Huang Jianjun

Bio: Huang Jianjun is an academic researcher from Hohai University. The author has contributed to research in topics: Solar energy & Pile. The author has an hindex of 5, co-authored 16 publications receiving 59 citations. Previous affiliations of Huang Jianjun include Worcester Polytechnic Institute.

Quantitative Biology: Theory, Computational Methods, and Models

Abstract: An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michal Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-Pars, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienaltowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr ulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber

Interaction of toroidal swimmers in Stokes flow.

Abstract: A doughnut-shaped object supporting surface rotations was a hypothetical construct proposed by both Taylor and Purcell as a swimmer that would be able to propel itself in a Stokesian fluid because of the irreversibility of its stroke. Here we numerically examine the hydrodynamic interaction of pairs and trios of these free toroidal swimmers. First, we study the axisymmetric case of two toroidal swimmers placed in tandem, and show that a single torus of a corotating pair is more efficient than when it swims alone, but less efficient when paired with a counterrotating partner. Using a regularized Stokeslet framework, we study the nonaxisymmetric case of toroidal swimmers whose axes are initially parallel, but not collinear. These perturbed in tandem swimmers can exhibit qualitatively different trajectories that may, for instance, repel the swimmers or have them settle into a periodic state. We also illustrate interesting dynamics that occur for different initial configurations of three tori.

Experimental Study on Influence of Pile Wall on Flow Field Around Pile-Supported Wharf

Abstract: Tidal flow has a significant influence on the mooring safety of vessels in deep-sea ports. In order to ensure the mooring safety of vessels, improving the structure form of the wharf can d...

Meshfree and efficient modeling of swimming cells

Abstract: We develop a tool for simulating three-dimensional locomotion in Stokes flow with highly resolved flow and swimming trajectories for multiple swimmers in the presence of surfaces. Key features include modularity, scalability, ease of implementation, and no need for mesh generation.

Efficient implementation of elastohydrodynamics via integral operators

Abstract: Many systems in physics and life sciences are characterised by microscopic flexible fibers interacting through viscous flow. We describe an efficient modeling framework taking into account nonlocal interactions, applied to sedimenting and shear flows with multiple fibers, and flagellar propulsion.

Sperm Motility: Models for Dynamic Behavior in Complex Environments

Abstract: Sperm–often considered the most diverse cell type known–present unique challenges for modeling frameworks. Responsible for fertilizing the egg, sperm are not only necessary for sexual reproduction, but also increasingly important to study given rising rates of infertility. In this review, we summarize aspects of sperm motility and interactions, which make it unique in comparison to other cells. The journey of a sperm involves swimming in different fluid environments, where emergent trajectories and waveforms are coupled to the fluid properties such as viscosity, the mechanics of the flagellum, as well as the relevant biochemistry. We emphasize that there is a range of modeling frameworks, each of which can bring an understanding to fundamental aspects of sperm motility, such as how a particular fluid or interaction with another swimmer can alter swimming speeds and trajectories. In order to study the emergent flagellar waveforms of sperm and compare to experiments, it is important to have accurate models of the relevant surfaces and interactions to capture the correct and relevant hydrodynamics. We discuss current challenges and describe aspects of sperm motility that models can elucidate in the future, ultimately to help solve the puzzle of how the sperm is able to reach and fertilize the egg.