The document summarizes simulations of liquid crystal molecular organizations at different resolutions, from atomistic to mesoscale. It discusses using the Gay-Berne potential to model nematic and columnar liquid crystal phases. It also describes using genetic algorithms to parameterize effective charges to mimic electrostatic interactions and reproduce ordering in columnar phases. Simulations are able to form nanoscale liquid crystal droplets and demonstrate how molecular shape and charge distributions influence self-assembly.
I gave 1 hour seminar at ANSTO (Australian Nuclear Science and Technology Organization) to introduce my approach to magnetism. I see myself as an experimental physicist who is studying magnetism by using neutron scattering techniques. Throughout my career, I had learned local structure analysis (PDF), magnetic structural analysis, and inelastic neutron scattering technique to investigate superconductor, multiferroics, antiferromagnets, helimagnets, and frustrated magnets. I was trying to explain my approach to magnetism as an experiment physicist to both professional scientists and novices.
I gave 1 hour seminar at ANSTO (Australian Nuclear Science and Technology Organization) to introduce my approach to magnetism. I see myself as an experimental physicist who is studying magnetism by using neutron scattering techniques. Throughout my career, I had learned local structure analysis (PDF), magnetic structural analysis, and inelastic neutron scattering technique to investigate superconductor, multiferroics, antiferromagnets, helimagnets, and frustrated magnets. I was trying to explain my approach to magnetism as an experiment physicist to both professional scientists and novices.
Kinetic pathways to the isotropic-nematic phase transformation: a mean field ...Amit Bhattacharjee
Here we illustrate the classic Ginzburg-Landau-de Gennes theory of isotropic nematic phase transition and show how fluctuations as well as deterministic kinetics can lead to phase equilibria.
The public trial lecture presented by Mohammadreza Nematollahi on 8th of October 2014 at Norwegian University of Science and Technology. The theoretical models and the experimental progress of highly mismatched alloys, as well as their optoelectronic applications are covered.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
Synthesis and analysis of electrical properties of Lead free Ba3Sr2LaTi3V7O30...inventy
Materials of tungsten-bronze (TB) structure belong to an important family of dielectric materials which are well known for their applications in various electrical devices, such as transducers, actuators, capacitors, and ferroelectric random access memory. The TB structure consists of a framework of distorted BO6 octahedral sharing corners in such a way that three different types of interstices (A, B and C) are available for a wide variety of cations occupying in a general formula (A1)2(A2)4(C)4(B1)2(B2)8O30. Our present work deals with the studies of preparation and characterization of the physical properties of a novel single-phase polycrystalline lead-free vanadate having Tungsten Bronze Structure with compound formula Ba3Sr2LaTi3V7O30.The X-ray diffraction analysis confirms the formation of single-phase compound with orthorhombic structure. The effect of temperature (32- 5000C) and frequency (102–106 Hz) on structural and electrical properties were studied using an impedance analyzer. Detailed studies of impedance parameters provide a better understanding of the electrical properties and type of relaxation processes in the material. The bulk resistance is observed to be decreased with rise in temperature showing a typical negative temperature coefficient of resistance (NTCR) behavior.
Structural and Dielectric Studies of Cerium Substituted Nickel Ferrite Nano P...theijes
Cerium substituted Nickel ferrite nanoparticles with general formula NiCeXFe2-XO4 (x=0.0, 0.05, 0.1, 0.15) have been synthesized by using sol-gel method. The crystalline structure and grain size of these particles were analyzed by using XRD; the particle size ranged from 12.22nm to 17.60nm.The decrease in value of the lattice parameter with doping suggests that there is shrinkage in unit cell. The single-phase cubic spinal structure was clearly indicated by the XRD patterns of pure NiFe2O4.The XRD pattern also show that all the samples had formed the cubic single phase spinal structure. Dielectric properties have been studied in the frequency range of 1 kHz to 5 MHz. Permittivity and tangent loss (tanδ) decreases with the substitution of Ce3+ in parent crystal structure.
Structural and Dielectric Properties of Lanthanum Substituted Lead ZirconateT...iosrjce
IOSR Journal of Applied Physics (IOSR-JAP) is a double blind peer reviewed International Journal that provides rapid publication (within a month) of articles in all areas of physics and its applications. The journal welcomes publications of high quality papers on theoretical developments and practical applications in applied physics. Original research papers, state-of-the-art reviews, and high quality technical notes are invited for publications.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
More Related Content
Similar to Zannoni Liquid Crystal Modeling BO_ECME8_Jun05e .pdf
Kinetic pathways to the isotropic-nematic phase transformation: a mean field ...Amit Bhattacharjee
Here we illustrate the classic Ginzburg-Landau-de Gennes theory of isotropic nematic phase transition and show how fluctuations as well as deterministic kinetics can lead to phase equilibria.
The public trial lecture presented by Mohammadreza Nematollahi on 8th of October 2014 at Norwegian University of Science and Technology. The theoretical models and the experimental progress of highly mismatched alloys, as well as their optoelectronic applications are covered.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
Synthesis and analysis of electrical properties of Lead free Ba3Sr2LaTi3V7O30...inventy
Materials of tungsten-bronze (TB) structure belong to an important family of dielectric materials which are well known for their applications in various electrical devices, such as transducers, actuators, capacitors, and ferroelectric random access memory. The TB structure consists of a framework of distorted BO6 octahedral sharing corners in such a way that three different types of interstices (A, B and C) are available for a wide variety of cations occupying in a general formula (A1)2(A2)4(C)4(B1)2(B2)8O30. Our present work deals with the studies of preparation and characterization of the physical properties of a novel single-phase polycrystalline lead-free vanadate having Tungsten Bronze Structure with compound formula Ba3Sr2LaTi3V7O30.The X-ray diffraction analysis confirms the formation of single-phase compound with orthorhombic structure. The effect of temperature (32- 5000C) and frequency (102–106 Hz) on structural and electrical properties were studied using an impedance analyzer. Detailed studies of impedance parameters provide a better understanding of the electrical properties and type of relaxation processes in the material. The bulk resistance is observed to be decreased with rise in temperature showing a typical negative temperature coefficient of resistance (NTCR) behavior.
Structural and Dielectric Studies of Cerium Substituted Nickel Ferrite Nano P...theijes
Cerium substituted Nickel ferrite nanoparticles with general formula NiCeXFe2-XO4 (x=0.0, 0.05, 0.1, 0.15) have been synthesized by using sol-gel method. The crystalline structure and grain size of these particles were analyzed by using XRD; the particle size ranged from 12.22nm to 17.60nm.The decrease in value of the lattice parameter with doping suggests that there is shrinkage in unit cell. The single-phase cubic spinal structure was clearly indicated by the XRD patterns of pure NiFe2O4.The XRD pattern also show that all the samples had formed the cubic single phase spinal structure. Dielectric properties have been studied in the frequency range of 1 kHz to 5 MHz. Permittivity and tangent loss (tanδ) decreases with the substitution of Ce3+ in parent crystal structure.
Structural and Dielectric Properties of Lanthanum Substituted Lead ZirconateT...iosrjce
IOSR Journal of Applied Physics (IOSR-JAP) is a double blind peer reviewed International Journal that provides rapid publication (within a month) of articles in all areas of physics and its applications. The journal welcomes publications of high quality papers on theoretical developments and practical applications in applied physics. Original research papers, state-of-the-art reviews, and high quality technical notes are invited for publications.
Similar to Zannoni Liquid Crystal Modeling BO_ECME8_Jun05e .pdf (20)
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
4. • Molecular Models
• Atomistic Models
Resolution
mesoscale
nanoscale
Liquid Crystal simulations at different resolutions
5. Molecular level models
•Molecular resolution:
•a particle corresponds
to 1 molecule.
•Current typical sample
sizes: N=103-104
particles.
•Applications:
Relating molecular
features to phase
properties.
6. The Gay-Berne intermolecular potential
,
,
,
(
,
,
(
'
4
,
,
(
6
12
0
c
j
i
c
c
j
i
c
j
i
r
r
U
r)
u
u
r)
u
u
r)
u
u
uj
ui
r =rr
15. Common nematogens are biaxial but ..do not give
biaxial nematics!
R F
F
F
R CN R CN
CF3
R
16. A uniaxial (left) and biaxial (right) Gay-Berne type potential
(x,x)
(y,y)
17. Biaxial Nematics
• Biaxial nematic
phases can be
obtained from system
of molecules with
repulsive and
attractive biaxiality of
opposite sign.
• Optimizing molecular
shape is not enough
to give a biaxial
nematic
R. Berardi, C. Zannoni, J.Chem. Phys. 113, 5971 (2000)
23. Some recent works on biaxial nematics
• J. L. Figueirinhas, C. Cruz, D. Filip, G. Feio, A. C. Ribeiro, Y. Frere, T.
Meyer and G. H. Mehl, Phys. Rev. Lett. 94, 107802 (2005)
• K. Merkel, A. Kocot, J. K. Vij, R. Korlacki, G. H. Mehl and T. Meyer, Phys.
Rev. Lett. 93, 237801 (2004).
• K. Severing and K. Saalwachter, Phys. Rev. Lett. 92, 125501 (2004)
• G. R. Luckhurst, Nature 430, 413 (2004).
• L. A. Madsen, T. J. Dingemans, M. Nakata and E. T. Samulski, Phys.
Rev. Lett. 92, 145505 (2004).
• B. R. Acharya, A. Primak and S. Kumar, Phys. Rev. Lett. 92, 145506
(2004).
• V. Channabasaveshwar, Y. Prasad, G. G. Nair, I. S. Shashikala, D. Rao,
C. V. Lobo and S. Chandrasekhar, Angew. Chem. Int. Ed. Engl. 43, 3429
(2004).
• D. W. Bruce, Chem. Rec. 4, 10 (2004).
24. J.L.Figueirinhas, C. Cruz, D. Filip, G. Feio, A. C. Ribeiro, Y. Frere, T.
Meyer, G. H. Mehl, Phys. Rev. Lett. 94, 107802 (2005).
25. Biaxial Nematics Switching. A molecular dynamics
simulation study
R. Berardi, L. Muccioli, C. Zannoni (2005)
29. Computer Simulation of Liquid Crystal
nanodroplet phase separation
R. Berardi, A. Costantini, L. Muccioli,
S. Orlandi, C. Zannoni (2005)
30. A simple model for the formation of liquid
crystal nanodroplets from an homogeneous
solution
• Method
– Phase separation of GB–LJ mixtures
– MD simulation of nanodroplets formation
• Study
– effect of temperature
– effect of solute–solvent affinity
31. Model
• Mixture of Lennard–Jones (isotropic solvent) and Gay–
Berne (solute) particles that can form I, N, Sm
organizations.
33. Model and thermodynamic conditions are setup to give:
(a) pure solvent in a liquid state
(b) pure solute forming isotropic, nematic, and smectic phases
GB-LJ=3 GB-LJ=(1.0, 2.0, 2.5, 3.0)
(c) Mixture with x=xGB=0.02,0.04,0.08
Methodology
58. What is realism? Can we reproduce transition
temperatures with atomistic modelling?
R. Berardi, L. Muccioli, C. Zannoni, ChemPhysChem 5,104(2004)
59. • Molecular dynamics: ORAC multi time step
engine
• Force field: AMBER like potential
• Sample: N=98 molecules of the n=0,1, 2
homologues (4214, 4508 and 4802 atoms),
• Conditions: NPT
• Periodic boundaries
• Electrostatics with Particle Mesh Ewald
Etotal = Ebonds + Eangle + Edihed + ELJ + Echarge
Atomistic simulation approach
60. Ab-initio equilibrium geometries (MP2/3-21G*) and partial
charges. We show the electrostatic potential (a.u./Å at 3Å1)
1CHelpG method. C. M.Breneman; K. B. Wiberg, J. Comput. Chem. 11, 361 (1990).
69. Not all “similar” discs assemble in columnar
phases! Can we understand why?
HTT: LC columnar HAT: not a liquid crystal
e.g. HOTT,K 313 Col 360 I e.g. HOAT,K1 307 K2 366 I
Y.H.Geerts et al. MCLC 396,35(2003) V.Lemaur et al. JACS 126, 3271 (2004)
70. The effect of charge distributions
• A detailed representation is needed, e.g. to
get interdigitation in smectics or proper
ordering of discotics in columns
• Standard way: place a partial charge on
every atom
• Handling a full atomistic distribution of Nq
charges is very time consuming in
simulations. Time grows with O(Nq
3/2)
• Multipoles cannot be reliably used for
anisometric molecules in contact
71. Mimicking electrostatic interactions with a set
of effective charges. A genetic algorithm.
R.Berardi, L.Muccioli, S.Orlandi, M.Ricci, C.Zannoni,
Chem. Phys.Lett., 389,373 (2004)
• Obtain first a QM level description of the
charge distribution and of the corresponding
reference electrostatic potential around the
molecule.
• Assume a certain number nq of effective
charges and determine their optimal positions
and values by fitting their electrostatic potential
surface to the reference one.
72. • We define N trial solutions or genomes gi as sets of nq
charge positions, kept ordered according to their x
component.
• Genomes are combined according to evolution rules
• Determine the charges optimal positions and values by
fitting their electrostatic potential surface to the reference
one.
Genetic algorithm
73. Influence of charge distribution on the
columnar packing
R.Berardi, L.Muccioli, S.Orlandi, M.Ricci,
C.Zannoni, 2005
74. Atomistic (left) and effective (right) charge
distribution for Hexathiotriphenylene (HTT)
QM charge distribution at MP2/6-311G+ level
75. Atomistic (left) and effective (right) charge
distribution for Hexa-thio-azo-triphenylene (HTAT)
76. GB discs parameterization
• GB parameterization by fitting pair energies and
molecular structures in the columnar phase
obtained from a small atomistic simulation.
• MD simulation of N=40 HOTT molecules
preliminarily arranged in a columnar way.
• P = 3 atm, T = 300K, no electrostatic charges
(AMBER FF), time ≈ 5 ns.
• The non-bonded LJ intermolecular energies of the
side-side and face-face configurations have been
fitted using a Gay-Berne potential
• Model disc dimensions σs and σf taken from the
maxima or the radial distribution function
79. Molecular level simulation
• (i) NPT Monte Carlo simulation of discotic particles,
without charges, enclosed in a box with periodic
boundary conditions.
• Number of particles N=1000
• Dimensionless pressure P* ≡ Pσo
3/o=3.5 (equivalent
to P = 25MPa.), 0=10Å, 0=1kcal/mol
• Then, simulations with two different sets of Nq fitted
charges:
• (ii) 12 for HOTT and
• (iii) 22 for HOTAT.
86. Ferroelectric response and field induced biaxiality in
the nematic phase of a banana-shaped mesogen
O. Francescangeli, V. Stanic, S.I. Torgova, A. Strigazzi,
N.Scaramuzza, C.Ferrero, I. Dolbnya, R. Berardi, L.Muccioli,
S.Orlandi, C. Zannoni (2005)
Cr Sm N I
115.1 oC 138.3 oC 262.5 oC
118.5 oC 140.0 oC 263.0 oC
Cr Sm N I
Cr Sm N I
115.1 oC 138.3 oC 262.5 oC
118.5 oC 140.0 oC 263.0 oC
87. Ferroelectric like Response in the Nematic Phase
0,0 0,2 0,4 0,6 0,8 1,0
-2
-1
0
1
2
= 1 Hz
T = 180 °C
t (s)
I (A)
-12
-8
-4
0
4
8
12
V (V)
0,0 0,2 0,4 0,6 0,8 1,0
-6
-4
-2
0
2
4
6
t (s)
I (A)
-12
-8
-4
0
4
8
12
= 1 Hz
T = 180 °C
V (V)
88. Modelling the banana molecule: single particle
QM calculations
DFT equilibrium geometry with two interatomic distances
measurements and atomic labels
rAF
90. Some findings from atomistic simuations
- The two alkyloxy chains (rAB, rEF ) have the same behavior
and their length decreases with temperature.
- The central fragment (oxadiazole and two phenyl rings) (rCD)
is rigid and has constant length.
-The “bent-core” is not completely rigid.
-The effective “wingspan” ( rAF )
depends on the conformational
distribution.
0.10
0.06
0.04
0.08
P(rAF)
92. T=300 °C T=225 °C T=160 °C
85
.
0
2
P
80
.
0
2
P
10
.
0
2
P
T=140 °C
88
.
0
2
P
0°, 180° 90°
0°, 360° 180°
Constant Pressure Monte Carlo simulations
N=1000
93. T=160 °C
s0 = 10 Å
s0 = 10 Å
ij
j
i
j
i
j
i
j
i
j
i
j
i
j
i
j
i
ij y
y
x
x
x
y
y
x
y
y
x
y
y
x
x
x
r
r
r
S ˆ
ˆ
ˆ
ˆ
2
ˆ
ˆ
ˆ
ˆ
2
ˆ
ˆ
ˆ
ˆ
ˆ
ˆ
ˆ
ˆ
5
1 2
2
2
2
0
,
2
,
2
2
,
2
Cybotactic Clusters
97. Conclusions
Modelling and simulations at molecular level have reached the
stage where they can help to explain the effect of a specific
molecular feature (shape, attraction range,..) on the phase
organization of systems of increasing complexity (including
some composite systems).
Atomistic simulations are becoming predictive, but they are still
so extremely demanding in resources that they can be of use
only in very specific cases.
Molecular level models enriched with specific geometrical and
electrostatic details obtained by auxiliary atomistic simulations
can provide a useful intermediate approach for current
modelling applications.
98. • Alberto Arcioni
• Corrado Bacchiocchi
• Roberto Berardi
• Cesare Chiccoli
• Marco Mazzeo
• Davide Micheletti
• Luca Muccioli
• Silvia Orlandi
• Paolo Pasini
• Adriana Pietropaolo
• Matteo Ricci
• Gregor Skacej
• Giustiniano Tiberio
• Ilaria Vecchi
Group Home page
http://www.fci.unibo.it/~bebo/z/index.html
Thanks to: Bologna University, INSTM, PRIN,FIRB, EU-NAIMO
99.
100. Nanoscale self-organizing
multifunctional organic materials
24 September - 2 October, 2005 – Erice, Sicily, ITALY
International School of Liquid Crystals 12th meeting
Directors: F.Biscarini, Y.Geerts, P.Pasini, C.Zannoni
Lecturers: F. Biscarini, A. Brillante, J. Cornil, D. de Leeuw, R. Friend, A.Furlani,
R.Garcia, Y.Geerts, N.Greenham, P.Heremans, A.Menon, K.Müllen,
M.M.Nielsen, C.Rovira, G.Schmidt, C.Taliani, A.Walker, C.Zannoni
http://www-th.bo.infn.it/islc/erice2005/index.html