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,