Posters
Po.1
Life at the Edge of Chaos, examples from the
kingdoms1
Enrique Balleza
Cub 45, Centro de Ciencias Fı́sicas, Universidad Nacional Autónoma de México,
Av. Universidad 1001, Colonia Chamilpa, Cuernavaca, Morelos, México, C.P.
62251, Mexico
Gene regulatory networks are recognized as the main component in charge
of cellular control. The coordinated expression of the different genes in an
organism is essential to achive proper cell function and cell differentiation.
Experimental data has been fitted to myriads of biochemically detailed models in order to explain the dynamics of very small parts of these networks.
However, their intrinsic complexity and size has hindered their global dynamical characterization. Here we show that real gene regulatory networks
of several organisms from different kingdoms exhibit a critical global dynamic
behaviour. In consequence, perturbations die out or have only a finite localized influence in network dynamics. Criticality, a precise, measurable and
well characterized property of dynamical systems, summarizes the idea that
robustness and adaptability coexist in organisms. Presumably this result will
be corroborated for a wide range of species when enough data becomes available giving rise to the general aceptance of criticality as an intrinsic property
of gene regulatory networks.
1
Poster session I (June 6th ), Panel 1
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XX Sitges Conference
Po.2
Experimental studies of the dynamics of supercooled
water in confinement or mixtures2
Rikard Bergman
Applied physics & Condensed Matter Physics, Chalmers University of
Technology, SE 412 96 Goteborg, Sweden
The dynamics of water is important for many biological processes. For
instance the function of proteins is directly related to the dynamics of the
surrounding water, which thus is of extreme importance for all living organisms. Yet very little is known about the dynamics of water and particularly
confined water that is of particular relevance in biological systems.
Here we present results from studies focused on solving two of the currently most debated questions regarding the dynamics of supercooled water.
Due to the difficulties of studying bulk water in the deeply supercooled regime
(due to unavoidable crystallisation), there is no consensus reached regarding
at which temperature the liquid to glass transition would occur. Furthermore, supercooled water has recently been proposed to have a ”fragile-strong”
transition at 228 K, i.e a transition from close to Arrhenius temperature dependence at low temperatures to highly non-Arrhenius dependence above the
transition temperature. However, this transition is experimentally elusive as
it would occur in the inaccessible temperature range of the supercooled bulk
water. Here we report on results from several studies using dielectric and
neutron spectrosco-py on water in various confinements or in mixtures in order to avoid the crystallization problem. We find that has been associated to
the commonly accepted glass transition temperature, Tg, is of a local nature
[1] and, hence, the Tg of water seems to be at a higher temperature (? 160
K) [1, 2] in agreement with recent thermodynamical arguments [3]. Since the
viscosity related ?-relaxation is absent in deeply supercooled confined water,
these types of studies show no direct evidence of the proposed fragile-strong
transition [4].
1. S. Cerveny, G.A. Schwartz, R. Bergman and J. Swenson, Phys. Rev.
Lett., 93, 245702 (2004)
2. S. Cerveny, G.A. Schwartz, A. Alegrı́a, R. Bergman and J. Swenson, J.
Chem. Phys., in press
2
Poster session I (June 6th ), Panel 11
54
Posters
3. V. Velikov, S. Borick and C.A. Angell, Science 294, 2335 (2001)
4. J. Hedström , J. Swenson, R. Bergman, H. Jansson and S. Kittaka,
Submitted to J. Phys. IV
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Po.3
Neuronal Growth: A Bistable Stochastic Process3
Timo Betz
University of Leipzig, Institut for Soft Matter Physics, Abt. PWM, Linnestraße
5, 04103 Leipzig, Germany
During the past decade, modeling biological systems as stochastic processes has given tremendous insight into nature’s working principles at the
level of networks, single cells, and molecules. However, the stochastic nature of neuronal growth has hardly been investigated. The basic step in the
correct neuronal wiring of a developing organism is the controlled advancement of a highly motile structure,called the growth cone, which is directed
by gradients of chemical guidance cues. We report on the first statistical
analysis of the stochastic fluctuation of a neuronal growth cone’s leading
edge movement. Describing the edge movement with a stochastic process allows inferring a bistable potential from the edge velocity distribution. Using
Kramer’s approach to calculate decay rates, an isotropic noise parameter can
be determined, which we used to consistently connect the measured edge velocity distribution and the residence time distribution. An according analysis
of the growth cone’s motility confirms the model, and predicts that linear
changes of the bistable potential might result in the directed growth cone
translocation. These results help to understand how the growth cone can
detect chemical gradients that are on the order of one molecule across its
diameter, even in the highly noisy environment of a developing organism.
– T. Betz, D. Lim, J. Kaes,”Neuronal Growth: A Bistable Stochastic
Process”, Phys. Ref. Lett. 96, 098103 (2006)
3
Poster session I (June 6th ), Panel 6
56
Posters
Po.4
Efficient electrolyte modeling in MD simulations of
transport in membrane channels4
Titus Beu
University Babes-Bolyai, Faculty of Physics, Cluj-Napoca, Romania
Various site-site water models are investigated in the context of nonequilibrium molecular dynamics simulations of transport through ion channels. The rigid-body dynamics of the water molecules is decomposed in
centre-of-mass translation and rotation about the centre-of-mass (in the quaternion formalism), thus substantially reducing the total number of degrees of
freedom (roughly by 1/3) and rendering a supplementary shake-type algorithm to preserve molecular structure unnecessary.
To account correctly for the long-range electrostatic interactions of the
charges and their periodic images, Ewald sum techniques are employed.
By using the P3M particle-particle/particle-mesh FFT-accelerated Ewald
method developed by Deserno and Holmes [1], simulations up to microseconds are possible, allowing for the current flow to be measured.
Considering the Na channel model proposed by Crozier et al. [2], we address such questions as the spatial voltage profile, the longitudinal and radial
density distribution of water and ions, the ion passage time, the channel selectivity for the ion species, and the influence of the pronounced polarization
of the water along the paths of the transiting ions.
1. M. Deserno and C. Holm, J. Chem. Phys. 109, 7678 (1998); J. Chem.
Phys. 109, 7694 (1998)
2. P.S. Crozier, R.L. Rowley, N.B. Holladay, D. Henderson, D.D. Busath,
Phys. Rev. Lett. 86, 2467 (2001)
3. T.A. Beu, J. Opt. Adv. Mat. 8, 160 (2006)
4
Poster session II (June 8th ), Panel 1
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XX Sitges Conference
Po.5
Rupture Rate of Biomembrane under Dynamic
Surface Tension5
Dominique J. Bicout
Institut Laue-Langevin, Theory Group, 6 Avenue Jules Horowitz, B.P. 156,
38042 Grenoble cedex 9, France
5
Poster session II (June 8th ), Panel 9
58
Posters
Po.6
Analysis of Physiological time series (ECG)6
Jean Bragard, P. Elizalde, J. Elorza and E. Diaz-Calavia
Universidad de Navarra, c. Irunlarrea (s/n),
31080 Pamplona, Spain
Heart rate variability has attracted much attention from researchers since
the early 1980s. It has long been understood that a perfectly periodic heart
rate is pathological, and that the healthy heart is influenced by multiple
neural and hormonal inputs that result in variations in interbeat (RR) intervals, at time scales ranging from less than a second to 24 hours. Using very
long time series of ECG (Holter of 24 hours) from two groups of subjects
(normal and severe heart disease), we have studied the RR intervals. The
distribution of RR intervals erases the time correlations and is therefore not
a good tool for characterizing the long term variability of the heart rate.
On the contrary, long time correlation and more precisely their fractal structure is a powerful tool for helping in classifying the subjects. Other kinds
of indicators are also used for analysing the heart variability. These indicators are borrowed from statistical physics (fractal structure and entropy of
the signal) and from electrical engineering techniques (Fourier analysis and
cross-correlation). We conclude that ECG analysis is still a very efficient toy
for helping in the detection of heart disease.
6
Poster session I (June 6th ), Panel 22
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XX Sitges Conference
Po.7
Dynamic instabilities in biological membranes7
Fèlix Campelo
Departament de Estructura i Constituents de la Matèria, Facultat de Fı́sica,
Universitat de Barcelona, Digonal 647, 08028 Barcelona, Spain
We study the pearling instability in biomimetic vesicles motivated by recent experiments. The pearling of tubular vesicles is induced by the anchorage of amphiphilic polymers. We use a phase-field model, which reproduce
both stationary and non-stationary shapes.
7
Poster session II (June 8th ), Panel 10
60
Posters
Po.8
Establishment of the Dorsal-Ventral Boundary in the
Drosophila Wing Imaginal Disc8
Oriol Canela Xandri
Parc Cientı́fic de Barcelona, Universitat de Barcelona, Spain
Herein, we present a gene-protein regulatory network for the establishment of the dorsal-ventral boundary in the Drosophila wing imaginal disc.
We perform in silico experiments by means of a modelling approach that reduces each transcriptional-translational dynamics into a single effective process where Hill-like functions are assumed as regulatory functions. Thus, we
show how short-range (receptor-ligand dynamics) together with long-range
(morphogen gradient signalling) interactions shape the border and constitute
the gene expression pattern that is observed in in vivo experiments. Our in
silico results are complemented with a robustness analysis of the regulatory
network.
8
Poster session I (June 6th ), Panel 2
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XX Sitges Conference
Po.9
A topological analysis of the periodic cell-cycle
network in fission yeast S. pombe9
Cecile Caretta Cartozo
Laboratoire de Biophysique Statistique, ITP-FSB, Ecole Polytechnique Federale
de Lausanne, CH-1015 Lausanne, Switzerland
Recently gene expression data on the cell cycle of fission yeast Schizosaccharomyces pombe from three independent studies, with several replicates
each, were made available (Rustici et al. 2004, Peng et al. 2005 and Oliva et
al. 2005). The result of the data analysis is the assignment of the cell-cycle
phase for each gene that has been detected as periodically regulated. We
propose a comparative study to underline the discrepancies as well as the
similarities between these results. We consider the cluster structure of the
corresponding network of cell-cycle periodic genes. Each node in the network represents a periodic gene while each link is assigned a weight that is a
function of the phase difference between the two linked vertexes. We discuss
the stability of the cluster structure through the computation of an entropy
parameter that describes the progression of the clustering procedure. Finally
we consider the networks corresponding both to the union and the intersection of the three data sets to investigate the degree of discrepancy between
the different studies. We find interesting results regarding the universality of
the cluster structure of the periodic cell-cycle network despite diferences in
the size of the data sets and in the specific phase assignement of each gene.
9
Poster session I (June 6th ), Panel 3
62
Posters
Po.10
Theoretical prediction of a liquid-liquid transition in
monocomponents fluids10
Luciano Armando Cervantes Garcı́a1 , Ana Laura Benavides1 ,
Fernando del Rı́o2
1
Instituto de Fı́sica de la universidad de Guanajuato, Loma del Bosque 103,
Fraccionamiento Lomas del campestre. Apartado Postal E-143. C.P. 37150 León,
Guanajuato, Mexico
2
Universidad Autónoma Metropolitana-Iztapalapa, Mexico
By using the Discrete Perturbation Theory [1] we present the phase diagram of several families of discrete potentials that are a sequence of squareshoulder + square-well potentials. These phase diagrams are very interesting
since they exhibit both gas-liquid and liquid-liquid transitions. The liquidliquid transitions in monocomponents fluids have recently been observed by
experimental observations for important real systems like: water, phosphorus, carbon, silica, among others [2,3]. In this work present a systematic
study of the effect of the variation of the intermolecular potential parameters. This study complements those previously obtained with the molecular
simulation and integral equation approaches [4,7]. Since a variety of phase
diagrams can be obtained by varying these parameters we analyse the role of
the atttractive and repulsive parts of the intermolecular potential model in
order to understand the mechanism that generates this type of transitions.
1. Benavides A.L., and Gil-Villegas, Mol. Phys. 97 (1999)
2. Harrington, S. et al, Phys. Rev. Lett. 78, 2409-2412 (1997)
3. Katayama, Y., Mizutani, T., Utsumi, W., Shimomura, O., Yamakata,
M. and Funakoshi, K. 2000 Nature (London) 403, 170.
4. Mishima, O. & Stanley, H.E., Nature 396 (1998)
5. Pool, P.H. Nature 360, 324
6. Skibinsky A., Buldyrev S. V., Franzese G., Male-scio G. and Stanley
H. E., Phys. Rev. E 69, (2004)
7. Gianpetro Malescio, Giancarlo Franzese, Anna Skibinsky, Sergey V.
Buldyrev, and H. Eugene Stanley, Physical Review E 71, 061504, (2005)
10
Poster session I (June 6th ), Panel 12
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Po.11
Immunological Synapse: a Stochastic Theory11
Amit Chattopadhyay
Dipartimento di Fisica ”G. Galilei”, Università degli Studi di Padova, via F.
Marzolo 8, 35131 Padova, Italy
We analyse the size and density of regions of close contact in thermally
fluctuating cell:cell contact interfaces in a glycoalyx potential. Our calculations indicate that these patches are of the order of one-tenth of a micron
and depend critically on the distance ∆ between the contact threshold depth
and the mean membrane separation width. The size of a patch decreases
as ∆ increases while the corresponding density decays exponentially. In the
process we generalise a theory to evaluate the probability of first crossing in
a system without reflection symmetry. The model is expected to represent
the patterning sequences during the early binding of an antigen receptor to
a T-cell in an immunological synapse.
11
Poster session I (June 6th ), Panel 7
64
Posters
Po.12
Translocation boost protein-folding efficiency of
double-barreled chaperonins12
Ivan Coluzza
The University Chemical Laboratory, University of Cambridge, Lensfield Road,
Cambridge, CB2 1EW, UK
Incorrect folding of proteins in living cells may lead to malfunctioning
of the cell machinery. To prevent such cellular disasters from happening, all
cells contain molecular chaperones that assist non-native proteins to fold into
the correct native structure. One of the most studied chaperone complexes
is the GroEL-GroES complex. The GroEL part has a double-barrel structure, which consists of two cylindrical chambers, joined at the bottom in a
symmetrical fashion. The hydrophobic rim of one of the GroEL chambers
captures non-native proteins. The GroES part acts as a lid that temporarily
closes the filled chamber during the folding process. Several capture-foldingrelease cycles are required before the non-native protein reaches its native
state. Here we report molecular simulations that suggest that translocation
of the non-native protein through the equatorial plane of the complex boost
the efficiency of the chaperonin action. If the target protein is correctly
folded after translocation it is released. However, if it is still non-native, it is
likely to remain trapped in the second chamber, which then closes to start a
reverse translocation process. This shuttling back and forth continues until
the protein is correctly folded. Our model provides a natural explanation for
the prevalence of double-barreled chaperonins. Moreover, we argue that internal folding is both more efficient and safer than a scenario where partially
refolded proteins escape from the complex before being recaptured.
12
Poster session II (June 8th ), Panel 4
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XX Sitges Conference
Po.13
A simple Functional Analysis of the E. coli
Transcription Network13
Marco Cosentino Lagomarsino1 and Giancarlo Franzese2
1
Institut Curie, Paris, UMR 168 CNRS/Institut Curie, 11 rue Pierre et Marie
Curie, 75231 Paris CEDEX 05 France
2
Departament de Fı́sica Fonamental, Universitat de Barcelona, C. Martı́ i
Franqués 1, 08028 Barcelona, Spain
Transcription networks are the basic switchboard of a living cell. Their
scope is to activate the relevant genes, given the information on the surrounding environment. This information is carried by specific DNA-binding
proteins, the transcription factors. Recently a significant fraction of these
networks has become available for a few organisms such as E. coli and S. cerevisiae. However, no simple tools exist for the functional analysis of mediumto large-sized networks and all functional studies are directed to small subnetworks, where detailed models can be used. The question that remains
open is how to define sub-net-works that are functionally independent from
each
other.
We introduce an elementary large-scale analyisis that includes all the
available functional information on the E. coli network, and proves to be
useful in gaining some insight in the network operating modes. This is done
using an extremely simple Boolean model for gene activation, that allows,
for small networks, to enumerate all the possible input-output configurations.
For larger ones, it is possible to analyze a statistically significant sub-class of
configurations. Our approach allows to define functional subgraphs in a very
natural way.
13
Poster session II (June 8th ), Panel 18
66
Posters
Po.14
Determination of the potential of mean force using
the non-equilibrium Crooks formula14
Gianni de Fabritiis
Centre for Computational Science, Department of Chemistry, University College
London, 20 Gordon Street, London WC1H 0AJ, UK
The permeation of ions in protein channels is important to control cell
activity. However, a direct measurement of the conductivity via molecular simulations is not possible because the time scales involved are too long
(micro-milli seconds). Rather, the potential of mean force (PMF) of the
crossing is computed and the conductance estimated from it. Here, we look
at a simple non-equilibrium method to compute the PMF which is based
on the Crooks non-equilibrium relation [Phys. Rev. E 61 2361 (2000)] over
the Gramicidin A membrane protein. The equilibrium PMF is reconstructed
from a set of controlled non-equilibrium pullings of ions trough the channel. This procedure also allows to compute the position dependent diffusion
coefficient.
14
Poster session II (June 8th ), Panel 19
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XX Sitges Conference
Po.15
Study of the influence of ethanol on the basic
fibrolast growth factor structure by molecular
dynamics simulations15
Gustavo H. Brancaleoni, Marcos R. Lourenzoni and Léo Degrève
Departamento de Quı́mica, Faculdade de Filosofia Ciências e Letras de Ribeirão
Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900,
14040-901 Ribeirão Preto, SP, Brasil
The growth of cells is controlled by stimulatory or inhibitory factors via
proteins interactions. In multicellular organisms, these proteins are known
as growth factors. One of them, the basic fibroblast growth factor (bFGF)
have proliferative activity for fibroblastic cells. bFGF can be inibited by
ethanol during the embryonary phase. In the present work, wild bFGF and
three mutants (M6B-bFGF, M1-bFGF and M1Q-bFGF ) were examined by
molecular dynamics simulations in aqueous solutions in the presence or not of
ethanol at 298K and physiological pH over 4.0ns using the gromacs package
and the gromos96 force field. The hydrogen bonds (HB) and hydration of
bFGF and mutants in the presence, or not, of ethanol establish that the
residues belonging to the beta-5 and beta-9 strands, specially SER-73(beta
5), and, in beta-9, in TYR-112, THR-114, TYR-115 and SER-117 are the
most affected region by ethanol by the substitution of hydration molecules
by ethanol that form HB with these residue being the CH3 tail located close
to a neighborly hydrophobic residue. Experimental data have previously
identified the role of TYR-112 and THR-114 in the bFGF docking on its
receptor. More experimental studies about the SER-73, TYR-115 and SER117 residues must be done to identify the exact role of these residues in the
bFGF activity. Our MD simulation were able to understand what is the
procedure for the inactivation of some residues by ethanol that may result in
numerous anomalies regarding fetus formation. Fapesp CNPq
15
Poster session I (June 6th ), Panel 8
68
Posters
Po.16
Cellulose Biosynthesis: a polymerization driven
molecular motor16
Fabiana Diotallevi
FOM Institute for Atomic and Molecular Physics, Institute AMOLF, P.O.Box
41883, 1009 DB Amsterdam, The Netherlands
Cellulose is the most abundant renewable resource in the biosphere. It
serves its most prominent role as the main architectural component of the
cell wall of higher plants, where it occurs in the form semi-crystalline cellulose microfibrils (CMFs). Despite the crucial role that cellulose plays in
nature and in many aspects of everyday life, the primary event of its biosynthesys still remains a mystery. Only recently has been established that this
biopolymer is sinthesized by hexagonal enzymes, called ”rosettes”, embedded in the plasma membrane of plant cells. Current studies are based on the
hypothesys that the rosette travels in the membrane powered by the force
arising form the cellulose synthesis itself. We present here the first detailed
theoretical understanding of the propulsion mechanism of the cellulose synthase. The model takes into account polymerization and crystallization as
driving forces, and the role of polymer flexibility and membrane elasticity as
force transducers. We show that the rosette exploits the thermal fluctuations
and the elasticity of the system as energy source for its motion. Our model
reproduces the experimental observations and, for typical values of the elastic constants, predicts a velocity of the cellulose synthase of 4.5 × 10−9 m/s,
in good agreement with the experimental value of 5.8 × 10−9 m/s.
16
Poster session II (June 8th ), Panel 5
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XX Sitges Conference
Po.17
A model for polar growth of the fission yeast cells17
Jure Dobnikar1 and Sasa Svetina2
1
2
Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
Institute of Biophysics, Faculty of Medicine, University of Ljubljana Lipiceva 2,
1000 Ljubljana, Slovenia
A growing fission yeast cell exhibits localized growth at one or both ends
of its cylindrically shaped body. Such a polarized growth is regulated by
mod5p through its anchoring of tea1p at cell ends. We present a possible
mechanism for the active co-localization of these two proteins.
17
Poster session I (June 6th ), Panel 10
70
Posters
Po.18
Ab-initio Calculation of Dominant Pathways in
Protein Folding18
Pietro Faccioli, M.Sega, F. Pederiva and H. Orland
Dipartimento di Fisica, Trento University and INFN,
14 Via Sommarive, Povo (Trento), Italy
We present a recently developed theoretical framework which allows to
simulate the entire protein folding reaction using an atomistic description.
The approach is based on the formal analogy between thermal and quantum diffusion: by writing the solution of the Fokker-Planck equation for the
time-evolution of a protein in a viscous heat-bath in terms of a path integral,
we derive a Hamilton-Jacobi variational principle from which we are able to
compute the most probable pathway of folding. Such a pathway corresponds
to an instanton in the quantum-mechanical language. We show that, by
employing the Hamilton-Jacobi formalism, the long-standing computational
difficulties associated with rare events are bypassed. As a result, it becomes
possible to simulate the entire folding reaction on presently available computers.
As a first exploratory application, the method is tested by studying the
folding of the Villin Headpiece Subdomain, in the framework of a Go-model.
We have found that, in this model, the transition occurs through an initial
collapsing phase driven by the starting coil configuration and a later rearrangement phase, in which secondary structures are formed and all computed
paths display strong similarities. This method is completely general, does not
require the prior knowledge of any reaction coordinate. It represent an efficient tool to perfom ab-initio simulations of the entire folding process with
available computers.
18
Poster session II (June 8th ), Panel 22
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XX Sitges Conference
Po.19
Overcharging in Biometic Membranes: Molecular
Dynamics Simulations19
Jordi Faraudo
Dept. Fı́sica, Facultat de Ciències,
Universitat Autónoma de Barcelona, Edifici CC, E-08193 Bellaterra, Spain
Ions near membranes play an important role in many processes (transport,recognition,...) and determine the interactions between membranes. Experimentally, it is known that concentrations of divalent ions above certain
thresold limits produce overcharging (i.e., charge inversion due to adsorption
of counterions) at amphiphilic interfaces (1). The consequences of membrane
overcharging are dramatic. However, the physical mechanisms underliying
this phenomenon are not well understood. Several theories propose different
mechanisms of charge correlation leading to overcharging (2,3). In addition,
ion hydration and dielectric overscreening near the membranes may have
a decisive role (4). In this work, we show large-scale molecular dynamics
simulations performed in the new BSC spanish national Supercomputing facility showing the physical mechanisms of overscreening in a phospholipid
biomimetic membrane. We performed simulations of a DMPA2− /water layer
in contact with Ba2+ counterions and added sat (BaCl2 ), in conditions similar to those observed experimentally (1). Our results allow us to identify the
physical mechanisms for overcharging in these systems and the role player
by Bjerrum correlations and ion hydration.
1. D. Vaknin et al. Phys. Rev. Lett. 90, 178102 (2003)
2. N. Grobech-Jensen et al., Phys. Rev. Lett. 78, 2477 (1997)
3. A. Travesset and D. Vaknin, Europhys. Lett. (accepted for publication,
2006)
4. J. Faraudo and F. Bresme, Phys. Rev. Lett. 92, 236102 (2004)
19
Poster session II (June 8th ), Panel 11
72
Posters
Po.20
Exhaustive comparison of molecular dynamics
simulationc force Fields20
Carles Ferrer-Costa
Parc Cientı́fic de Barcelona – Institut de Recerca Biomèdica, Josep Samitier 1-5,
08028 Barcelona, Spain
The improvement of force fields is a subject in molecular dynamics in
constant development in order to reproduce experimental data. Several
force fields are available actually for protein molecular dynamics. In this
poster we show an exhaustive comparative for 4 different force fields (Amber
PARM99, Charmm 22, OPLS for charmm and gromos 43a1 for gromacs)
running using amber, namd and gromacs packages. In this comparisons we
analyze up to 4x35 10 ns molecular dynamics simulations. Those 35 different proteins represent 35 different metafolds included in PDB database.
Here we present different analysis for comparisons from standard rmsd or
radius of gyration to PCA and entropy. This project is hosted by MoDEL
database (http://mmb.pcb.ub.es/MODEL) and Barcelona Supercomputing
Center (http://www.bsc.org.es).
20
Poster session I (June 6th ), Panel 21
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XX Sitges Conference
Po.21
Search dynamics of cooperatively and specifically
binding transcription factors21
Nico Geisel
DPG (German physical society), Lehrstuhl Prof. Dr. E. Frey, Theresienstr 19,
80333 München, Germany
Cooperative binding of two proteins to adjacent and specific sites on the
genomic DNA is indispensable for many genetic mechanisms, in particular
transcription regulation.
The equilibrium and non-equilibrium properties of this process are strongly
affected by the presence of the genomic background.
We consider a model which explicitly takes this heterogeneous background
into account and investigate the search dynamics of two cooperative transcription factors (TF) for two adjacent operators, aiming insight into the
design of TF-TF and TF-DNA interaction.
We find that first operator occupation generally takes place out of equilibrium and in dependence of the cooperativity strength. Furthermore this
is likely to happen by independent binding of each single TF, which has
implications to the response times of genetic logic gates.
21
Poster session II (June 8th ), Panel 17
74
Posters
Po.22
Ionic current enhancement and modulation by DNA
translocation22
Nélido González-Segredo and Daan Frenkel
AMOLF Amsterdam, The Netherlands
We study the ionic current as a DNA oligomer immersed in an electrolyte
translocates through a nano-pore under an applied electric field. Our method
consists in solving the electrokinetic equations at the Pois-son-Boltzmann
level for the microions, coupled to a lattice-Boltzmann equation for the solvent hydrodynamics. We find ionic current enhancement for large enough
screening lengths. If a localised charge probe is placed on the wall of the
nanopore, we observe ionic current modulations which, albeit small, should
be experimentally observable.
– S. Reboux, F. Capuani, N. Gonzalez-Segredo and D. Frenkel, “LatticeBoltzmann Simulations of Ionic Current Modulation by DNA Translocation” J. Chem. Theor. Comput. DOI:10.1021/
ct050340g (2006)
22
Poster session II (June 8th ), Panel 8
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XX Sitges Conference
Po.23
Deformations of lipid membranes due to external
stimuli23
Wojciech Gozdz
Institute of Physical Chemistry Polish Academy of Sciences, Kasprzaka 44/52,
01-224 Warsaw, Poland
We investigate the shape of lipid membranes influenced by external stimuli, within the framework of the curvature energy model. A few different
systems are studied. The deformations of tubular vesicles due to the temperature change are examined. The deformation of the vesicles with large
spontaneous curvature due to a growing microtubulus are investigated. The
interface width between domains in multicomponent vesicles with coherent
domains of one component are studied.
23
Poster session II (June 8th ), Panel 12
76
Posters
Po.24
Solvent impact on helix formation24
Hendrik Hansen-Goos
Max-Planck-Institut für Metallforschung,
Heisenbergstr. 3, 70569 Stuttgart, Germany
Proteins in the cellular environment frequently are found in helical conformations. While the polypeptide backbone is tightly bound by covalent
bonds, the folding structure is stabilized by the much weaker noncovalent
bonds. This gives rise to the question whether the solvent containing the
protein has an influence on the stability of different folding structures. We
study this influence by solvation free energy calculations for various helical
conformations of a tube, modeling the protein. The method we use is the
so-called morphometric approach which, based on a theorem from integral
geometry, allows to separate the tasks of calculating thermodynamic solvent
properties and geometric protein quantities. We present results for the simple
hard-sphere solvent and an attractive solvent, more appropriate to model water. The solvent properties are determined through density functional theory.
Hydrophilic and hydrophobic proteins are modeled by an external potential
acting on the solvent. Our results suggest that the presence of a solvent
stabilizes helices by offering them a (local) energy minimum. The tendency
to helix unwinding suggested by the Asakura Oosawa model is shown to be
suppressed by the hard-sphere solvent interaction.
24
Poster session I (June 6th ), Panel 14
77
XX Sitges Conference
Po.25
Knot Statistics and Entaglement for Biomolecules25
Dieter W. Heermann, P.M. Diesinger and M. Brill
Insitute for Theoretical Physics, Heidelberg University, Philosophenweg 19,
D-69120 Heidelberg, German
We present an analysis on the average number of knots in macromolecules
given a certain chain length. We study the power law behaviour for the
number of knot-monomers and consider the situation of macromolecules in
constrained space as it occurs within the cell. As an example we present
results for a model drosophila system.
25
Poster session I (June 6th ), Panel 20
78
Posters
Po.26
Fractional diffusion in periodic potentials26
Els Heinsalu
Institute of Theoretical Physics, Tartu University,
Tähe 4, 51010 Tartu Estonia
Theoretische Physik I, Institut für Physik, Universität Augsburg, Universitätsstr.
1, D-86135 Augsburg, Germany
26
Poster session I (June 6th ), Panel 13
79
XX Sitges Conference
Po.27
Are hydrodynamic interactions important for active
transport in cells?27
Dion Houtman
University of Amsterdam (HIMS),
Nieuwe Achtergracht 166, 1018WV, Amsterdam, The Netherlands
We present a model to account for hydrodynamic interactions between
molecular motors moving unidirectionally along biofilaments and the surrounding viscous environment. In our simple lattice model we include excluded volume, active transport and hydrodynamic interactions. The latter
is important to properly account for the interaction of the molecular motors
with their environment, something that was not taken into account so far
[1,2].
Our model shows that the hydrodynamic interactions enhance the flux of
particles along biofilaments, the highways in cells. This increase depends on
the biofilament occupation. We find an optimal occupation at which transport takes place most efficiently. Moreover, the hydrodynamic forces induced
by the bound motors give rise to a non-negligible flux of unbound particles
(e.g. organelles) or other cargo close to the filament. In fact, the flow field
set-up by an ensemble of molecular motors with cargo can explain transport
of larger objects as organelles in plant cells, as is the case of cytoplasmic
streaming, where cargo has to travel long distances.
1. Lipowsky R., Klumpp, S and Nieuwenhuizen T.M., Phys. Rev. Lett.,
87 (2001), 108101
2. Nédélec F., Surrey T. and Maggs A.C., Phys. Rev. Lett., 86 (2001),
3192
27
Poster session II (June 8th ), Panel 2
80
Posters
Po.28
Solute escape from a vesicle28
Marco A. P. Idiart, Yan Levin and Jeferson J. Arenzon
Instituto de Fı́sica - UFRGS - Porto Alegre-Brazil,
Av. Bento Gonçalves 9500, Caixa Postal 15051,
91501-970 Porto Alegre, RS, Brazil
We present both analytical and simulational results for the dynamics of
solute release from an osmotically ruptured vesicle. There are two release
mechanisms: osmotic outflux of solvent and solute effusion. The convection
dynamics is modeled using the continuity equation and an expression for the
energy of the lipidic membrane. We find that dependent on the internal solute concentration and vesicle size, liposomes can stay pore-free, nucleate a
short lived oscillatory pore, or nucleate a long-lived pore. The phase diagram
of pore stability is obtained, and the different scaling regimes are deduced
analytically. Solute effusion is studied using Monte Carlo simulations combined with scaling analysis. It is found that for small vesicles with radius
less than 500nm diffusion is the dominant mechanism for solute release.
– Idiart MA, Levin Y. PHYSICAL REVIEW E 69 (6): Art. No. 061922
Part 1 JUN 2004
– Levin Y, Idiart MA, Arenzon J. PHYSICA A 354, 95-100 AUG 15
2005
28
Poster session II (June 8th ), Panel 13
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XX Sitges Conference
Po.29
How affects the molecular crowding to the enzymatic
cytoplasmatic reactions? An in silico Monte Carlo
study 29
Adriana Isvoran1 , Eudald Vilaseca2,3 , Francesc Mas2,3
1
Department of Chemistry, University of the West Timisoara, Str. Pestalozzi 16,
300311 Timisoara, Romania
2
Theoretical Chemistry Research Centre (CeRQT) of Scientific Park of
Barcelona (PCB), Spain
3
Physical Chemistry Department, Barcelona University (UB), Spain
In silico studies of enzymatic reactions, following Michaelis-Menten mechanism, taking place in crowded media, as a model of the cellular cytoplasm,
have recently been performed by Berry [1] and Schnell and Turner [2], using a Monte Carlo algorithm of diffusion controlled reactions in 2D, showing
fractal kinetics behaviour [3], where the rate coefficients for the diffusion
controlled reactions are not constants but they are depending on time. We
generalize the Berry’s algorithm for situations more physically realistic in
the cellular media [4, 5], as different degrees of mobility and different sizes
for big molecules and obstacles. We use a reformulation of Zipf-Mandelbrot
distribution [2]: k(t) = k0 (1 + t/τ )−h , in terms of the kinetic coefficient,
k0 , which will be only dependent on the conditions of the crowded media,
and not on initial conditions of reactants, and we refer as a classical kinetic
coefficient of the reaction. The other parameters will be dependent on the
initial conditions of the reactants and also on the crowded media. These
simulations suggest that in crowded media we always deal with a fractal-like
kinetics, but with different types of fractality depending on the crowding and
on the topological dimension (2D or 3D) of the cellular cytoplasm where the
reaction takes place.
1. Berry H., ”Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation”, Biophysical Journal, 83
(2002), 1891-1902
2. Schnell S., Turner T. E., ”Reaction kinetics in intracellular environments with macromolecular crowding”, Progress in Biophysics and Molecular Biology, 83 (2004), 235-251
29
Poster session II (June 8th ), Panel 7
82
Posters
3. Kopelman R., ”Rate processes on fractals: theorey, simulations and
experiments”, J. Stat. Phys., 42 (1986), 185-193
4. Isvoran A., Vilaseca E., Ortega. F., Cascante M., Mas F., ”About
implementing a Monte Carlo simulation algorithm for enzymatic reactions in crowded media”, Journal of Serbian Chemical Society, 71
(2005), 75-86
5. Isvoran A., Vilaseca E., Ortega. F., Garces J.L, Cascante M., Mas
F., ”Monte Carlo simulations of enzymatic reactions in 2D and 3D
croded media”, European Biophysical Journal with Biophysics Letters,
34 (2005), 566
83
XX Sitges Conference
Po.30
Single-chain folding of duplex DNA simulated by
association of loop structures: From an all-or-none
transition to an intra-chain phase segregation30
Takafumi Iwaki
Okayama Institute for Quantum Physics, Kyoyama 1-9-1, Okayama city,
Okayama 700-0015, Japan
Physical properties of DNA, in particular, physical changes of its structure
would be important in considering the relation of DNA to cellular activities.
Folding of a single duplex DNA chain is one of such structural transitions.
This transition has two physical aspects of a change in density and a parallel
ordering of segments. For example, it is widely known that a toroidal structure appears as a condensate of a T4 DNA molecule. In the present poster
presentation, we try to understand this phenomenon through the association
of loop structures. The double equilibrium of the formation of loops and
their association is considered. Free energy of a molecular chain and the
average number of aggregates on the chain are first calculated for a system
of aggregates with a typical surface energy. It is shown that the profiles
of these quantities essentially change according to the chemical potential of
loop structures. This suggests that the bending rigidity or formability of
the chain changes the nature of the transition from continuous aggregation
of loops to aggregation as a first-order phase transition, and further, to an
all-or-none folding transition of a single toroidal structure. In addition, we
consider a charged aggregate for which the interior is completely neutralized
by counter-ions. The analytical result of this model is shown and the relationship between the morphology and stability of a partially folded structure
is discussed.
30
Poster session II (June 8th ), Panel 23
84
Posters
Po.31
Folding pathways in single protein force experiments31
Ivan Junier
Departament de Fı́sica Fonamental, Facultat de Fı́sica, Universitat de Barcelona,
Digonal 647, 08028 Barcelona, Spain
Many biomolecules, such as proteins and RNA’s, relax in a two-state kinetic process. Upon cooling below the corresponding theta temperature, they
first collapse into a compact state (the ”molten globule” in the case of singledomain proteins) to subsequently fold into the native state. In the presence
of force, such scenario is still expected to be valid, and the two conformations (molten globule and native state) observable during a single-molecule
experiment. Recent experiments at constant force have shown a switch between the unfolded and a compact structure, presumably the molten-globule,
before reaching the native structure (see figure).
We have numerically studied the folding of on-latti-ce heteropolymers
under stretching forces. We found that in some condition (hydrophobic
monomers, low temperature) one could reproduce the three-state be-haviour
observed in the experiments. The intermediate state then corresponds to the
state which first forms during a force jump experiment. Depending on the
geometry, it can also be (or not) the intermediate state which early forms
during the thermal folding process, i.e. at zero force.
We also determined whether the observed intermediate states were always
on-pathway; in the presence of an off-pathway state, the heteropolymer needs
to unfold back before folding. We then propose force-jump protocols, that
can be applied to any biomolecule exhibiting a three-state behaviour, to
quantify the proportion of on/off-pathway states.
31
Poster session II (June 8th ), Panel 21
85
XX Sitges Conference
Po.32
Hydrodynamic Interactions between semiflexible
filaments32
Isaac Llopis
Departament de Fı́sica Fonamental, Facultat de Fı́sica, Universitat de Barcelona,
Digonal 647, 08028 Barcelona, Spain
Some biological filaments at physiological temperatures behave as semiflexible filaments, they are described by the worm-like chain model. The
cytoskeletal structure of the cell is constituted of actin filaments and microtubules, which are semiflexible. The DNA is another semiflexible filament.
They are mesoscopic objects that are suspended in a fluid, they live in
a low Reynolds number regime and the hydrodynamic interactions (HI) are
relevant to study their collective dynamics. We present a model that solves
numerically the equations of motion of a discretized and inextensible filament
suspended in a fluid, taking into account the HI:
1) The motion of a filament under a uniform field is already studied [1].
Here, we analyze in detail how this motion and morphology changes by
the presence of other filaments.
2) We modelize a flagella as a semiflexible filament driven at one end. The
velocity of a flagella changes by the presence of other driven filaments
and these changes depend on the flexibility of the chain and on the
number of flagella in the suspension.
1. M. Cosentino Lagomarsino, I. Pagonabarraga and C.P. Lowe, Phys.
Rev. Lett. 94, 148104 (2005).
32
Poster session I (June 6th ), Panel 15
86
Posters
Po.33
Force dependent fragility in RNA hairpins33
Maria Mañosas
Departament de Fı́sica Fonamental, Facultat de Fı́sica, Universitat de Barcelona
Diagonal 647, 08028 Barcelona Spain
We apply Kramers theory to investigate the dissociation of multiple bonds
under mechanical force and interpret experimental results for the unfolding
/ refolding force distributions of an RNA hairpin pulled at different loading
rates using laser tweezers. We identify two different kinetic regimes depending on the range of forces explored during the unfolding and refolding process.
The present approach extends the range of validity of the two-states approximation by providing a theoretical framework to reconstruct free-energy landscapes and identify force-induced structural changes in molecular transition
states using single mole-cule pulling experiments. The method should be
applicable to RNA hairpins withmultiple kinetic barriers.
33
Poster session II (June 8th ), Panel 20
87
XX Sitges Conference
Po.34
The role of tuning interactions of colloids in
sedimentation-difusion, stationary electrophoresis
and thermophoresis34
Miguel Mayorga
Facultad de Ciencias, Univ. Aut. Edo. Mex., Av. Instituto Literario 100, Toluca,
CP 50000, Mexico
Applying the mesoscopic thermodynamics scheme [1], we show how to obtain the density profile of a suspension of weakly interacting charged colloids
in a steady state situation. In the case of diffusophoresis, we analyze the
role of tuning interactions to reproduce experimental sedimentation profiles
[2]. For globular proteins under stationary electrophoresis, tuning the pair
interactions between particles permit a better interpretation of the experimental profiles [3] in terms of the collective diffusion and the electrophoretic
velocity [4]. On the other hand, we find that control of thermal diffusion
effects in colloidal dispersions can be accomplished upon tuning interactions
between particles [5]. Our results are compared with experiments in micellar
dispersions [6] and in DNA trapped by thermophoresis [7].
1. D. Reguera, J. M. Rubı́, J. M. G. Vilar, J. Phys. Chem. B 109 (2005)
21502
2. R. Piazza, T. Bellini, V. Degiorgio, Phys. Rev. Lett. 71 (1993) 4267
3. J. E. Godfrey, Proc. Natl Acad. Sci. 86 (1989) 4479
4. M. Mayorga, O. A. Hernández-Flores, J. Phys: Cond. Matter 16 (2004)
1
5. O. Hernández-Flores, M. Mayorga, L. Romero-Salazar, J.M. Rubı́ (in
preparation)
6. R. Piazza, A. Guarino, Phys. Rev. Lett. 88, 208302 (2002).
7. D. Braun, A. Libchaber, Phys. Rev. Lett. 89 (2002) 188103-1.
34
Poster session I (June 6th ), Panel 16
88
Posters
Po.35
MoDEL: Molecular Dynamics Extended Library35
Tim Meyer
Universitat Barcelona, Spain
Here we present the first analysis of protein family dynamics based on
the MoDEL Database. Today MoDEL contains over 1300 different proteins
which are considered representative for the over 30.000 proteins listed in the
PDB. All Simulations are run for 10ns using explicit water and ion representation and state of the art forcefields and simulation codes. Simulation data
is accessible on our webserver on:
http://mmb.pcb.ub.es/model.
35
Poster session I (June 6th ), Panel 22
89
XX Sitges Conference
Po.36
The precision of genetic oscillators and clocks36
Luis G. Morelli
Max Planck Institute for the Physics of Complex Systems, Biological Physics
Group, Nöthnitzer Str. 38, 01187 Dresden, Germany
Genetic oscillations are known to play a major role in driving important cellular processes, for example in circadian clocks, in the cell cycle, and
patterning the vertebrate body axis. Due to the stochastic nature of gene
expression, the period of these oscillations is subject to fluctuations. These
fluctuations limit the precision of the oscillator, which can be characterized
by the quality factor. We study the precision of genetic oscillators in a
simple but general stochastic feedback system. We show that high quality
oscillations are possible even when the number of molecules is low and amplitude fluctuations relatively large. We relate our results to circadian clocks
in bacteria, where high quality oscillations have been observed in single cell
experiments, in the absence of environmental cues.
36
Poster session I (June 6th ), Panel 5
90
Posters
Po.37
Depletion effects and loop formation in self-avoiding
polymers37
Minh Toan Ngo
SISSA – The International School for Advanced Studies, Via Beirut 2-4, Trieste,
34014 Italy
We deploy extensive Langevin dynamic simulations to study the looping
kinetics of a self-avoiding polymer both in an ideal buffer and in a crowded
solution of spherical colloidal particles, which models the nucleoplasm of an
eukaryotic cells. Crowding is treated effectively a-la Asakura-Oosawa, by
introducing a density-dependent viscosity and a two-body depletion interaction between different segments of the polymer. Our results are consistent
with a Rouse scaling for the mean first passage time as a function of length.
For very short chains we find that crowding increases the time that the ends
need to meet, due to the enhanced solvent viscosity. As the chain length
increases, our data display a crossover to another regime in which depletion
attractions render looping both more probable and more persistent. We discuss the relevance of our results to chromatin looping in vitro and in vivo,
where looping of several thousands of kilo-bases spontaneously form during
transcription in interphase.
37
Poster session I (June 6th ), Panel 17
91
XX Sitges Conference
Po.38
Domain formation of protein complexes in a
photosynthetic membrane38
Josep C. Pàmies, Raoul N. Frese and Daan Frenkel
FOM-Institut AMOLF, Kruislaan 407, 1098SJ, Amsterdam, The
Netherlands
The photosynthetic apparatus of purple photosynthetic bacteria contains
primarily two different, functionally connected pigment-protein complexes:
the peripheral light-harvesting LH2 and the core reaction-centre light-harvesting
RC-LH1. Atomic force microscopic (AFM) images and polarised-light spectroscopic data have shown these complexes to reside in two co-existing domains: highly-curved disordered domains comprised of LH2 only, and crystalline domains of long-range ordered RC-LH1. Here we show that these
features can arise solely from close packing and different preferential curvature of the proteins, without specific protein-protein interactions. Monte
Carlo simulations of a crowded model membrane demonstrate that the size
and shape asymmetry of the proteins is sufficient to induce lateral segregation with varying order. This may be of key importance in photosynthesis,
where both close packing and diffusion are a functional necessity.
38
Poster session II (June 8th ), Panel 14
92
Posters
Po.39
Cardiac dynamics: modelling the Brugada syndrome39
Angelina Peñaranda
Universitat Politècnica de Catalunya, EPSEB, Departament de Fı́sica Aplicada,
Dr. Marañon, 44-50, 08028 Barcelona, Spain
The Brugada syndrome is associated with an abnormal electrocardiogram
(ECG), characterized by an elevation of the ST-segment. Since its discovery
in 1992, it has gained increasing recognition, and today is believed to be
responsible for 4% to 12% of all sudden deaths and around 20% of deaths in
patients with structurally normal heart. Recently it has been discovered that
it is caused by a mutation in a specific gene (SCN5A), resulting in dysfunction
of the sodium channel in the membrane of cardiac cells. However, the link
between this channelopathy and the occurrence of arrhythmias or ventricular
fibrillation is, as yet, not completely understood. We have constructed a
simplified ionic model that reproduces well the action potential observed in
the Brugada syndrome. With its help, possible mechanisms for the induction
of reentrant waves (spirals) will be discussed.
39
Poster session I (June 6th ), Panel 24
93
XX Sitges Conference
Po.40
Relationship between DNA physical properties and
nucleosme structure40
Alberto Pérez
Universitat de Barcelona, Parc Cientı́fic de Barcelona, Josep Samitier,1-5, 08028
Barcelona, Spain
We use physical properties like the intrinsic flexibility of the different base
pair parameters to study the structure of the nucleosome.
40
Poster session I (June 6th ), Panel 25
94
Posters
Po.41
Functional dynamics of proteins and normal modes
at working temperatures41
Francesco Piazza
Ecole Politechnique Fédérale de Lausanne, Laboratoire de Biophysique
Statistique, LBS/ITP/SB, BSP-720, CH 101, Lausanne, Switzerland
The large-scale displacements involved in functional dynamics of proteins
are often well reproduced within the harmonic approximation of fluctuations close to the native state. In particular, in many cases only a few
low-frequency collective modes seem to provide the major contribution to
the spectral decomposition of relevant conformational changes.
We provide an example of this conceptual framework by reporting some
results for the PDZ binding domain, where we investigate the binding dynamics of the domain through normal modes calculations from elastic network
theory and simulations of an off-lattice native-centric coarse-grained model.
In general, however, the harmonic approximation is only justified in close
proximity of the equilibrium configuration. In this sense, the normal mode
patterns are traditionally interpreted as precursory displacement correlations
rooted in the protein structure.
In this study, we perform temperature-dependent Brownian dynamics unfolding simulations of selected binding domains with a native-centric, coarsegrained model. Our aim is to investigate the evolution with temperature of
the spectral weight associated with relevant normal modes in reconstructing
the fluctuations away from the native structure. Remarkably, we find that
structural fluctuations are well described by a limited number of modes even
at temperatures close to the protein working point. In the examined cases,
these modes are the same that express the displacement patterns correlated
with the biological activity of the protein.
41
Poster session II (June 8th ), Panel 26
95
XX Sitges Conference
Po.42
Microscopic swimming arising from reaction
diffusion equations42
Christopher Pooley
Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble
Road, Oxford, OX1 3NP, UK
We propose a mechanism for a micron-scale artificial propulsion system.
Movement is achieved by producing non-reversible, snake-like distortions in
a long, thin piece of responsive material lying in a fluid. By responsive
material, we refer to a material that can expand or contract in response to a
chemical concentration change. The concentrations of the chemical species
are modeled by simple reaction diffusion equations. We make no specific
assumptions about the nature of the reactions, and, with the use of a genetic
algorithm, find efficient swimmer solutions. To understand the behavior of
the evolved solutions, a simplified set of equations is proposed, which captures
the salient features of the system. This allows us to place bounds on different
parameters within the model, and accordingly permits the mapping of the
results onto a real system.
42
Poster session II (June 8th ), Panel 6
96
Posters
Po.43
A physical interpretation of the microbial growth rate
temperature dependence43
Clara Prats
Escola Superior d’Agricultura de Barcelona, Departament de Fı́sica i Enginyeria
Nuclear, Campus del Baix Llobregat, Universitat Politècnica de Catalunya, Av.
del Canal Olı́mpic s/n, 08860 Castelldefels, Barcelona, Spain
Ratkowsky et al. (1982, 1983) looked for an experimental relationship
between the microbial growth rate and the temperature. They established
an empirical non-linear regression model which is known as Ratkowsky’s
model. This equation has been fitted with success to many data from different bacterial cultures at different temperature ranges, from psycrophilic to
thermophilic conditions. A physical or chemical explanation for this experimental dependence is necessary.
We propose a microscopic explanation based on the brownian behaviour
of the nutrient particles. The premise is that the cell growth is limited by
the total nutrient particles that enter the cell per unit of time. Both nutrient
concentration and system temperature fix the amount of nutrient particles
that are accessible for the cell during a certain time interval, which is the
first limiting factor. Another limiting factor is the fraction of the cellular
surface where the nutrient particles entrance is allowed. We have checked this
model with Individual-based Modelling simulations (Ginovart et al., 2002),
using Blackman’s kinetics to model the nutrient uptake and growth of each
individual cell. The results show that the Ratkowsky’s culture behaviour
emerges from these simple physical rules.
This physical interpretation can be generalized to other systems where
there is not a biological control of the temperature, like the growth of certain fish or vegetables under some specific conditions. It can also be used to
understand the quadratic dependence with the temperature of other experimental parameters of the bacterial cultures, such as salinity or water activity
among others.
– Ratkowsky, D.A., Lowry, R.K., McMeekin, T.A., Stokes, A.N. and
Chandler, R.E., 1983. ”Model for bacterial culture growth rate throughout the entire biokinetic temperature range”, J. Bacteriol. 154, 12221226
43
Poster session I (June 6th ), Panel 9
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– Ratkowsky, D.A., Olley, J., McMeekin, T.A., and Ball, A., 1981. ”Relationship between temperature and growth rate of bacterial cultures”,
J. Bacteriol. 149, 1-5
– Ginovart, M., Lpez, D., Valls, J., 2002. ”INDISIM, and individual
based discrete simulation model to study bacterial cultures”, J. theor.
Biol. 214, 305-319
98
Posters
Po.44
Thin film formation of electrosprayed polymer
Solutions; Can nonequilibrium thermodynamics be
applied?44
Ivo Rietveld, Kei Kobayashi, Hirofumi Yamada, Kazumi Matsushige
Kyoto University, Dept. of Electronic Science and Engineering, A1-326 Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
Ultra thin polymer films are difficult to make. Electrospray appears to
be a promising, fast method to produce nanoscale polymer films. However,
as in all nanoscale engineering methods, many parameters have an influence
on the eventual film morphology; therefore polymer films have been prepared
under varying conditions and have been studied with AFM to single out the
major factors contributing to film morphology.
The electrospray method consists of a liquid spray induced by a strong
electric field. Generally a liquid is led through a thin capillary with a high
potential in the order of 5 kV. At the tip of the nozzle a liquid cone will
form from which a jet emanates. The jet breaks up into small monodisperse
droplets of about 1 micron in diameter. Electrospray has been thoroughly
studied and most parameters that control droplet size and droplet charge
are well understood. By adding a solute to the sprayed liquid, monodisperse
particles can be produced. These particles can be used in aerosol applications
or for the production of thin films.
The process of thin film production with electrospray can be divided into
four subprocesses: 1) steady state cone-jet, 2) droplet formation 3) droplet
evolution 4) deposition and film formation. Subprocess 1 and 2 have already
been studied in relation to electrospray [1, 2]. Droplet evolution (3) is fairly
well understood. However the combination of these four subprocesses is
much less studied. One of the major difficulties is that parameters with a
particular effect in one of the subprocesses can have a different effect in other
subprocesses. Parameters, affecting various subprocesses, are for example the
solvent, the conductivity of the solution and the temperature.
Making use of the knowledge of the subprocesses 1 to 3, this study is
focused on the effects of parameters during droplet evolution (3) and deposition (4). The main parameters are droplet size (evaporation time and
particle size), spray distance (drying of the droplet/particle), initial polymer
concentration (particle size at deposition), temperature (evaporation time
44
Poster session I (June 6th ), Panel 18
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XX Sitges Conference
and polymer mobility on the substrate) and spray time (film thickness) [3].
Different morphologies have been observed depending on the parameters.
Under wet conditions films containing polymer crystals can form. Smooth
continuous polymer film can be found for drop-lets with a higher polymer
concentration. Dry particles will create rough films.
With global control over film morphology we intend in a future approach
to make use of Mesoscopic Nonequilibrium Thermodynamics (MNET), developed among others by Prof. Rubi [4], to describe the film formation process
in the case of the continuous polymer films. Flow is expected to play a major role in this process. MNET could provide understanding of how viscosity
and droplet size can be used to control film morphology. This may lead to
an improvement of the films made with electrospray; for example it may improve the control over the crystallinity in the film, which is often a desired
property in applications.
1. R.P.A. Hartman et al., J. Aerosol Sci., 31 (2000) 65
2. A.M. Ganan-Calvo, Phys. Rev. Lett., 79(2) (1997) 217
3. I.B. Rietveld et al., J. Colloid Interface Sci., 298(2) (2006) 639
4. D. Reguera et al., J. Phys. Chem. B 109, (2005), 21502
100
Posters
Po.45
Finite-size effects in intracellular microrheology45
Ivan Santamaria-Holek
Departamento de Fı́sica, Facultad de Ciencias, Universidad Nacional Autónoma
de México, Circuito Universitario Exterior 04510, Mexico
We propose a model to explain finite-size effects in intracellular microrheology observed in experiments. The constrained dynamics of the particles in
the intracellular medium, treated as a viscoelastic medium, is described by
means of a diffusion equation in which interactions of the particles with
the cytoskeleton are modelled by a harmonic force. The model reproduces
the observed power-law behavior of the mean-square displacement in which
the exponent depends on the ratio between particle-to-cytoskeleton-network
sizes.
45
Poster session I (June 6th ), Panel 19
101
XX Sitges Conference
Po.46
Fluctuation theorems for chemical reaction networks46
Tim Schmiedl
Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57 / III,
D-70550 Stuttgart, Germany
For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent
nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy,
applied (chemical) work and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the
entropy of the network itself and the entropy of the medium. The latter is
given by the exchanged heat identified through the first law. Total entropy
production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem
for networks in the steady state. Further exact relations like a generalized
Jarzynski relation and a generalized Clausius inequality are discussed. We
illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different
steady states.
46
Poster session I (June 6th ), Panel 4
102
Posters
Po.47
Defining the local temperature of adsorbed argon in a
nanoporous zeolitic membrane47
Jean-Marc Simon, Dick Bedeaux and Signe Kjelstrup
Department of Chemistry, Norwegian University of Science and Technology, NO
7491 Trondheim, Norway
The temperature of an adsorbed phase under equilibrium conditions is
supposed to be homogeneous and equal to the surroundings. In this study
we investigated the local temperature of adsorbed argon in a membrane of
nanoporous zeolite, the silicalite, in equilibrium with a gas of argon using
molecular dynamics simulations under different temperatures. Temperatures
were calculated in two ways, using the kinetic energy, the kinetic temperature Tkin, and using the instantaneous configurations, the configurational
temperature Tconf. These temperatures were computed for each molecule
separately along their trajectories and averaged locally.
As expected, the results showed that the global temperature of the adsorbed phase was identical to the gaseous phase within the statistical uncertainties both for Tkin and Tconf. This verified the equipartition principle
for the global temperature. We also verified that the two approaches for
Tkin and Tconf gave the same value of the local temperature. However, a
surprisingly strong dependance of the local values of these temperatures was
observed with the interaction potential energy of the adsorbed molecules with
the zeolite. The temperatures increased with the interaction energy. For a
simulation at a global temperature of 200 K their values ranged from 50 to
280 K, for example. An analysis of the time averaged local velocities exhibited also a surprising strong dependance on the acceleration. These results
showed that the local thermodynamics properties of the adsorbed molecules
are strongly influenced by their near surroundings, with stabilized hot and
cold spots separated by a few angstroms of distance.. The existence of these
spots means that for the system studied the transfer of energy is not efficient
enough to equilibrate the local temperatures. Consequently the minimum
size of a thermodynamics system, which can be considered to be in local
equilibrium, must be at least of the order of a crystalline cell.
47
Poster session II (June 8th ), Panel 15
103
XX Sitges Conference
Po.48
Monte-Carlo simulations of discrete vesicular
membranes48
Maarten van Wieren
EURANDOM, Postbox 513, 5600 MB, Eindhoven, The Netherlands
One possible approach in finding relations between physics and biology, is
to go back to the roots of life. Within this context, one would like to estimate
the probability of spontaneous fission of vesicles as a function of the relevant
parameters, since it would provide a simple and efficient alternative to the
highly structured forms of cell-fission observed in life today. Here we present
the results of Monte Carlo simulations of discrete membranes bahaving according to the spontaneous curvature model introduced by Helfrich. In this
way we may take into account the influence of fluctuations of the shape as
the surface to volume ratio increases during growth. They offer insight into
the relevance of spontaneous fission for applications in artificial life as well
as for possible early vesicular life forms.
48
Poster session II (June 8th ), Panel 16
104
Posters
Po.49
Protein Folding in All-Atom Models by Zipping and
Assembly49
G. Albert Wu
Dept. of Pharmaceutical Chemistry, University of California, UCSF Box 2240,
San Francisco, CA 94143-2240, USA
We present zipping and assembly (ZA) as a new folding principle for small,
single-domain proteins. ZA suggests that local structuring occurs along the
chain at early times, followed by either substructure growth (zipping) or
coalescence with other substructures (assembly). We have implemented a
ZA-based computer algorithm that uses replica exchange molecular dynamics with the AMBER7 force fields and the GB/SA implicit solvent model.
The algorithm has been applied to the folding of 9 proteins (residues 25-73,
both alpha and beta) starting from extended chains, with 8 of them folded to
within an average of 2.2 Angstroms rmsd from the experimental structures
in 300 CPU days or less. In addition, experimental Phi values, where available on these proteins, are consistent with the predicted routes. This work
shows that physics-based protein structure prediction may be competitive
with bioinformatic methods for small proteins.
49
Poster session II (June 8th ), Panel 25
105
XX Sitges Conference
Po.50
Transporting of a Cell-Sized Phospholipid Vesicle
Across Water/Oil Interface50
Ayako Yamada
Department of Physics, Kyoto University, 3-2-501 Tanaka Genkyo-cho, Sakyo-ku,
Kyoto City, Kyoto 606-8201, Japan
We transferred a cell-sized phospholipid W/O emulsion from an oil phase
to a water phase across the water/oil interface to make a liposome.
50
Poster session II (June 8th ), Panel 3
106