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    Metode Komputasi - Simulasi Biomaterial

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    Rizky Wahyu Febriyanto
    Computational modeling and simulation allow scientists to investigate physical phenomena beyond the limits of manageable mathematics and feasible experiments. There are several approaches ranging from atomistic to continuum methods. Atomistic methods use empirical or ab initio force fields to determine properties of systems containing thousands to millions of atoms. Mesoscale methods introduce simplifications to study larger, more complex systems up to billions of atoms. Continuum methods treat matter as continuous fields to model macroscopic systems of any size. Each method has tradeoffs between system size, timescales possible to study, and ability to physically interpret results. Multi-scale modeling combines approaches to bridge across scales.

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    Metode Komputasi - Simulasi Biomaterial

    Uploaded by

    Rizky Wahyu Febriyanto
    31 views61 pages
    Computational modeling and simulation allow scientists to investigate physical phenomena beyond the limits of manageable mathematics and feasible experiments. There are several approaches ranging from atomistic to continuum methods. Atomistic methods use empirical or ab initio force fields to determine properties of systems containing thousands to millions of atoms. Mesoscale methods introduce simplifications to study larger, more complex systems up to billions of atoms. Continuum methods treat matter as continuous fields to model macroscopic systems of any size. Each method has tradeoffs between system size, timescales possible to study, and ability to physically interpret results. Multi-scale modeling combines approaches to bridge across scales.

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    DESAIN BIOMAT

    Original Title

    KULIAH-DESAIN-BIMATERIAL

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    Computational modeling and simulation allow scientists to investigate physical phenomena beyond the limits of manageable mathematics and feasible experiments. There are several approaches ranging from atomistic to continuum methods. Atomistic methods use empirical or ab initio force fields to determine properties of systems containing thousands to millions of atoms. Mesoscale methods introduce simplifications to study larger, more complex systems up to billions of atoms. Continuum methods treat matter as continuous fields to model macroscopic systems of any size. Each method has tradeoffs between system size, timescales possible to study, and ability to physically interpret results. Multi-scale modeling combines approaches to bridge across scales.

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    © All Rights Reserved
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    Download as ppt, pdf, or txt
    31 views61 pages

    Metode Komputasi - Simulasi Biomaterial

    Uploaded by

    Rizky Wahyu Febriyanto
    Computational modeling and simulation allow scientists to investigate physical phenomena beyond the limits of manageable mathematics and feasible experiments. There are several approaches ranging from atomistic to continuum methods. Atomistic methods use empirical or ab initio force fields to determine properties of systems containing thousands to millions of atoms. Mesoscale methods introduce simplifications to study larger, more complex systems up to billions of atoms. Continuum methods treat matter as continuous fields to model macroscopic systems of any size. Each method has tradeoffs between system size, timescales possible to study, and ability to physically interpret results. Multi-scale modeling combines approaches to bridge across scales.

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    Metode Komputasi – Simulasi

    Biomaterial
    Modeling and scientific computing
    • Continuous advances in computer technology make possible the simulation
    approach to scientific investigation as a third stream together with pure theory
    and pure experiment
    • Experiment: primary concerned with the accumulation of factual information
    • Theory: mainly directed towards the interpretation and ordering of the
    information in coherent patters to provide with predictive laws for the behavior of
    matter through mathematical formulations
    • Computation: push theories and experiments beyond the limits of manageable
    mathematics and feasible experiments
    – Properties of materials under extreme conditions (temperature, pressure,
    etc.)
    – Study of properties of complex systems - a solid crystal is already an
    unmanageable system for a microscopic mathematical model!
    – Testing of theories vs. experimental observation
    – Suggestion of experiments for validation of the theory
    • Steps to set up a meaningful computational model:
    – Individuate the physical phenomenon to study
    – Develop a theory and a mathematical model to describe the phenomenon
    – Cast the mathematical model in a discrete form, suitable for computer
    programming
    – Develop and/or apply suitable numerical algorithms
    – Write the simulation program
    – Perform the computer experiment
    • A good computational scientist has to be a little bit of:
    – A theorist, to to develop new approaches to solve new problems
    – An applied mathematician, to be able to translate the theory in a
    mathematical form suitable for computation
    – A computer scientist/programmer, to write new scientific codes or modify
    existing ones to fit the needs and deal with the always changing world of
    advanced and high-performance computing
    – An experimentalist, to be able to define a meaningful path of computer
    experiments that should lead to the description of the physical phenomenon
    Multi-scale modeling
    • Challenge: modeling a physical phenomenon from a broad range of
    perspectives, from the atomistic to the macroscopic end

    Continuum
    TIME (s) Based on SDSC Blue Horizon (SP3) Methods
    512-1024 processors
    1.728 Tflops peak performance
    CPU time = 1 week / processor
    100

    Atomistic Mesoscale methods


    (ms) 10-3 Simulation
    Finite elements
    Methods methods

    (s) 10-6

    Semi-empirical
    (ns) 10-9 methods
    Monte Carlo
    Molecular dynamics
    (ps) 10-12 Ab initio
    methods
    tight-binding
    (fs) 10-15

    10-10 10-9 10-8 10-7 10-6 10-5 10-4


    (nm) (m)
    LENGTH (m)
    Multi-scale modeling
    • Ab initio methods: calculate materials properties from first principles, solving the
    quantum-mechanical Schrödinger (or Dirac) equation numerically
    • Pros:
    – Give information on both the electronic and structural/mechanical behavior
    – Can handle processes that involve bond breaking/formation, or electronic
    rearrangement (e.g. chemical reactions).
    • Methods offer ways to systematically improve on the results, making it easy
    to assess their quality.
    • Can (in principle) obtain essentially exact properties without any input but the
    atoms conforming the system.
    • Cons:
    • Can handle only relatively small systems, about O(102) atoms.
    • Can only study fast processes, usually O(10) ps.
    • Numerically expensive!
    • Semi-empirical methods: use simplified versions of equations from ab initio
    methods, e.g. only treat valence electrons explicitly; include parameters fitted to
    experimental data.
    • Pros:
    • Can also handle processes that involve bond breaking/formation, or
    electronic rearrangement.
    • Can handle larger and more complex systems than ab initio methods, often
    of O(103) atoms.
    • Can be used to study processes on longer timescales than can be studied
    with ab initio methods, of about O(10) ns.
    • Cons:
    • Difficult to assess the quality of the results.
    • Need input from experiments or ab initio calculations and large parameter
    sets.
    • Atomistic methods: use empirical or ab initio derived force fields, together with
    semi-classical statistical mechanics (SM), to determine thermodynamic (MC,
    MD) and transport (MD) properties of systems. SM solved ‘exactly’.
    • Pros:
    • Can be used to determine the microscopic structure of more complex
    systems, O(104-6) atoms.
    • Can study dynamical processes on longer timescales, up to O(1) s
    • Cons:
    • Results depend on the quality of the force field used to represent the
    system.
    • Many physical processes happen on length- and time-scales inaccessible
    by these methods, e.g. diffusion in solids, many chemical reactions, protein
    folding, micellization.
    • Mesoscale methods: introduce simplifications to atomistic methods to remove
    the faster degrees of freedom, and/or treat groups of atoms (‘blobs of matter’)
    as individual entities interacting through effective potentials.
    • Pros:
    • Can be used to study structural features of complex systems with O(108-9)
    atoms.
    • Can study dynamical processes on timescales inaccessible to classical
    methods, even up to O(1) s.
    • Cons:
    • Can often describe only qualitative tendencies, the quality of quantitative
    results may be difficult to ascertain.
    • In many cases, the approximations introduced limit the ability to physically
    interpret the results.
    • Continuum methods: Assume that matter is continuous and treat the
    properties of the system as field quantities. Numerically solve balance
    equations coupled with phenomenological equations to predict the
    properties of the systems.
    • Pros:
    – Can in principle handle systems of any (macroscopic) size and dynamic
    processes on longer timescales.
    • Cons:
    – Require input (elastic tensors, diffusion coefficients, equations of state,
    etc.) from experiment or from a lower-scale methods that can be difficult
    to obtain.
    – Cannot explain results that depend on the electronic or molecular level
    of detail.
    Pemodelan dan Simulasi
    Biomaterial/ Material Implan,

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