Multiscale And Multiphysics Computational Frameworks For Nano And Bio Systems

This volume develops multiscale and multiphysics simulation methods to understand nano- and bio-systems by overcoming the limitations of time- and length-scales. Here the key issue is to extend current computational simulation methods to be useful for providing microscopic understanding of complex experimental systems. This thesis discusses the multiscale simulation approaches in nanoscale metal-insulator-metal junction, molecular memory, ionic transport in zeolite systems, dynamics of biomolecules such as lipids, and model lung system. Based on the cases discussed here, the author suggests various systematic strategies to overcome the limitations in time- and length-scales of the traditional monoscale approaches.

This book examines the latest research results from combined multi-component and multi-scale explorations. It provides theory, considers underlying numerical methods and presents brilliant computational experimentation. Engineering computations featured in this monograph further offer particular interest to many researchers, engineers and computational scientists working in frontier modeling and applications of multicomponent and multiscale problems. Professor Geiser gives specific attention to the aspects of decomposing and splitting delicate structures and controlling decomposition and the rationale behind many important applications of multi-component and multi-scale analysis. Multicomponent and Multiscale Systems: Theory, Methods and Applications in Engineering also considers the question of why iterative methods can be powerful and more appropriate for well-balanced multiscale and multicomponent coupled nonlinear problems. The book is ideal for engineers and scientists working in theoretical and applied areas.

Theory, Models, and Applications in Engineering explains how to solve complicated coupled models in engineering using analytical and numerical methods. It presents splitting multiscale methods to solve multiscale and multi-physics problems and describes analytical and numerical methods in time and space for evolution equations arising in engineering problems. The book discusses the effectiveness, simplicity, stability, and consistency of the methods in solving problems that occur in real-life engineering tasks. It shows how MATLAB (R) and Simulink (R) are used to implement the methods. The author also covers the coupling of separate, multiple, and logical scales in applications, including microscale, macroscale, multiscale, and multi-physics problems. Covering mathematical, algorithmic, and practical aspects, this book brings together innovative ideas in coupled systems and extends standard engineering tools to coupled models in materials and flow problems with respect to their scale dependencies and their influence on each time and spatial scale

The three-volume set LNCS 3514-3516 constitutes the refereed proceedings of the 5th International Conference on Computational Science, ICCS 2005, held in Atlanta, GA, USA in May 2005.The 464 papers presented were carefully reviewed and selected from a total of 834 submissions for the main conference and its 21 topical workshops. The papers span the whole range of computational science, ranging from numerical methods, algorithms, and computational kernels to programming environments, grids, networking, and tools. These fundamental contributions dealing with computer science methodologies and techniques are complemented by papers discussing computational applications and needs in virtually all scientific disciplines applying advanced computational methods and tools to achieve new discoveries with greater accuracy and speed.

Nanorobots represent a nanoscale device where proteins such as DNA, carbon nanotubes could act as motors, mechanical joints, transmission elements, or sensors. When these different components were assembled together they can form nanorobots with multi-degree-of-freedom, able to apply forces and manipulate objects in the nanoscale world. Design, Modeling and Characterization of Bio-Nanorobotic Systems investigates the design, assembly, simulation, and prototyping of biological and artificial molecular structures with the goal of implementing their internal nanoscale movements within nanorobotic systems in an optimized manner.

Computational Multiscale Modeling of Multiphase Nanosystems: Theory and Applications presents a systematic description of the theory of multiscale modeling of nanotechnology applications in various fields of science and technology. The problems of computing nanoscale systems at different structural scales are defined, and algorithms are given for their numerical solutions by the quantum/continuum mechanics, molecular dynamics, and mesodynamics methods. Emphasis is given to the processes of the formation, movement, and interaction of nanoparticles; the formation of nanocomposites; and the processes accompanying the application of nanocomposites. The book concentrates on different types of nanosystems: solid, liquid, gaseous, and multi-phase, consisting of various elements interacting with each other, and with other elements of the nanosystem and with the environment. The book includes a large number of examples of numerical modeling of nanosystems. The valuable information presented here will be useful to engineers, researchers, and postgraduate students engaged in the design and research in the field of nanotechnology.

Part of a four-volume set, this book constitutes the refereed proceedings of the 7th International Conference on Computational Science, ICCS 2007, held in Beijing, China in May 2007. The papers cover a large volume of topics in computational science and related areas, from multiscale physics to wireless networks, and from graph theory to tools for program development.

In this white paper, a road map is presented to establish a multiphysics simulation capability for the design and optimization of sensor systems that incorporate nanomaterials and technologies. The Engineering Directorate's solid/fluid mechanics and electromagnetic computer codes will play an important role in both multiscale modeling and integration of required physics issues to achieve a baseline simulation capability. Molecular dynamic simulations performed primarily in the BBRP, CMS and PAT directorates, will provide information for the construction of multiscale models. All of the theoretical developments will require closely coupled experimental work to develop material models and validate simulations. The plan is synergistic and complimentary with the Laboratory's emerging core competency of multiscale modeling. The first application of the multiphysics computer code is the simulation of a ''simple'' biological system (protein recognition utilizing synthesized ligands) that has a broad range of applications including detection of biological threats, presymptomatic detection of illnesses, and drug therapy. While the overall goal is to establish a simulation capability, the near-term work is mainly focused on (1) multiscale modeling, i.e., the development of ''continuum'' representations of nanostructures based on information from molecular dynamics simulations and (2) experiments for model development and validation. A list of LDRDER proposals and ongoing projects that could be coordinated to achieve these near-term objectives and demonstrate the feasibility and utility of a multiphysics simulation capability is given.

This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the mesoscale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer’s usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com).

In this Special Issue, one review paper highlights the necessity of multiscale CFD, coupling micro- and macro-scales, for exchanging information at the interface of the two scales. Four research papers investigate the hydrodynamics, heat transfer, and chemical reactions of various processes using Eulerian CFD modeling. CFD models are attractive for industrial applications. However, substantial efforts in physical modeling and numerical implementation are still required before their widespread implementation.