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invited

VIEWS: 7 PAGES: 20

									                                                                                    Invited Contributions


I01 - Computational design of nanostructures            Lett. 89, 196803, (2002). [2] J-Y. Raty, G.
and nanostructured materials                            Galli, A.Van Buuren and L. J. Terminello, Phys.
Galli G. 1                                              Rev. Lett.90, 037401 ( 2003); J-Y Raty and
1 Lawrence Livermore National Laboratory,               G.Galli, Nature Materials 2, 792 (2003). [3] A.
Livermore USA                                           Puzder, A. J. Williamson, J. C. Grossman and G.
                                                        Galli, J. Chem. Phys. 117, 6721 (2002); Phys.
Computational tools are playing an increasingly         Rev. Lett. 88, 097401 (2002) and JACS 125,
important role in understanding and control-            2786 (2003). [4] E. Draeger, J. Grossman, A.
ling matter at the microscopic scale, by pre-           Williamson and G. Galli Phys. Rev. Lett. 90,
dicting with quantitative, thermodynamic accu-          167402 (2003). [5] F.Reboredo, E.Schwegler
racy the property of materials based on their           and G.Galli, JACS 125, 15243 (2003).
atomic and molecular constituents. In the next          I02 - Self-standing and metal-supported
decade, we expect the coming of age of first             molecular nanostructures
principles theories of matter and related com-          Di Felice R. 1
putational techniques –as well as the growth of         1 INFM-S3 Modena, Italy
computer power– to allow for simulations of a
wide variety of alternative materials with de-          The drive towards novel electronic devices at
sired properties, and thus for the engineering of       the nanoscale has attracted the interests of re-
optimized materials from first principles.               searchers worldwide to study molecules and
   In this talk, computer simulations using First       molecular materials. A huge investigation ef-
Principles Molecular Dynamics (FPMD) and                fort is currently devoted to understanding the
Quantum Monte Carlo (QMC) techniques are                structural and electronic properties of several
employed to solve specific nanoscience prob-             candidates for technological exploitation in me-
lems, in particular to investigate the physical         chanical and electrical devices. The application
properties of group IV semiconductor nanos-             of first-principle DFT calculations to complex
tructures and their possible use as chemical and        molecules and molecular overlayers is playing
biological labels.                                      an ever growing prominent role in unraveling
   While robust experimental results have been          the intimate features of the charge carriers in
established for II-VI nanocrystals in the last          free molecules and at their interface with inor-
decade, group IV elemental nanostructures are           ganic substrates.
much less well characterized. The interplay be-            In this presentation I will give a brief
tween quantum confinement effects and surface            overview about the simulation of selected
properties has not been fully understood, and the       biomolecular nanowires [A. Calzolari, R. Di Fe-
effects of preparation conditions on the physi-         lice, E. Molinari, A. Garbesi, Electron chan-
cal properties of Group IV nanoparticles remain         nels in biomolecular nanowires, J. Phys. Chem.
an open issue. Our simulations are aimed at             B 108, 2509 (2004); R. Di Felice, H. Zhang,
understanding the physical and chemical prop-           A. Calzolari, Ferromagnetic alignment of metal
erties of C, Si, SiC and Ge nanoparticles with          ions in a DNA-mimic double helix, preprint
diameters up to 2-3 nm. In particular, we will          (2004)] and nanoglobules [S. Corni, F. De
present investigations of optical gaps [1,2] and        Rienzo, R. Di Felice, E. Molinari, Redox ac-
surface properties[2,3], and simulations of the         tivity at the Azurin active site by means of ab-
effect of different preparation conditions [4] on       initio electronic structure calculations, preprint
the structure of Si nanoparticles. Recent simu-         (2004)], to illustrate the kind of information that
lation results on the early stages of quantum dot       can be extracted about their potential electrical
functionalization will also be discussed [5].           behavior. Then I will focus on the interface
   [1] A. J. Williamson, J.C. Grossman, R.Q.            between thiols (cysteine and methanethiol) and
Hood, A. Puzder and G. Galli, Phys. Rev.                the gold (111) surface. The ammino acid cys-

                                                    9
Invited Contributions


teine is used both to make self-assembled or-        at least at moderate temperatures. The “icy” gi-
ganic monolayers, and to link complex macro-         ants Uranus and Neptune are instead thought to
molecules (DNA, proteins, etc.) to the inor-         be mostly composed of the so-called planetary
ganic world. I will discuss the structure and        “ices”: water, ammonia, and methane. High-
the enegetics of partial cysteine monolayers [R.     pressure and high-temperature simulations in-
Di Felice and A. Selloni, Adsorption Modes           dicate however that these molecules do not
of Cysteine on Au(111): Thiolate, Amino-             sustain extreme conditions, and become fully
Thiolate, Disulfide, J. Chem. Phys. 120, 4906         ionised (water and ammonia) or disproportion-
(2004); R. Di Felice, A. Selloni, E. Molinari, A     ate (methane), with important implications for
DFT study of cysteine adsorption on Au(111),         planetary models. Terrestrial planets are finally
J. Phys. Chem B 107, 1151 (2003)], showing           composed of an iron core surrounded by a man-
the relative role of different functional groups     tle of silicates and oxides. Simulations of iron
(SH, NH2, SS) in metal-molecule bonding. I           can provide constraints on the temperature at
will then present a thorough analysis of the         the Earth’s center and explain why seismic shear
electronic structure, that allows one to identify    waves are anomalously slow in the solid core.
the metal-molecule hybridization, the degree of      Unfortunately, a number of crucial high-P high-
chemisorption versus physisorption, the modifi-       T properties of mantle minerals such as viscos-
cation of the molecular orbitals upon deposition     ity, thermal conductivity, thermoelasticity, and
onto the inorganic support, and the HOMO-EF          rheology, are presently very difficult to address
alignment that determines the injection barriers     with ab-initio methods, due to their intrinsi-
at electrodes. I will finally show an application     cally large time and size scales. The problem is
of DFT simulations to compute the energy bar-        presently coped with by constructing effective
rier for methanethiol pulling from a Au surface      classical potential tailored to the ab-initio dy-
[A. Calzolari and R. Di Felice, unpublished],        namics. Very encouraging results obtained for
which is relevant for the mechanical properties      liquid silica and magnesium oxide will be pre-
and in AFM measurements.                             sented.
I03 - Exploring planetary interiors with ab-         I04 - Ab-initio simulation of NMR and EPR
initio molecular dynamics                            spectra in solids
Scandolo S. 1                                        Mauri F. 1 Pickard C. 2 Yates J. 3
1 The Abdus Salam International Cen-                 1 Laboratoire de Minralogie-Cristallographie de
tre for Theoretical Physics (ICTP) and               Paris, France , 2 Cavendish Laboratory, Cam-
INFM/Democritos National Simulation Center,          bridge, Uk , 3 Cavendish Laboratory, Cam-
Trieste, Italy                                       bridge, Uk

Because the conditions of pressure and tempera-      The orbital magnetic response is at the origin of
ture of relevance for planetary interiors, includ-   important physical properties that are exploited
ing the Earth, extend beyond those currently         to determine the microscopic structure of ma-
achievable in laboratory experiments, ab-initio      terials using the electron paramagnetic reso-
atomistic simulations are instrumental to pre-       nance (EPR) or the nuclear magnetic resonance
dict how planetary matter behaves at extreme         (NMR). Indeed, the knowledge of the orbital
conditions. The giant planets Jupiter and Sat-       currents linearly-induced by a uniform external
urn, for example, are mostly composed of hy-         magnetic field, allows us to compute two impor-
drogen, which is known to loose its molecu-          tant quantities measured in magnetic resonance
lar character and become metallic at sufficiently     spectroscopies: the EPR g-tensor of defects in
high pressures. Ab-initio simulations indicate       solids and the NMR chemical shifts.
that the transition of fluid hydrogen from molec-        I will present a formalism for the ab initio
ular to non-molecular is likely to be first-order,    calculation of NMR chemical shits, and elec-

                                                 10
                                                                                 Invited Contributions


tric field gradients, and of the EPR g-tensor,         by molecular evolution, define the pathways of
in molecules and solids based on density func-        folding and ensure the avoidance of misfolded
tional theory.                                        conformations. In another application, results
   The reconstruction of the all-electron prop-       from protein engineering experiments are used
erties with the Projector-Augmented-Waves             to determine the transition state for folding for
(PAW) and the Gauge-Including-PAW (GIPAW)             several proteins. An analysis of the resulting
approaches, the use of the scalar-relativistic cor-   structures suggests that, in the nucleation con-
rections and of ultra-soft pseudopotentials allow     densation mechanism for folding, the transition
us to describe most of the atoms of the periodic      state is reached when the native-like interac-
table, and to deal with systems containing hun-       tions of few key residues are formed. Taken to-
dreds of atoms in the unit cell.                      gether, these results illustrate how a combina-
   The accuracy of the predicted NMR and EPR          tion of computational and experimental data al-
spectra establishes our method as an useful tool      lows the investigation of the general principles
to interpret and analyze the NMR and EPR spec-        of macromolecular self-organization.
tra of real materials.                              I06 - Models of Solvation for Complex So-
   I will illustrate our approach with applications lutes
to bio-molecular and inorganic systems.             Marchi M. 1 Borgis D. 2
                                                                      ´
I05 - Determination of partially folded states 1 Commissariat a l’Energie Atomique, DSV-
of proteins at atomic resolution                    DBJC-SBFM, Centre d’Etudes de Saclay, F-
Vendruscolo M 1                                                                 e
                                                    91191 Gif sur Yvette C´ dex, FRANCE ,
1 Department of Chemistry, University of Cam-           e                                  e
                                                    2 D´ partement de Physique et Mod´ lisation,
bridge, UK                                                                 e
                                                    Laboratoire de Mod´ lisation des Syst` mes e
                                                        e                                 e
                                                    Mol´ culaires Complexes, Universit´ d’Evry,
A combination of computational and experi- 91025 Evry C´ dex, FRANCE
                                                                   e
mental methods is making it possible to describe
protein folding pathways at atomic resolution. We have introduced novel methods to describe
Much of the recent progress has been driven by the solvation of complex solutes in computer
advances in experimental techniques that pro- simulation. Two classes of techniques have been
vide residue-specific information about the suc- developed which represent the solvent either
cessive intermediate states that are populated with a dielectric continuum approach or with
during the folding process. Detailed molecular a particle–based model. Both methods enforce
dynamics simulations have been used to com- the requirement that they yield either an exact or
plement the experimental results and to suggest approximate representation of the macroscopic
new measurements. In an alternative approach laws of electrostatics.
that I present here, experimental data are used       In a first approach1 , the solvent is described
directly to build an artificial energy function that by dielectric continuum and the interaction be-
guides computer simulations to sample the re- tween the solvent and the molecular degrees of
gions of the conformational space of a protein freedom is described by means of a polariza-
most compatible with the experimental results. tion density free energy functional which is min-
In one recent application, NMR data obtained imum at electrostatic equilibrium. After a pseu-
at increasing concentrations of denaturant were dospectral expansion of the polarization and a
used for the determination of the free energy discretization of the functional, we construct the
landscape of the molten globule state at pH 2 equations of motion for the system based on a
of alpha-lactalbumin. The resulting landscape Car–Parrinello technique. In the limit of the adi-
is characterized by deep valleys that are ro- abatic evolution of the polarization field vari-
bust against changes in the external conditions. ables, our method provides the solution of the
These deep valleys in the landscape, created dielectric continuum problem “on the fly”, while

                                                  11
Invited Contributions


the molecular coordinates are propagated.           water phase. We compute the effect of the chain
   In the particle–based method2 , electrostatics   length of the alcohol on the phase behaviour of
of continuous media is formulated in terms of       the membrane. At low concentrations of alco-
a polarization density free energy functional,      hol the membrane has domains of the interdigi-
which is projected on randomly distributed dis-     tated phase that are in coexistence with the nor-
crete Lennard-Jones pseudoparticles. The re-        mal membrane phase. We use our model to clar-
sulting model is that of a polarizable fluid, in     ify some of the experimental questions related to
which the induced dipoles describe both orien-      the structure of the interdigitated phase and put
tational and electronic polarization. This model    forward a simple model that explains the alco-
has been implemented in molecular dynamics          hol chain length dependence of the stability of
simulations and its solvation properties have       this interdigitated phase.
been compared to continuous electrostatics for
                                                    I08 - Phase transitions, micellization and
simple solutes such as spherical ions or ion
                                                    shear alignment in polymer and surfactant
pairs.
                                                    systems
   The computational efficiency of both meth-
ods have also been tested against more com-         Panagiotopoulos A. 1
plex solutes such as proteins. We have shown        1 Princeton University
how our implicit solvent molecular dynamics
methods can be successfully applied to hydrated     This presentation summarizes recent work in the
biomolecules, with low cost compared to free        author’s group on modeling phase transitions in
energy simulations with explicit solvent.           model polymer and surfactant systems. A key
                                                    characteristic of these fluids is the close inter-
  1 M. Marchi, D. Borgis, N. Levy, and P. Bal-      play between microstructure and macroscopic
    lone, J. Chem. Phys. 114, 4377 (2001).          properties and the existence of interactions on
                                                    multiple length and time scales. Two com-
  2 T. HaDuong, S. Phan, M. Marchi, and D.          plementary approaches are used to render the
    Borgis, J. Chem. Phys. 117, 541 (2002).         computational problem tractable, namely dras-
                                                    tic simplification of the model studied to retain
I07 - Mesoscopic simulations of phase transi-       only essential physical characteristics and de-
tions in biological membranes                       velopment of appropriate sampling methodolo-
Smit B. 1                                           gies to avoid getting trapped in local free en-
1 University of Amsterdam, The Netherlands          ergy minima. We have developed a methodol-
                                                    ogy based on grand canonical Monte Carlo com-
Various factors can induce phase transitions        bined with histogram reweighting to distinguish
in biological membranes. To understand the          between phase separation on one hand and mi-
molecular mechanisms underlying these transi-       cellization to finite-size aggregates on the other.
tions, we have developed a mesoscopic mem-          The effects of chain flexibility on polymer and
brane model. Molecular simulations on this          surfactant phase and aggregation behavior have
model nicely reproduce the experimental phase       been examined in detail. Ongoing investiga-
diagrams. A particular example the will be          tions of surfactant systems under shear will also
discussed is the effect of alcohol molecules or     be described, in connection to the development
other small amphiphilic molecules. In the cell      of long-range order observed experimentally in
membrane these molecules can induce signifi-         PS-PEP thin films.
cant changes in the structure of the membrane.
We find that alcohol can induce an interdigitated    I09 - Fluid and kinetic simulations of inertial
structure in which the normal bilayer structure     confinement fusion plasmas
changes into monolayer in which the alcohol         Atzeni S. 1 Schiavi A. 2 Temporal M. 3 Cali-
molecules screen the hydrophobic tails from the     fano F. 4 Cattani F. 5 Cornolti F. 6 Lisseikina

                                                12
                                                                                Invited Contributions


T. 7 Macchi A. 8 Pegoraro F. 9                       matter interaction, plasma and radiation trans-
1 Dipartimento di Energetica, Universit` di   a      port processes, realistic materials equation-of-
Roma “La Sapienza” and INFM, Italy , 2 Dipar-        state, fusion reactions and transport of fusion
timento di Energetica, Universit` di Roma “La
                                    a                products. As sample applications we show sim-
Sapienza” and INFM, Italy , 3 ETSII, Universi-       ulations of the complete evolution of a laser-
dad de Castilla-La-Mancha, Ciudad Real, Spain        driven target, and of the linear and nonlinear
, 4 Dipartimento di Fisica, Universit` di Pisa and
                                       a             evolution of multi-mode RTI during the forma-
INFM, Italy , 5 Dipartimento di Fisica, Univer-      tion of the central hot spot. We also present sim-
sit` di Pisa and INFM, Italy , 6 Dipartimento
   a                                                 ulations of beam-induced ignition of precom-
di Fisica, Universit` di Pisa and INFM, Italy
                     a                               pressed fuels, which have helped to determine
, 7 Dipartimento di Fisica, Universit` di Pisa
                                         a           the beam requirements for ignition of both DT
and INFM, Italy , 8 INFM and Dipartimento di         and T-lean fuels.
Fisica, Universit` di Pisa, Italy , 9 Dipartimento
                 a                                      We have studied key aspects of the fast ignitor
di Fisica, Universit` di Pisa and INFM, Italy
                    a                                scheme using relativistic electromagnetic codes.
                                                     Particle-in-Cell simulations show that the inter-
We outline the main features of codes we devel-      action of an ultraintense laser beam with a solid
oped to study inertial confinement fusion (ICF)       surface stimulates surface instabilities and re-
physics problems, and present recent results on      sults in the formation of fast electron jets with
selected key issues.                                 characteristic energy and angular distributions.
   Essential ingredients of ICF are compression      Relativistic 3D collisionless fluid simulations
of the deuterium-tritium (DT) fuel to at least one   have been used to study electron beam prop-
thousand times solid density and heating of a hot    agation in the dense plasma. The simulations
spot which triggers a fusion burn wave. Com-         provide valuable results concerning the devel-
pression is obtained by laser- or beam-driven        opment of the Weibel instability caused by the
implosion of a spherical hollow shell, contain-      interaction of the beam current with the neutral-
ing a frozen DT layer. The hot spot can either       izing return current provided by the cold plasma.
be produced at the center of the imploded shell
by hydrodynamic cumulation (central hot spot         I10 - Simulating the Ether: Local algorithms
ignition) or generated in the compressed fuel by     for Coulombs Law
an ultraintense laser or particle beam (fast igni-   Maggs A.C. 1
tor scheme).                                         1 ESPCI, Paris, France.
   Key issues for ICF are limitation of plasma
instabilities (hindering coupling of the laser       We have introduced a local algorithm for the
energy to the plasma) and hydrodynamic               Monte-Carlo simulation of charged systems in-
Rayleigh-Taylor instabilities, RTI (hindering        teracting via the long ranged Coulomb potential.
shell acceleration and compression, and, in cen-     This local algorithm is very efficient (with O(N)
tral ignition, hot spot formation). Fast ignition    scaling) when compared with traditional meth-
relaxes hydro-stability requirements, but relies     ods based on Ewald summation. It Is based on
on not fully understood relativistic laser plasma    the constrained dynamics of an auxiliary vector
processes.                                           field coupled to the physical charge density.
   ICF target physics involves multiple time-           In this talk we will discuss recent progress
and space-scales, and requires the use of both ki-   in applying cluster methods to further improve
netic and fluid models. We study full target per-     the efficiency of the updates. We demonstrate
formance and sensitivity to hydrodynamic in-         a considerable improvement in the efficiency of
stabilities using the 2D hydro-radiative-nuclear     the algorithm compared with our original local
DUED code. It employs a multi-temperature,           Metropolis formulation, especially when work-
single-fluid model, including collisional laser-      ing with low densities of charged particles.

                                                 13
Invited Contributions


   Generalizations to molecular dynamics are framework has also a solid microscopic founda-
also possible.                                     tion that has allowed us, in particular, to derive
                                                   from microscopic principles the hydrodynamic
I11 - Routes to gel formation
                                                   equations of a fluid mixture that can phase sepa-
Sciortino F. 1
                                                   rate. The essential assumption is that of van der
1 Dipartimento di Fisica, Universita’ La Waals (separation of the molecular potential in
Sapienza Roma Italy                                a repulsive and attractive parts, the latter being
                                                   treated in mean field). The continuum equations
I will discuss some recent numerical studies
                                                   have surface tension terms in a form common to
of colloidal models which undergo dinamical
                                                   other diffuse interface models. Yet, some ambi-
structural arrest. Both glass and gel states will
                                                   guities concerning the definition of internal en-
be discussed. In particular I will focus on mod-
                                                   ergy are clarified in the derivation.
els where the gel line can be approached from
                                                      The continuum equations are the basis for a
the equilibrium liquid side. Finally I will dis-
                                                   construction, again within the GENERIC frame-
cuss the possibility that gel formation can be in-
                                                   work, of a discrete model of fluid particles.
terpreted in the same theoretical frameworks de-
                                                   Smoothed particle hydrodynamics, which is a
veloped for glass formation.
                                                   Lagrangian discretization of the Navier-Stokes
   References:
                                                   equation and other continuum equations, is used
   Saika-Voivod, E. Zaccarelli, F. Sciortino, S.V.
                                                   in order to express the different terms of the
Buldyrev, P. Tartaglia Effect of bond lifetime
                                                   discrete equations not specified by GENERIC
on the dynamics of a short-range attractive col-
                                                   in a way that ensures that the discrete model
loidal system cond-mat/0403320
                                                   is a faithful representation of the continuum
   Francesco Sciortino,         Stefano Mossa, equations. We present numerical simulations in
Emanuela Zaccarelli, Piero Tartaglia A simple cases (binary mixtures without viscous
new route to the formation of colloidal gels: processes) to show the potential of the model.
Short range attraction and long range repulsion Non-equilibrium non-isothermal phase separat-
cond-mat/0312161                                   ing processes can be studied with full inclusion
I12     -    Thermodynamically         consistent of cross effects of the Soret type.
Smoothed Particle Hydrodynamic model
for phase separating fluids                         I13 - Adaptive sampling techniques to deter-
      ˜
Espanol P. 1 Thieulot C.A.P. 2                     mine transition pathways, free energy, and
1 U.N.E.D Madrid (Spain) , 2 Dept. of Chemi- rates in complex systems
cal Engineering, Groningen (The Netherlands) Vanden-Eijnden E. 1
                                                   1 Courant Insitute, USA
Phase separating fluids are challenging due to
the delicate interplay between the complex equi- Various techniques have been developed to sam-
librium thermodynamic behavior and the hy- ple efficiently the free energy associated with
drodynamic behavior of the fluid. In order to some reaction coordinates. Most of these ap-
approach the construction of models for these proaches presuppose that the reaction coordi-
systems, we have found that the recently intro- nate appropriate to the description of some rare
duced framework known as GENERIC (Gen- transition event is known beforehand. This as-
eral Equation for Non-Equilibrium Reversible- sumption, however, may lead to a free energy
Irreversible Coupling) offers an invaluable tool. landscape that has no dynamical significance in
This framework captures in an elegant and eco- the sense that it cannot be used to determine
nomic way the contents of the First and Sec- the transition region for the rare event, nor its
ond Laws and has great potential for the gen- rate. In this talk, I will present a new tech-
eration of new models for complex fluids. The nique, termed the string method, which allows

                                                 14
                                                                              Invited Contributions




Figure 1: [I12] Four needles at undercritical temperature are introduced in a supercritical mixture.
The mixture starts phase separating as a consequence.

to search adaptively for the right reaction co-    Nose’-Hoover chain, isokinetic scheme allows
ordinate associated with some rare event, and      molecular dynamics time steps on the order of
thereby determine the correct free energy for the  100 femtoseconds to be employed without loss
event and the associated transition rate.          of accuracy, thus, ameliorating, considerably,
                                                   the multiple time scale problem. Applications
I14 - New methods for sampling rough energy
                                                   of both methods to model and realistic problems
landscapes
                                                   are presented.
Martyna G.J. 1
1 IBM Research, Division of Physical Sciences, I15 - Computing the mechanism, reaction co-
Yorktown Heights, USA                              ordinate, transition states and rate constants
                                                   of complex processes with path sampling.
Atomistic computer simulation studies of com- Bolhuis P.G. 1
plex phenomena allow new insights to be ob- 1 University of Amsterdam, The Netherlands
tained that would be difficult to achieve via ex-
perimental studies or analytical theory. Indeed, In this presentation I will give a brief overview
simulations which give access to the positions of the transition path sampling (TPS) method.
and velocities of atoms at all times during im- Designed for studying activated processes in
portant events can be used to probe structure, complex environment, the TPS technique har-
reactivity and mechanism at an extraordinary vests a collection of transition paths that connect
level of detail. However, many processes are the reactant with the product states. This en-
impeded by high barriers which are difficult to semble of true dynamical paths allows detailed
cross except at very long times inhibiting simu- understanding of the kinetics and mechanism
lation from impacting many classes of problems of the reaction. In addition, rate constants can
from protein folding to the formation of com- be computed. The main advantage is that the
plex interfaces in semiconductor manufacture. method does in principle not need prior knowl-
Similarly, significant separations in time scales edge of the reaction coordinate. Processes as
make designing new methods difficult. For in- diverse as cluster isomerization, auto dissocia-
stance, in protein folding, large scale structural tion of water, ion pair dissociation, the folding
rearrangements take place on the time scale of of a polypeptide and reactions in aqueous solu-
microseconds while carbon-carbon bond vibra- tion have been studied with TPS (see Ref.[1] for
tions occur on the femtosecond scale. In this an overview).
talk, two new approaches will be described.           The rate constant calculation is rather time
The first, the reference system potential warping consuming and improvements in efficiency were
scheme permits barriers to be overcome with- achieved by the introduction of the Transition
out changing the equilibrium distribution speed- Interface Sampling approach. This approach is
ing configurational sampling by many orders of based on the sampling of paths that cross hy-
magnitude. The second, the multiple time step, persurfaces in phase spaces defined by an or-

                                                15
Invited Contributions


der parameter that does not have to be equal to       chanical Properties of Nanostructures
the reaction coordinate. TIS allows for a vari-       Louie S.G. 1
able path length, thus greatly enhancing effi-         1 Department of Physics, University of Califor-
ciency. Recently, we improved the efficiency           nia at Berkeley, and Materials Sciences Divi-
even more for the calculation of rate constants       sion, Lawrence Berkeley National Laboratory,
for the case diffusive processes by sampling          Berkeley, CA 94720 USA
only partial paths. Having introduced the meth-
ods I will show their applicability by giving a       Calculation of the various properties of materi-
few examples.                                         als often requires very different theoretical and
   There are also disadvantages to TPS, TIS and       computational approaches because of the com-
related techniques. For instance, qualitatively       plex interactions and diverse behaviors in con-
different reactive pathways are hard to sample.       densed matter. In particular, the restricted ge-
Another problem is the existence of unknown           ometry and symmetry of nanostructures often
local traps (metastable states) in trajectory space   give rise to interesting quantum confinement,
which can hamper the sampling. I will discuss         enhanced many-electron interaction, and other
the problems occurring in the sampling of paths       effects related to reduced dimensionality. These
and their possible solutions.                         effects can lead to novel physical properties and
   [1] P.G. Bolhuis, D. Chandler, C.Dellago, and      phenomena, which also are potentially useful in
P.Geissler, Annu. Rev. Phys. Chem., 53, 291           applications. In this talk, I will discuss some
(2002).                                               of our recent studies on the electron transport,
I16 - Time correlation functions for mixed            optical, and mechanical properties of nanotubes
quantum classical dynamics                            and molecular junctions. For examples, molec-
Coker DF 1 Bonella S 2 Causo S 3 Ciccotti G           ular electronic devices, i.e., electrical transport
4                                                     through a single molecule can produce highly
                                                      nonlinear I-V characteristics. The optical spec-
1 Boston University, U.S.A , 2 Boston Univer-
                                                      tra of small diameter carbon nanotubes exhibit
sity, U.S.A , 3 University of Rome, La Sapienza,
                                                      dramatic excitonic effects. Also friction on the
Italy , 4 University of Rome, La Sapienza, Italy
                                                      nanoscale may be very different from that on
A new method is developed for computing ther-         the human scale. The talk will be on the the-
mal equilibrium time correlation functions of         ory and computation of these phenomena. We
quantum subsystem operators. The trajectory           will present results on the nonlinear transport
based approach is obtained from a rigorous sta-       behavior of molecular junctions calculated us-
tionary phase approximation to the full path in-      ing a newly developed ab initio scattering-state
tegral expression for the correlation function.       method, the optical response of nanotubes em-
The method is implemented using adiabatic ap-         ploying a first-principles many-particle Greens
proximations to the thermal and temporal propa-       function approach, and the behaviors of me-
gators and we explore how nonadiabatic dynam-         chanical energy dissipation in double-walled
ical effects can be incorporated. The approach is     carbon nanotube oscillators from molecular dy-
tested on a suite of model problems where exact       namics simulations. The physical origin of the
results can be obtained and, as a proof of princi-    calculated behaviors will be examined.
ple check, is employed to test the Green-KuboI18 - Combining ab-initio and classical ap-
relation for excess electron transport in metal
                                             proaches for the simulation of complex ma-
molten salt solutions. The method will also be
                                             terials: the case of semiconductor-dielectric
employed to study vibrational relaxation in con-
                                             interfaces.
densed phase systems.                        Curioni A. 1
I17 - Optical, Electrical Transport, and Me- 1 IBM Research Zurich Research Laboratory

                                                  16
                                                                              Invited Contributions


Understanding the properties of semiconductor-      scription of complex phenomena of the type de-
dielectric interfaces is of paramount importance    scribed above. The methodologies are based on
in the search for an alternative to silicon diox-   density functional theory approaches at the mi-
ide as a gate dielectric in CMOS devices. Mod-      croscopic scale, on molecular dynamics simu-
elling such interfaces is complex and extremely     lations at the mesoscopic scale and on contin-
challenging, as demonstrated by the unsatisfac-     uum (computational or phenomenological) ap-
tory comparison of theory and experiments so        proaches at the macroscopic scale. We describe
far obtained. For this reason we developed a        the key ideas behind the links across the scales
novel approach that combines the accuracy of        and how these are implemented in specific ex-
quantum calculations with the speed and flex-        amples.
ibility of classical molecular dynamics. The
physical properties of these interfaces could be       Acknowledgement: This work was per-
thus obtained in an unbiased way and compared       formed in collaboration with Paul Maragakis,
satisfactorily with a number of different experi-   Nick Choly, Gang Lu, Greg Smith, Umesh
ments.                                              Waghmare and Ellad Tadmor, and supported by
                                                    the Materials Research Science and Engineer-
I19 - Multiscale simulations of mechanical
                                                    ing Center and the Nanoscale Science and En-
and electrical behavior
                                                    gineering Center of Harvard University, which
Kaxiras E. 1
                                                    are funded by NSF, and by a MURI grant from
1 Department of Physics and Division of Engi-
                                                    AFOSR through Brown University.
neering and Applied Sciences, Harvard Univer-
sity, Cambridge MA 02138, U.S.A.                    I20 - Deformation of glasses: Bulk rheology
                                                    and the molecular origins of friction
A variety of physical phenomena involve multi- Robbins M.O. 1 Rottler J. 2 Muser M.H. 3 He
ple length and time scales in their manifestation. G. 4
Some interesting examples of practical impor- 1 Johns Hopkins Univ., USA , 2 Princeton Univ.,
tance are: (a) the mechanical behavior of crys- USA , 3 Univ. Western Ontario, Canada , 4
tals and in particular the interplay of chemistry Univ. Pittsburgh, USA
and mechanical stress in determining the macro-
scopic brittle or ductile response of solids; (b) Simulations have been used to study deforma-
the response of piezoelectic crystals to compet- tion of amorphous glasses as a function of stress
ing external electric and stress fields; (c) the al- state, temperature, confinement, and deforma-
teration of the structure and electronic proper- tion rate and amplitude. The initial yield be-
ties of macromolecular systems due to external havior in models of amorphous metals and poly-
forces, as in stretched DNA nanowires or carbon mers is quite similar. The octahedral stress σy
nanotubes.                                          at which shear occurs can be described by the
   In these complex physical systems, the pressure-modified von Mises (PMVM) criterion
changes in bonding and atomic configurations at σy = τ0 + αp, where p is the pressure. By vary-
the microscopic level have profound effects on ing the potential, we show that the value of τ0
the macroscopic properties, be they of mechan- is determined by adhesive interactions between
ical or electrical nature. Linking the processes molecules while α is determined by geometry.
at the two extremes of the length scale spectrum The yield stress drops linearly with temperature,
is the only means of achieving a deeper under- but the shear rate dependence is surprisingly in-
standing of these phenomena and of ultimately sensitive to temperature. At sufficiently nega-
being able to control them. In this presenta- tive pressures, the mode of failure changes from
tion we will discuss the development of method- shear to cavitation. Chain connectivity leads
ologies for simulations across disparate length to shear hardening at large strains in entangled
scales with the aim of obtaining a detailed de- polymer glasses. We show that thin contaminant

                                                17
Invited Contributions


films between bulk solids are also trapped in        on a dual scale simulation scheme are presented
glassy states. The yield behavior of these films     as well, covering coarse grained and atomisti-
also follows the PMVM criterion and can nat-        cally resolved motion for times up to the total re-
urally explain the familiar macroscopic laws of     laxation time of chains of up to 10 entanglement
friction. In particular, we find that the friction   lengths. The work presented is done in collabo-
force increases linearly with load, and that the    ration with R. Everaers and C. Svaneborg (both
slope is nearly independent of parameters that      now at MPI for Physics of Complex Systems,
are not controlled in macroscopic experiments.      Dresden, Germany), G. S. Grest (Sandia Nat.
                                                    Lab., USA), S. Sukumaran, A. Sivasubramanian
                                                    and S. Leon.
I21 - Hydrophobic attraction between
protein-like solutes in water                       I23 - Hierarchical Modelling of Amorphous
 Dzubiella J. 1 Hansen J.P. 2                       Polymers
1 University of Cambridge, UK , 2 University of     Theodorou D.N. 1
Cambridge, UK                                       1 National Technical University of Athens,
                                                    Greece
The effective, solvent-induced forces between
nanometer scale solutes in water are determined
by constant pressure MD simulations. Macro-  Predicting the physical properties of amorphous
                                             polymers from their chemical structure consti-
scopic considerations predict a strong reduction
of the hydrophobic attraction between solutestutes a serious challenge, because of the very
when the latter are uniformly charged. This  broad spectra of length and time scales that
is confirmed by the simulations of oppositely govern these properties. We will discuss some
                                             recent hierarchical simulation work aimed at
charged solutes, while like-charged solutes lead
                                             meeting this challenge by (a) invoking coarse-
to significantly different behaviour between pos-
                                             graining strategies to reduce the number of de-
itively and negatively charged pairs. The lat-
ter exhibit the phenomenon of like-charge at-grees of freedom in the description of macro-
traction, previously observed in some charge-molecules; (b) utilizing powerful connectivity-
                                             altering Monte Carlo algorithms to achieve
stabilized colloidal dispersions. The hydropho-
                                             equilibration of long-chain polymer melt mod-
bic interaction turns out to be very sensitive to
                                             els at all length scales; (c) mapping long dy-
details of the charge pattern on the solute sur-
face.                                        namical trajectories onto mesoscopic theoreti-
                                             cal models, such as the Rouse and reptation
I22 - Entangled Polymer Systems              model, in order to estimate rheological proper-
Kremer K. 1                                  ties. Measures of computational efficiency will
1 Max Planck Institute for Polymer Research, be discussed, and comparisons against experi-
Ackermannweg 10, 55128 Mainz, Germany        ment will be presented.
                                                    I24 - Local Dynamics in Polymer Melts :
Extensive computer simulations are used to
                                                    From Individual Jumps to Diffusive Coarse-
study the dynamics and rheology of entangled
                                                    Grained Dynamics.
polymeric systems ranging from semidilute so-
lutions of flexible polymers to melts of rather      Ryckaert J.P. 1 Arialdi G. 2 Karatasos K. 3
stiff chains. A topological analysis is used        1 Polymer Physics, CP223, Universite Libre
to predict the entanglement molecular weight        de Bruxelles, Brussels, Belgium , 2 Polymer
without any adjustable parameter from confor-       Physics, CP223, Universite Libre de Bruxelles,
mations only and shown to yield quantitatively      Brussels, Belgium. , 3 Polymer Physics, CP223,
correct results for the plateau modulus. Simula-    Universite Libre de Bruxelles, Brussels, Bel-
tions of the dynamics of specific polymers based     gium.

                                                18
                                                                                   Invited Contributions


Local dynamics relaxation functions in polymer          observed phenomena is discussed.
melts which are probed by NMR and neutron                  1) M. W. Deem and H. Y. Lee, “Sequence
scattering experiments can be obtained from             Space Localization in the Immune System Re-
molecular dynamics simulations. The molecu-             sponse to Vaccination and Disease,” Phys. Rev.
lar processes which are responsible for the var-        Lett. 91 (2003) 068101.
ious relaxations can be analyzed more directly             2) J.-M. Park and M. W. Deem, “Correlations
from the simulations. Our data on polyethylene          in the T Cell Response to Altered Peptide Lig-
(PE) indicate how coarse-graining the analysis          ands,” Physica A, to appear.
of local motion, a diffusive behaviour emerges
at low diffusion vectors. This diffusive process        I26 - Analysis of DNA-chip and Antigen-chip
separates from more localized motions which             data: applications to studies of cancer, stem
could be at the origin of the relaxation processes      cells and autoimmune diseases.
detected in the amorphous domains of semi-              Domany E. 1
cristalline PE and more generally may reflect            1 Weizmann Institute of Science, Israel
the so called alpha-beta splitting in amorphous
polymers.                                               DNA chips are novel experimental tools that
I25 - Random Energy Model of the Immune                 have revolutionized research in molecular biol-
Response to Viruses, Vaccines, and Cancer               ogy and generated considerable excitement. A
Deem M.W. 1                                             single chip allows simultaneous measurement of
1 Physics and Astronomy, Rice University, 6100          the level at which thousands of genes are ex-
Main Street - MS 61, Houston, TX USA                    pressed. A typical experiment uses a few tens of
                                                        such chips, each devoted to one sample - such as
Adaptive vertebrate immune system is a won-             material extracted from a tumor. Hence the re-
der of modern evolution. Under most circum-             sults of such an experiment consist of a table, of
stances, the dynamics of the immune system              several thousand rows (one for each gene) and
is well-matched to the dynamics of pathogen             50 - 100 columns (one for each sample). Ex-
growth during a typical infection.             Some     tracting relevant information from such a large,
pathogens, however, have evolved escape mech-           complex and noisy data set requires develop-
anisms that interact in subtle ways with the            ment of novel methods of analysis.
immune system dynamics. In addition, nega-                 In this talk I will briefly explain how gene
tive interactions the immune system, which has          expression is measured by DNA chips, and
evolved over 400 000 000 years, and vacci-              demonstrate how we combine standard statis-
nation,which has been practiced for only 200            tical analysis with novel unsupervised methods
years, are possible. For example,vaccination            to mine expression data obtained from various
against the flu can actually increase susceptibil-       types of cancer. I will show that studies of gene
ity to the flu in the next year. As another exam-        expression in human stem cells led to the dis-
ple, vaccination against one of the four strains        covery of a new design principle used by stem
of dengue fever typically increases susceptibil-        cells.
ity against the other three strains. Immunodom-            If time permits, I will describe a novel exper-
inance also arises in the immune system con-            imental tool - antigen chips - and the manner
trol of nascent tumors–the immune system rec-           it can be used to predict whether an individual
ognizes only a small subset of the tumor specific        (mouse) will or will not become diabetic.
antigens, and the rest are free to grow and cause
tumor growth.                                           I27 - Driven elastic manifolds in random me-
   In this talk, I present a physical theory of orig-   dia: Exact algorithms, new insights
inal antigenic sin and immunodominance. How             Krauth W. 1
localization in the immune system leads to the          1 Ecole Normale Superieure, Paris, France

                                                    19
Invited Contributions


                                                     f


                                i




                                     hi              h’
                                                      i

     Figure 1: [I27] Schematic view of continuous-time algorithm (come to talk for details!).

I present the algorithmic ideas which allow          for the use of environmentally-aware self en-
to compute the ultimate pinned d-dimensional         ergies in soft matter simulation.
manifold in a finite d+1-dimensional sample,          Warren P. 1
both on a discrete lattice, and in the continuum.    1 Unilever R&D Port Sunlight
I report on calculations of the roughness ex-
ponents at depinning for short-range and long-       Dissipative particle dynamics (DPD) can be ex-
range elasticity, and of several experimentally      tended so that a one-component fluid of soft
relevant fluctuation properties.                      spheres exhibits vapour-liquid coexistence, with
                                                     a sharp vapour-liquid interface, and a vapour
I28 - Mesoscopic models for complex fluids:           phase of vanishingly small density [1]. This is
from non-ideal to charged mixtures                   done by allowing the pairwise soft repulsions to
Pagonabarraga I. 1                                   become dependent on a local density [1–3]. The
1 Universitat de Barcelona, Departament de           application to capillary problems is illustrated
Fisica Fonamental, Carrer Marti i Franques 1,        by simulations of a pendant drop (see Figure)
08028 Barcelona, Spain                               [1], and of novel coarsening kinetics in vapour-
                                                     liquid phase separation [4]. The model is an
In this talk I will describe different strategies    example of a soft-sphere liquid with a poten-
to model the dynamics of complex fluids in            tial energy built out of local-density-dependent
the presence of general geometries, paying par-      one-particle self-energies. More generally, I
ticular attention tot he difficulties that arise in   argue that the use of ‘environmentally-aware’
charged fluids. I will concentrate then in how        many-body self-energies is simpler than the use
to couple such models to analyze the dynamics        of many-body pair potentials, and offers the
of colloidal suspensions, and I will assess the      promise to open up new directions for simula-
models’ capabilities by analyzing some particu-      tion of soft condensed matter.
lar examples.                                           [1] P. B. Warren, Phys. Rev. E 68, 066702
I29 - Vapor-liquid coexistence in many-body          (2003).
dissipative particle dynamics—a manifesto               [2] I. Pagonabarraga and D. Frenkel, J. Chem.

                                                 20
                                                                                  Invited Contributions


Phys. 115, 5015 (2001).                               I32 - Adaptive Kinetic Monte Carlo Method
  [3] S. Y. Trofimov et al, J. Chem. Phys. 117,        for Long Time Scale Simulations
9383 (2002).                                          Jonsson H 1 Henkleman G 2 Uberuaga B.P. 3
  [4] P. B. Warren, Phys. Rev. Lett. 87, 225702       1 Univ. of Iceland, Reykjavik, Iceland , 2 Univ.
(2001).                                               of Texas, Austin TX, USA , 3 Los Alamos Labs,
                                                      New Mexico, USA
I30 - The Adaptive Integration Method
Swendsen R.H. 1                                       Diffusion and chemical reactions in and on the
1 Carnegie Mellon University, USA                     surface of solids typically involve a climb over
                                                      an energy barrier. A typical ’fast’ event on
This lecture will present an adaptive Monte           laboratory time-scale may have an energy bar-
Carlo approach to the calculation of generalized      rier of 0.5 eV and occur thousands of times
free energies as a function of some parameter         per second. In a direct classical dynamics sim-
of interest. The Adaptive Integration Method          ulation such an event is, however, impossibly
(AIM), which was recently developed in collab-        slow even when simple interaction potentials
oration with Marc Fasnacht and John M. Rosen-         are used, requiring thousands of CPU-years be-
berg, uses a biasing potential based on the aver-     cause of the small time step required to faith-
age derivative of the Hamiltonian with respect to     fully represent atomic vibrations. A different
the parameter of interest to calculate the free en-   approach is needed for long time scale simu-
ergy and accelerate the simulation. The method        lations. We present an extension of the kinetic
is particularly effective in dealing with high free   Monte Carlo (kMC) algorithm - Adaptive KMC
energy barriers. AIM is simple and capable of         - where the mechanism and rate of transitions
high accuracy. It also allows a substantial im-       are found within harmonic transition state the-
provement in resolution over the more common          ory [1]. A search method based on finding just
histogram methods. Comparison calculations            the lowest frequency normal mode [2] is used
show that the convergence for AIM is compa-           to search for saddle points on the potential en-
rable to or better than the well-known Wang-          ergy rim surrounding the basin corresponding
Landau method for the models tested.                  to a given state of the system. In this way, the
                                                      need for a predefined event table and lattice ap-
I31 - Computing time scales by milestoning
                                                      proximation typically employed in KMC simu-
 Faradjian T. 1 Elber R 2
                                                      lations is eliminated. Application of this algo-
1 Cornell University, USA , 2 Cornell Univer-
                                                      rithm to the dissociation of boron clusters in sil-
sity, USA
                                                      icon will be presented [3]. There, atomic forces
                                                      obtained by density functional theory are used
An algorithm is presented to compute time
                                                      directly. Another application is multiple time
scales of complex processes following pre-
                                                      scale simulations of the growth of metal surfaces
determined milestones along a reaction coordi-
                                                      using an empirical EAM potential. A screen
nate. A non-Markovian hopping mechanism is
                                                      saver has been developed and used to distribute
assumed and constructed from underlying mi-
                                                      the computations on over a hundred PCs (see
croscopic dynamics. General analytical analy-
                                                      http://eon.chem.washington.edu).
sis, a pedagogical example, and numerical so-
lutions of the non-Markovian model are pre-              [1] G. Henkelman and H. Jonsson, J. Chem.
sented. No assumption is made in the theoretical      Phys., 115, 9657 (2001). [2] G. Henkelman and
derivation on the type of microscopic dynamics        H. Jonsson, J. Chem. Phys., 111, 7010 (1999).
along the reaction coordinate. However, the de-       [3] Blas Uberuaga et al., Physica Status Solidi
tailed calculations are for Brownian dynamics         B, 233, No. 1 (2002)
in which the velocities are uncorrelated in time I33 - Two dimensional model colloids: phase
(but spatial memory remains).                    transitions, effects of external potentials and

                                                  21
Invited Contributions




                  Figure 1: [I29] Many-body DPD simulation of a pendant drop.

quantum effects                                       ion similar to charge stabilised colloids which
 Binder K. 1 Lohrer M. 2 Nielaba P. 3 Sengupta        are known to undergo an initial freezing, fol-
S. 4 Strepp W. 5                                      lowed by a re- melting transition as the ampli-
1 Physics Department, University of Mainz,            tude of the imposed, modulating field produced
55099 Mainz, Germany , 2 Physics Department,          by crossed laser beams is steadily increased.
University of Konstanz, 78457 Konstanz, Ger-          Detailed analysis of the simulation data shows
many , 3 Physics Department, University of            several features consistent with a recent disloca-
Konstanz, 78457 Konstanz, Germany , 4 S.N.            tion unbinding theory of laser induced melting.
Bose National Centre for Basic Sciences, Block        The differences and similarities of systems with
JD, Sector III, Salt Lake, Calcutta 700098, India     soft potentials (DLVO, 1/r12 , 1/r6 ) and the rela-
, 5 Physics Department, University of Konstanz,       tion to experimental data is analysed. Besides
78457 Konstanz, Germany                               these classical studies we discuss the validity of
                                                      our results on atomic length scales.
The nature of the melting transition for a system        The modifications of the phase diagram for
of hard disks with translational degrees of free-     quantum hard disks with finite particle masses,
dom in two spatial dimensions has been anal-          obtained by path integral Monte Carlo simula-
ysed by a combination of computer simulation          tions indicate a new quantum melting scenario,
methods and a novel finite size scaling tech-          absent in the classical case.
nique. The behaviour of the system is consistent      I34 - Simulating Vapor-Liquid Equilibria
with the predictions of the KTHNY theory.             from First Principles
   Hard and soft disks in external periodic (light-    McGrath M.J. 1 Siepmann J.I. 2 Kuo I.F.W. 3
) fields show rich phase diagrams including            Mundy C.J. 4
freezing and melting transitions when the den-        1 University of Minnesota , 2 University of Min-
sity of the system is varied. Monte Carlo simu-       nesota , 3 Lawrence Livermore National Labo-
lations for detailed finite size scaling analyses of   ratory , 4 Lawrence Livermore National Labo-
various thermodynamic quantities like the order       ratory
parameter, its cumulants etc., have been used
in order to map the phase diagram of the sys-         Efficient Monte Carlo algorithms are combined
tem for various values of the density and the         with the Quickstep energy routines of CP2K
amplitude of the external potential. For hard         to develop a program that allows for Monte
disks we find clear indication of a reentrant liq-     Carlo simulations in the canonical, isobaric-
uid phase over a significant region of the pa-         isothermal, and Gibbs ensembles using a first-
rameter space. The simulations therefore show         principles description of the physical system.
that the system of hard disks behaves in a fash-      Configurational-bias Monte Carlo techniques

                                                  22
                                                                                Invited Contributions


and pre-biasing using an inexpensive approx-         culated Hugoniot, including phase boundaries
imate potential are employed to increase the         and transformation kinetics, particularly in com-
sampling efficiency and to reduce the frequency       bination with recent developments in ultrafast
of expensive ab initio energy evaluations. The       X-ray diffraction measurements of shocked, ori-
new Monte Carlo program has been validated by        ented single crystals. Reactive potentials such as
extensive comparison with molecular dynamics         ReaxFF and AIREBO for organic systems offer
simulations using CPMD and CP2K. Results for         insight into the initial energy redistribution and
the vapor-liquid coexistence curve of water us-      chemical reaction events in the detonation of
ing the BLYP functional will be presented.           RDX, TATB, and other energetic single crystals.
                                                     Using selected examples from various groups, I
I35 - Large-scale (106 to 1010 -atom) classi-        will try to convey the state-of-the-art in molecu-
cal molecular dynamics studies of shock com-         lar dynamics shock wave studies, including both
pression and fluid instabilities                      the limitations and the (largely untapped) poten-
                                                     tial such studies have in contributing to model-
Germann T.C. 1 Holian B.L. 2 Kadau K. 3
                                                     ing meso-scale behavior. I will also describe re-
Lomdahl P.S. 4 Ravelo R. 5
                                                     cent simulations of the Rayleigh-Taylor fluid in-
1 Los Alamos National Laboratory (USA) ,
                                                     stability in 2 and 3 dimensions, developing from
2 Los Alamos National Laboratory (USA) , 3
                                                     an intially perfect interface between a heavy
Los Alamos National Laboratory (USA) , 4 Los
                                                     fluid on top and a light fluid on bottom, with
Alamos National Laboratory (USA) , 5 Univer-
                                                     only thermal fluctuations seeding the eventual
sity of Texas - El Paso (USA)
                                                     turbulent mixing.
Classical non-equilibrium molecular dynamics         I36 - Statistical mechanics of proteins: per-
simulations have been increasingly used with         spective from analytical theory, evolutionary
great success over the past several years to study   analysis and simulations
complex dynamic processes in both solids and         Shaknovich E. 1
fluids. Several independent factors have con-         1 Chemistry and Chemical Biology, Harvard
tributed to this growing field. The development       University, 12 Oxford, Cambridge, MA 02138
of efficient parallel algorithms and the availabil-
ity of inexpensive PC-based clusters have en-        We will disscuss recent developments in protein
abled routine large-scale simulations with 106       theory that allow a unified statistical-mechanical
to 1010 atoms, to study the shock compression        view of protein folding and evolution. Specif-
of solids on sub-micron length scales and sub-       ically we will present a mean-field picture of
nanosecond time scales. Simplified model po-          protein evolution that, along with Monte-Carlo
tentials, such as the Lennard-Jones pair poten-      design in sequence space allows to rational-
tial for close-packed solids and reactive empiri-    ize most of the conservatism patterns in pro-
cal bond-order (REBO) potentials for energetic       tein families and folds. Further, we will present
materials, have been used to explore generic         novel Monte-Carlo simulations of protein fold-
shock processes, including plasticity, solid-solid   ing in which all heavy atoms are represented
and solid-melt phase transformations, spalla-        as interacting hard spheres of various sizes cor-
tion, ejecta, grain boundary and polycrystal ef-     responding to their van-der-Waals radii. This
fects, void collapse-induced hot spots, and the      model includes all degrees of freedom rele-
propagation and failure of detonation waves.         vant to folding - all sidechain and backbone
Modern semiempirical force fields, including          torsions- and uses a range of force-fields - from
the embedded atom method (EAM) potential for         structure-based Go potential to sequence-based
simple metals and the modified EAM (MEAM)             fully transferable atom-atom potentials. By
potential for metals with partially covalent be-     recording many folding events over over a wide
havior, can be rigorously tested through the cal-    range of temperatures a possible microscopi-

                                                 23
Invited Contributions


cally detailed folding mechanism for three dif-      I39 - Symmetries in Nature and their realiza-
ferent proteins - three-helix bundle, crambin and    tion on the lattice
protein G is obtained. Further, using combi-         Hasenfratz P. 1
nation of experimental, infoarmation, simula-        1 University of Bern, Switzerland
tions and evolutionary analysis we were able to
fully characterize Transition State Ensemble of      Symmetries are the most important guiding
a number of proteins providing detailed predic-      principle in the search for the fundamental laws
tions that can be further tested by experiments.     of Nature. Some of the relevant symmetries are
These results present a proof-of-principle for the   realized on the lattice in a way which will influ-
possibility of a solution of protein folding prob-   ence our perception of a symmetry in general.
lem at an all-atom level, provided that one has a
realistic all-atom potential energy function that
correctly favors the native state. In a separate     I40 - Going Chiral: testing new formulations
development this algorithm helped to solve the       of lattice QCD
”side-chain packing problem” by providing a          Jansen K. 1
rigorous estimate of the number of side-chain        1 John von Neumann-Institute for Computing
packing conformations that are compatible with
a given backbone of a native protein.                One of the most relevant questions in lattice
                                                     Quantum Chromodynamics is, whether it is pos-
I37 - Heavy and light quarks in a hypercubic         sible to reach quark masses that correspond
box                                                  to the physical values as measured in experi-
Becirevic D. 1                                       ments.We will compare two formulations of lat-
                                ´
1 Universite Paris Sud, Centre dOrsay                tice QCD, the chiral invariant overlap fermion
                                                     and the twisted mass lattice QCD approaches.
I discuss the issues related to the lattice QCD      It is shown that with both kind of fermions it is
studies of the phenomenologicaly relevant quan-      indeed possible to reach pion masses of about
tities which involve heavy and light quarks. A       200MeV. The prospects for future dynamical
special attention is devoted to the problem of       simulations in QCD are discussed.
finiteness of the size of the lattice, the effects
of which may significantly change the chiral be-      I41 - Computational Cosmology
havior to a number of quantities of interest. I      Moore B 1
will explain how the problem can be tackled an-      1 University of Zurich, Switzerland
alytically and indicate how it can be handled nu-
                                              I will review some of the grand challenge prob-
merically. I will then discuss a specific example
                            ¯          0 ¯0
of the calculation of K 0 -K 0 and Bs -Bs mix-lems in computational cosmology, from planet
                                              formation to galaxy formation. The range of
ing amplitudes and present some new results for
these quantities.                             scales and diverse physical phenomenon ob-
                                              served in the Universe are highly challenging to
I38 - A lattice perspective on weak interac-
                                              model and require sophisticated hardware and
tion phenomenology
                                              software solutions. I will discuss the horizon
Lellouch L. 1                                 project in which we plan to construct one the
                                e
1 CNRS-Centre de Physique Th´ orique, Case worlds largest supercomputers in Switzerland
907, CNRS Luminy F-13288 Marseille Cedex based on a novel new design.
9 France
                                              I42 - High performance computing for self-
I will review recent lattice QCD calculations gravitating systems
and their impact on the phenomenology of weak Capuzzo Dolcetta R. 1
processes involving quarks.                   1 Dep. of Physics

                                                 24
                                                                               Invited Contributions


The simulation of the evolution of astrophysical    Rev. Lett., 90, 136401 (2003).
systems (gaseous and/or stellar) is made difficult
by the dominant role of self-gravity. A discus-     I44 - Wave function optimization for accurate
sion of the various problems posed by a correct     quantum Monte Carlo calculations
treatment of the gravitational interaction in the   Filippi C. 1 Schautz F. 2
study of stellar systems, with particular atten-    1 Instituut-Lorentz, Universiteit Leiden, The
tion to stellar dynamics as a classical gravita-    Netherlands , 2 Instituut-Lorentz, Universiteit
tional N-body problem, is discussed, as well as     Leiden, The Netherlands
a scheme of their solution in the frame of high
performance computing is presented.                 We present an efficient method to optimize
                                                    Jastrow-Slater wave functions for both ground
I43 - Slater Determinant Quantum Monte
                                                    and excited states. The approach is within the
Carlo for Realistic Systems
                                                    framework of the so-called energy fluctuation
Zhang Shiwei 1
                                                    potential method which minimizes the energy
1 College of William and Mary, Williamsburg,        in an iterative fashion based on Monte Carlo
VA 23187, USA                                       sampling and a fitting of the local energy fluc-
Accurate and robust calculations to treat elec-     tuations. The orbitals are optimized together
tron interactions are crucial for the reliable      with the configuration interaction coefficients
prediction of many materials properties. We         through the use of additional single excitations
have developed a quantum Monte Carlo (QMC)          to a set of external orbitals. An improved set
method [1] to interface with and improve upon       of orbitals is then obtained from the natural or-
more traditional electronic structure approaches    bitals of this enlarged expansion. For excited
for real materials. The method takes the form       states, the approach is extended to treat state-
of importance-sampled random walks in a space       averaging for the optimization of multiple states
of Slater determinants. It allows direct in-        of the same symmetry. The performance of our
corporation of state-of-the-art techniques from     approach is illustrated with the lowest states of
the very best mean-field calculations (non-local     several organic molecules, where a careful con-
pseudopotentials; high quality basis sets) into     struction of the wave function and the reopti-
a many-body framework. Electron correlation         mization of its determinantal part are required to
effects are recovered by stochastic sampling of     obtain accurate excitation energies within fixed-
mean-field solutions (Slater determinants). The      node diffusion Monte Carlo.
Monte Carlo phase problem is controlled by          I45 - Quantum-Classical Reactive Dynamics
an approximation with a trial wave function.        Kapral R. 1 Sergi A. 2 Hanna G. 3
Any one-particle basis can be used. Using a         1 Canada , 2 Canada , 3 Canada
plane-wave basis and non-local pseudopoten-
tials, we have applied the method to Be, Si, P,     Many chemical reactions, such as proton and
S atoms and dimers, molecules containing tran-      electron transfer processes, have an important
sition elements such as TiO, and bulk Si. Sin-      quantum character and are often studied in con-
gle Slater determinants from density functional     densed phase or other complex environments. In
theory (DFT) or Hartree-Fock calculations were      such circumstances a quantum mechanical de-
used as the trial wave function, with no addi-      scription of the entire system is not possible.
tional optimization. The calculated dissociation    Instead, we describe a mixed quantum-classcial
energies of molecules and the cohesive energy       approach where the environment is treated clas-
of bulk Si are in excellent agreement with ex-      sically and the reactive degrees of freedom are
periment and are comparable to or better than       considered to be quantum mechanical. Reac-
the best existing theoretical results.              tive flux correlation function expressions for the
   [1] Shiwei Zhang and Henry Krakauer, Phys.       rate constants of non-adiabatic chemical reac-

                                                25
Invited Contributions


                                    Relative error in computed dissociation energy
                                                measured against experimental value

                                   0.50         present work
                                                Density functional theory (LDA)
                                   0.40
                                                diffusion Monte Carlo (DMC)


                  relative error
                                   0.30         DMC (with multi-det. twf)

                                   0.20

                                   0.10

                                   0.00

                               -0.10

                               -0.20
                                          Si2       P2          S2         TiO        PbO

Figure 1: [I43] Present QMC results were obtained using single determinant trial wave functions
(twf) from LDA. Standard DMC results (Grossman, JCP 117, 1434 (2002); Wagner and Mitas,
CPL 370, 412 (2003)) used optimized Jastrows times single- or multi-det. as twf.

tions occurring in such quantum-classical sys-                  assignment of the measured spectral lines has
tems will be presented. Methods for their sim-                  not been possible.
ulation, which are applicable to general classi-
                                                                I47 - Holistic Simulation
cal condensed phase environments, will be de-
scribed. The formalism and simulation schemes                   Sato T. 1
will be illustrated by calculations on models of                1 The Earth Simulator Center
non-adiabatic reaction dynamics where the en-
vironement is treated either deterministically in               The Earth Simulator Project started in July of
full detail or as a stochastic bath.                            2002 at the Earth Simulator Center of JAM-
                                                                STEC has already demonstrated several epoch-
I46 - Computational spectroscopy of doped                       making products in the global atmosphere and
Helium clusters                                                 ocean circulation simulation, the earth’s interior
Moroni S. 1                                                     dynamic simulation, nano-material simulation,
1 INFM SMC, University of Rome La Sapienza,                     tera-hertz oscillator design, exact lattice-QCD
Italy                                                           solution, etc., that have never been obtained by
                                                                the conventional computers. Those results en-
Rotational spectra of various molecular species                 sure us that the Earth Simulator has enabled us
solvated with Helium atoms are calculated by                    to make simulation of the whole system at once.
a reptation quantum Monte Carlo algorithm.                      This fact is far more revolutionary and signif-
Computer simulations allow us to establish a                    icant than one would expect. This is because
relation between the dynamical properties of                    one has finally obtained a scientific tool to be
the solvated molecule and the structure of the                  able to see the future evolution of environment
He solvent. Our results, in excellent agree-                    and future design of technologies and manufac-
ment with the available spectroscopic informa-                  turing products. Thus, the new field of science
tion, provide a more detailed microscopic pic-                  and technology, the revolutionary way of manu-
ture than inferred from experiments. They ex-                   facturing, the symbiotic, safe and secured life of
tend our knowledge to cluster sizes where the                   humans would be brought.

                                                             26
                                                                                Invited Contributions


   However, the Earth Simulator is far too small    sensory paths while ensuring that critical infor-
to deal with an entire system in a true sense       mation is not lost will be at the forefront of com-
that is organized by inseparable numerous in-       putational science.
teraction forces, microscopic and macroscopic.
                                                  I49 - Computer Simulation of Multiscale
I come up with here a holistic simulator that
                                                  Phenomena in Colloidal Liquid Crystals
would be able to simulate as self-consistently as
possible the evolution of an entire system.       Allen M.P. 1
                                                  1 Centre for Scientific Computing, University of
I48 - Beyond-Petascale Computing– The End
                                                  Warwick, United Kingdom
Of The Beginning Or the Beginning Of The
End?
                                                  This talk will summarize recent studies of in-
Camp W.J. 1 Debenedictis E.P. 2 Leland R.W.
                                                  homogeneous liquid crystals in the vicinity of
3
                                                  spherical and nonspherical colloidal particles,
1 Sandia National Laboratories, Albuquerque,
                                                  using molecular dynamics simulation with a do-
NM 87185, USA , 2 Sandia National Labora-
                                                  main decomposition algorithm, on massively
tories, Albuqueruqe, NM 87185 USA , 3 Sandia
                                                  parallel computers. These studies employed rel-
National Laboratories, Albuquerque, NM 87185
                                                  atively large systems, up to a million particles,
USA
                                                  and relatively long simulation runs, of order sev-
As we move beyond Petascale computing, we eral million timesteps.
are facing fundamental issues in computing: On       We have studied a isolated spherical ob-
the one hand we must deal with the physical       jects, representing small colloidal particles or
limits of computing machinery. In the not-too- droplets, suspended in a nematic liquid crys-
distant future, computing engines may be lim- tal matrix modelled with the soft ellipsoid po-
ited by the thermodynamic and heat transfer is- tential. Homeotropic boundary conditions and
sues highlighted by Landauer. At the same time, strong anchoring create a hedgehog director
reliability of computation will become a domi- configuration on the particle surface and in its
nant problem. New architectures and algorithms vicinity; we have studied the defect structure
are needed that provide redundancy and other around the particle which cancels this hedgehog
mechanisms to deal with ensembles of comput- defect and produces a uniform director field at
ing components that are at best probablistically large distances. We observe both ring and satel-
available and software whose full correctness is lite defects, broadly consistent with the predic-
imposible to check. The difficulties of the cou- tions of the simplest elastic theory. By study-
pling between multiple length and time scales ing density and order-parameter maps, we are
in computational simulations must be faced and able to examine behaviour near the particle sur-
overcome. Finally, we must cope with Feyn- face, and in the disclination core region, where
man’s observation that any computing engine the elastic theory is inapplicable. In a similar
capable of describing a complex system is of ne- way we have studied pairs of spherical colloid
cessity at least as complex as the system it pur- particles embedded in a nematic liquid crystal
ports to describe. In scientific computing this host, observing the surrounding director struc-
means that computer experiments may become ture, and calculating the forces on the particles
as hard to prepare and interpret as the physical as functions of their separation and their orien-
experiments they simulate. The questions (1) tation with respect to the nematic director.
of how to prepare a description of the system        Related studies of elongated colloidal parti-
to be modelled; (2) of how to provide adequate cles, measuring the torque on a particle as a
programming tools to characterize the solution function of tilt angle with respect to the direc-
methods; and (3) of how to probe the data pro- tor, and the interactions between pairs of highly
duced in a way comprehensible to finite human elongated particles, have also been carried out.

                                                27
Invited Contributions


I50 - Multiscale Computation: From Multi-
grid solvers to systematic upscaling
Brandt A. 1
1 Weizmann Inst. of Science, Rehovot, IL

Most numerical methods for solving physical
problems tend to be extremely costly, for several
general reasons that will be explained. Model
studies have shown that each of these reasons
can in principle be removed by multiscale (e.g.,
multigrid) algorithms. These algorithms em-
ploy separate processing at each scale of the
physical space, combined with interscale intera-
tive interactions, in ways which use finer scales
very sparingly. Having been developed first
and well known as solvers for elliptic PDEs,
highly efficient multiscale techniques have more
recently been developed for non elliptic and
time-dependent problems, and for many other
types of computational tasks, including: in-
verse PDE problems; highly indefinite (e.g.,
standing wave) equations; Dirac equations in
disordered gauge fields; fast computation and
updating of large determinants (as needed in
QCD); general fast integral transforms; inte-
gral equations; astrophysics; molecular dynam-
ics of macromolecules and fluids; many-atom
electronic structures; global and discrete-state
optimization; practical network and graph prob-
lems; image segmentation and recognition; to-
mography (medical imaging); fast Monte-Carlo
sampling in statistical physics; real-time path in-
tegrals; and general, systematic methods of up-
scaling (accurate numerical derivation of large-
scale equations from microscopic laws), either
deterministic or stochastic. The potential for
fundamental achievements in physics and chem-
istry will be outlined.




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