi sistem dilakukan berdasarkan eksperimen (pengambilan data terbang) dan digunakan struktur model state-space. Terdapat tiga tahapan dalam penelitian ini, pemodelan gerak terbang pesawat, pengambilan data terbang, dan identifikasi model terbang. Melalui tiga tahapan tersebut, diperoleh model terbang pesawat sayap tetap jenis Bixler yang dapat merepresentasikan gerak terbang pesawat yang terbagi dalam 2 mode, mode longitudinal dan mode lateral.Diperoleh model terbang mode longitudinal pesawat udara tanpa awak sayap tetap jenis Bixler menggunakan 13 parameter menggunakan struktur model state-space orde 4. Model terbang mode lateral pesawat udara tanpa awak sayap tetap jenis Bixler menggunakan 11 parameter menggunakan struktur model state-space orde 4. Kata kunci—UAV, Identifikasi Sistem, Pemodelan AbstractFlight model is one of importing thing in fixed-wing unmanned aerial vehicle (UAV) control system development, mainly in the aircraft autopilot. Through this flight model, the aircraft motion can be represented and simulated.In this research, the flight model is obtained through system identification and system modelling of Bixler fixed-wing unmanned aerial vehicle. System identification is based on experiment data and use state-space model structure. There are three stages in this research, aircraft motion system modelling, flight data collecting, and flight model identification. Through those three stages, Bixler fixed-wing unmanned aerial vehicle flight model is obtained as represented in two modes, longitudinal mode and lateral modeThe Bixler fixed-wing unmanned aerial vehicle longitudinal mode flight model is obtained using 13 parameters. The lateral mode is obtained using 11 parameters. All modes are in 4th order state space model structure. Keywords— UAV, System Identification, Modelling
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Amir, Shahizat, Mohamed Nor Sabirin, and Siti Aishah Hashim Ali. "Using Polymer Electrolyte Membranes as Media to Culture Fractals: A Simulation Study." Advanced Materials Research 93-94 (January 2010): 35–38. http://dx.doi.org/10.4028/www.scientific.net/amr.93-94.35.
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In the authors' laboratory, fern-like fractals have been cultured in polymer electrolyte membranes of polyethylene oxide (PEO) doped with ammonium iodide (NH4I). The simulation study was then carried out utilizing the Diffusion Limited Aggregation (DLA) based on random motion of aggregating particles modelling technique. The fractal dimension values and the forms of the simulated fractals are comparable to those observed in the PEO polymer membranes. These indicate that the simulation using the DLA model done in this study has resulted outputs that are in abidance with the original fractals cultured in the polymer membranes.
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Brandani, Giovanni B., and Shoji Takada. "Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA." PLOS Computational Biology 14, no. 11 (November 5, 2018): e1006512. http://dx.doi.org/10.1371/journal.pcbi.1006512.
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Feng, Jean, David A. Shaw, Vladimir N. Minin, Noah Simon, and Frederick A. Matsen IV. "Survival analysis of DNA mutation motifs with penalized proportional hazards." Annals of Applied Statistics 13, no. 2 (June 2019): 1268–94. http://dx.doi.org/10.1214/18-aoas1233.
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Tikhonova, Polina, Iulia Pavlova, Ekaterina Isaakova, Vladimir Tsvetkov, Alexandra Bogomazova, Tatjana Vedekhina, Artem V. Luzhin, et al. "DNA G-Quadruplexes Contribute to CTCF Recruitment." International Journal of Molecular Sciences 22, no. 13 (June 30, 2021): 7090. http://dx.doi.org/10.3390/ijms22137090.
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G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment.
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MacIsaac, Kenzie D., and Ernest Fraenkel. "Practical Strategies for Discovering Regulatory DNA Sequence Motifs." PLoS Computational Biology 2, no. 4 (April 28, 2006): e36. http://dx.doi.org/10.1371/journal.pcbi.0020036.
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Eden, Eran, Doron Lipson, Sivan Yogev, and Zohar Yakhini. "Discovering Motifs in Ranked Lists of DNA Sequences." PLoS Computational Biology 3, no. 3 (March 23, 2007): e39. http://dx.doi.org/10.1371/journal.pcbi.0030039.
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Pasau, Guntur, and Adey Tanauma. "PEMODELAN SUMBER GEMPA DI WILAYAH SULAWESI UTARA SEBAGAI UPAYA MITIGASI BENCANA GEMPA BUMI." JURNAL ILMIAH SAINS 15, no. 1 (October 31, 2011): 202. http://dx.doi.org/10.35799/jis.11.2.2011.208.
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PEMODELAN SUMBER GEMPA DI WILAYAH SULAWESI UTARA SEBAGAI UPAYA MITIGASI BENCANA GEMPA BUMI 1) Guntur Pasau2) dan Adey Tanauma2); e-mail: pasaujunior@gmail.com1)Penelitian IPTEK dan Seni dengan Biaya DIPA Unsrat Tahun 2011 2)Progran Studi Fisika FMIPA Universitas San Ratulangi Manado, 95115 ABSTRAK Pemodelan sumber gempa di wilayah Sulawesi Utara telah dilakukan. Pemodelan sumber gempa menggunakan teori probabilitas total merupakan salah satu upaya mitigasi dalam mengetahui besarnya percepatan suatu gerakan tanah yang diakibatkan oleh suatu gempa bumi. Analisis perhitungan percepatan tanah maksimum di batuan dasar meliputi probabilitas terlampaui 10% dalam 50 tahun. Hasil analisis pemodelan sumber gempa yang telah dilakukan didapatkan bahwa nilai percepatan tanah pada beberapa kota besar di Sulawesi Utara cukup tinggi. Nilai percepatan tanah maksimum yang tertinggi adalah Kota Gorontalo dengan nilai percepatan sekitar 0,5g kemudian disusul oleh Kota Bitung sebesar 0,4g, dan Kota Manado sebesar 0,25g. Kata Kunci: pemodelan, sumber gempa, probabilitas, percepatan, batuan dasar. EARTHQUAKE SOURCE MODELING OF NORTH SULAWESI REGION AS AN EFFORT OF EARTHQUAKE DISASTER MITIGATION ABSTRACT Earthquake source modeling of North Sulawesi region was carried out. The earthquake source modeling using the theory of total probability is one of the mitigation efforts in knowing the magnitude of the acceleration of the ground motion caused by an earthquake. Analysis of the calculation of the maximum ground acceleration at bedrock includes the probability of exceedance 10% in 50 years. The results of the earthquake source modeling analysis has been done found that the ground acceleration values in some major cities in North Sulawesi is quite high. The maximum ground acceleration value of the highest is the of Gorontalo City with a value of about 0.5 g acceleration was followed by the Bitung City of 0.4 g, and the Manado City of 0.25 g. Keywords: modeling, earthquake source, probability, accelearation, bedrock
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SIPES, TAMARA B., and SUSAN M. FREIER. "PREDICTION OF ANTISENSE OLIGONUCLEOTIDE EFFICACY USING AGGREGATE MOTIFS." Journal of Bioinformatics and Computational Biology 06, no. 05 (October 2008): 919–32. http://dx.doi.org/10.1142/s0219720008003795.
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Antisense oligonucleotide technology allows the targeted reduction of mRNA expression through the in vitro application of short (~20 nt) DNA molecules. Oligonucleotides are valuable both in the study of gene regulation and for having potential therapeutic effects. In theory, a base sequence complementary to a region of the transcript would hybridize to its mRNA target. Nevertheless, in practice some complementary antisense oligonucleotides are more active and more potent than others in suppressing specific gene expression. We present a novel computational approach to modeling oligonucleotide efficacy that uses aggregate motifs, which are flexible tetramotifs that expand the predictive ability of the data descriptors and the attribute space. We also demonstrate our findings on the largest dataset yet reported in the literature. It was shown that the prediction accuracy was significantly enhanced, offering more than eightfold improvement compared to the traditional methods.
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Asrizal, Asrizal, Yohandri Yohandri, and Zulhendri Kamus. "Studi Hasil Pelatihan Analisis Video dan Tool Pemodelan Tracker pada Guru MGMP Fisika Kabupaten Agam." JURNAL EKSAKTA PENDIDIKAN (JEP) 2, no. 1 (May 24, 2018): 41. http://dx.doi.org/10.24036/jep/vol2-iss1/84.
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Experiment is important in physics to explain and describe a physical phenomenon and its characteristics. For this reason physics teachers should conduct the physics experiment activities to motivate students in learning and to improve scientific process skills, scientific attitudes, and student understanding in physics learning. However, in the experiment activities of physics were found many problems such as experiment equipment was insufficient, there is no equipment, equipment can�t operated well, and so on. An alternative solution to solve this problem was to do the video analysis and modeling tool tracker on physics teacher. The purpose of this research was to investigate the effects of the implementation the tracker video analysis and modeling tool on physics teachers. The research design was pretest and postest for one group sample. The sample of research was 26 physics teachers of Physics MGMP teacher in Agam district of West Sumatera. Instruments to collect the data consist of pretest and postest sheet, performance assessment sheet of video analysis product and questionnaires sheet of physics teachers. Data analysis techniques include descriptive statistical analysis, normality test, homogeneity test and paired comparison test for one group sample. From the data analysis, it can be stated that: 1). the average value of video analysis products from physics teachers is 85.10 and this value can be classified into very good category, 2). the average value of responses of physics teachers on training implementation of video analysis and tool modeling is 73.81 and this average value can be grouped into good category, and 3). the implementation of video analysis training of object motion video by using tracker software is effective to improve the understanding the physics MGMP teachers in Agam district on learning material of tracker video analysis and modeling tool, but the average value of understanding still in the low category.
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Guturu, Harendra, Andrew C. Doxey, Aaron M. Wenger, and Gill Bejerano. "Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1632 (December 19, 2013): 20130029. http://dx.doi.org/10.1098/rstb.2013.0029.
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Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis -regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF–TF–DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein–protein interactions, potentially indirect interactions and ‘through-DNA’ interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex .
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Osmer, Patrick S., Gatikrushna Singh, and Kathleen Boris-Lawrie. "A New Approach to 3D Modeling of Inhomogeneous Populations of Viral Regulatory RNA." Viruses 12, no. 10 (September 29, 2020): 1108. http://dx.doi.org/10.3390/v12101108.
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Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.
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Cahyono, Mohammad Ardi, and Rahmat Suwandi. "PEMODELAN MATEMATIK SISTEM HIDROLIK PADA MAIN LANDING GEAR EXTENSION DAN RETRACTION PESAWAT BOEING 737-900ER DENGAN PROGRAM MATLAB-SIMULINK." Angkasa: Jurnal Ilmiah Bidang Teknologi 9, no. 1 (August 22, 2017): 43. http://dx.doi.org/10.28989/angkasa.v9i1.110.
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The problem that often arises in the hydraulic system when the main landing gear is done extension and retraction is the control o f the hydraulic motion and the fluid motion is very big influence on the hydraulic work process where the fluid flow must be ensured or arranged in such a way as to work properly. To overcome this problem, a mathematical modeling system is used to create a representation or an imitation o f the actual system, which links the output o f the system with its input in a mathematical relationship and its parameter values. The research was conducted by observation method and literature study to obtain the data and its calculation. The results o f this study obtained a description o f the response and dynamic characteristics o f the PID controller in the transfer function o f the hydraulic system when the main landing gear extension and retraction o f the nearest Boeing 737-900ER aircraft is the 5th time experiment by inputting PID controller value P = 13 I = 4 D = 3 with an error value o f 0.01887 and an overshoot o f1,0002. With a small error value or a 2% value limit and the response picture is not experiencing a large overshoot, then the picture o f the response in accordance with the expected in the 5th experiment where the error value o f 0.01887 and overshoot o f 1,0002. With an overview o f the response with this small overshoot then the accuracy o f the system will stop at the point corresponding to the actual system. By using this modeling, the response o f the main landing gear extension and retraction movements can be well studied thus providing a good understanding o f the performance of the hydraulic system.
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Bredesen, Bjørn André, and Marc Rehmsmeier. "DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements." Nucleic Acids Research 47, no. 15 (July 24, 2019): 7781–97. http://dx.doi.org/10.1093/nar/gkz617.
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Abstract Polycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the seven motifs previously used, PREs are enriched in the GTGT motif, recently associated with the sequence-specific DNA binding protein Combgap. We investigated whether models trained on genome-wide Polycomb sites generalize to independent PREs when trained with control sequences generated by naive PRE models and including the GTGT motif. We also developed a new PRE predictor: SVM-MOCCA. Training PRE predictors with genome-wide experimental data improves generalization to independent data, and SVM-MOCCA predicts the majority of PREs in three independent experimental sets. We present 2908 candidate PREs enriched in sequence and chromatin signatures. 2412 of these are also enriched in H3K4me1, a mark of Trithorax activated chromatin, suggesting that PREs/TREs have a common sequence code.
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Qi, Yaping, John William Warmenhoven, Nicholas Thomas Henthorn, Samuel Peter Ingram, Xie George Xu, Karen Joy Kirkby, and Michael John Merchant. "Mechanistic Modelling of Slow and Fast NHEJ DNA Repair Pathways Following Radiation for G0/G1 Normal Tissue Cells." Cancers 13, no. 9 (May 3, 2021): 2202. http://dx.doi.org/10.3390/cancers13092202.
Full textAbstract:
Mechanistic in silico models can provide insight into biological mechanisms and highlight uncertainties for experimental investigation. Radiation-induced double-strand breaks (DSBs) are known to be toxic lesions if not repaired correctly. Non-homologous end joining (NHEJ) is the major DSB-repair pathway available throughout the cell cycle and, recently, has been hypothesised to consist of a fast and slow component in G0/G1. The slow component has been shown to be resection-dependent, requiring the nuclease Artemis to function. However, the pathway is not yet fully understood. This study compares two hypothesised models, simulating the action of individual repair proteins on DSB ends in a step-by-step manner, enabling the modelling of both wild-type and protein-deficient cell systems. Performance is benchmarked against experimental data from 21 cell lines and 18 radiation qualities. A model where resection-dependent and independent pathways are entirely separated can only reproduce experimental repair kinetics with additional restraints on end motion and protein recruitment. However, a model where the pathways are entwined was found to effectively fit without needing additional mechanisms. It has been shown that DaMaRiS is a useful tool when analysing the connections between resection-dependent and independent NHEJ repair pathways and robustly matches with experimental results from several sources.