Date :

 13, 16 April 2012

Place :

 The auditorium on 1st floor, Institute of Physics, Academia Sinica, Taipei

 National Center for Theoretical Sciences (Critical Phenomena and Complex Systems focus group)

 Institute of Physics, Academia Sinica (Taipei)

 Miss Chia-Chi Liu (Secretary, Physics Division, NCTS)
 Tel:(886)-2-33665566; Fax:(886)-2-33665565; E-mail: ccliu@phys.ntu.edu.tw

Speakers :

Prof. Ping Ao

Shanghai Center for Systems Biomedicine and Department of Physics, Shanghai Jiao Tong University, Shanghai, China

E-mail: aoping@u.washington.edu

Towards a Universal Dynamical Structure for Nonequilibrium Processes: biological perspective

Recently motivated by study in biology a new approach to nonequilibrium processes was found. A pronounced feature of such approach is its natural solution to the outstanding problem of absence of detailed balance. In the presentation I will discuss the key steps of this approach, along with two other provocative implications: generalized Einstein relation and implication of stochastic integration beyond classical Ito process. The experimental verifications will be discussed, too.

References:

[1] Potential in Stochastic Differential Equations: Novel Construction, P. Ao, J. Phys. A 37 L25-L30 (2004). http://www.iop.org/EJ/abstract/0305-4470/37/3/L01/
[2] Structure of Stochastic Dynamics near Fixed Points, C. Kwon, P. Ao, and D.J. Thouless, Proc. Natl. Acad. Sci. (USA) 102 (2005) 13029-13033. http://www.pnas.org/content/102/37/13029.full.pdf+html
[3]  Nonequilibrium Approach to Bloch-Peierls-Berry Dynamics, J.C. Olson and P. Ao, Phys. Rev. B 75, 035114 (2007). http://link.aps.org/abstract/PRB/v75/e035114
[4] Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics, P. Ao, Communications in Theoretical Physics 49 (2008) 1073-1090. http://ctp.itp.ac.cn/qikan/Epaper/zhaiyao.asp?bsid=2817
[5] Constructive Proof of Global Lyapunov Function as Potential Function. Ruoshi Yuan, Yian Ma, Bo Yuan, Ping Ao. Submitted.
http://arxiv.org/PS_cache/arxiv/pdf/1012/1012.2721v1.pdf
　

Prof. Ya-Hui Chou

Institute of Cellular and Organismic Biology, Academia Sinica, Taiwan

E-mail: yhchou@gate.sinica.edu.tw

The Assembly and Wiring Variability of Drosophila Olfactory Circuit

Neuronal diversity and variability are two general phenomena of neuronal circuits.  Yet, largely due to the complexity of nerve systems, little has been known how neuronal variability of a circuit is achieved nor its consequence to individual behaviors. Drosophila olfactory system is a great model to study mechanisms of neural circuit wiring and variability in terms of its similar but simpler composition than mammalian systems and its tremendous capacity of instructing diverse delicate behaviors. Our previous study with comprehensively sampling more than 1500 olfactory local interneurons (LNs) demonstrates that these neurons not only exhibit extensive diversity but also variability. The variability signature of LNs offers an unprecedented system to study the mechanisms underlying neuronal variability and the consequence of neuronal variability to individual behaviors. In my talk I will first introduce our ongoing LN projects, followed by a deeper discussion of the unpublished TC LN system.

References:

[1] Chou, Y.H., Spletter, M.L., Yaksi, E., Leong, J.C.S., Wilson, R.I. and Luo, L., Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe,  Nat. Neurosci. 13, 439-449 (2010).

Prof. Marek Cieplak

Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland

E-mail: mc@ifpan.edu.pl

1. Mechanostability of Proteins and Virus Capsids

  Molecular dynamics of proteins within coarse grained models have become a useful tool in studies of large scale systems. The talk will discuss two applications of such modeling. The first is a theoretical survey of proteins' resistance to constant speed stretching as performed for a set of 17134 simple and 318 multidomain proteins. The survey has uncovered new potent force clamps.
  They involve formation of cysteine slipknots and lead to characteristic forces that are exceeding significantly larger than the shear-based clamp observed in
titin. The second application involves studies of nanoindentation processes in virus capsids and elucidates their molecular aspects by showing deviations in behavior compared to the continuum shell model.

References:

[1]  M. Sikora, J. I. Sulkowska, and M. Cieplak, Mechanical strength of 17134 model proteins and cysteine slipknots. PLoS Computational Biology,5, e1000547 (2009).

[2] M. Sikora, J. I. Sulkowska, B. S. Witkowski, and M. Cieplak BSDB: the Biomolecule Stretching Database, Nucl. Acid. Res. 39, D443-D450 (2011).

[3] M. Cieplak and M. O. Robbins, Nanoindentation of virus capsids in a molecular model. J. Chem. Phys. 132, 015101 (2010).

2.Denaturation of Proteins near Polar Surfaces

  All-atom molecular dynamics simulations for proteins placed near a model mica surface indicate existence of two types of evolution. One type leads to the surface-induced unfolding and the other just to a deformation. The two behaviors are characterized by distinct properties of the radius of gyration and of a novel distortion parameter that distinguishes between elongated, globular, and planar shapes. They also differ in the nature of their single site diffusion and two-site distance fluctuations. The two proteins chosen for the studies, the tryptophan cage and protein G, are small to allow for a fair determination of the forces generated by the surface as the effects of finite cutoffs in the Coulombic interactions are thus minimized. When the net charge on the surface is set to zero artificially, infliction of deformation is seen to persists but no unfolding is observed.

References:

[1] A. Starzyk and M. Cieplak, Denaturation of proteins near polar surfaces,J. Chem.Phys. 135, 235103 (2011).

3.From Gene Expressions to Genetic Networks

  A method based on the principle of entropy maximization is used to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles [1]. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher order correlations. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabollic oscillations identifies a gene interaction network that reflects the intracellular communication pathways. These pathways adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems. The time-dependent behavior of the genetic network is found to involve only a few fundamental modes [2,3].

References:

[1]  T. R. Lezon, J. R. Banavar, M. Cieplak, A. Maritan, and N. Fedoroff, Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns, Proc. Natl. Acad. Sci. (USA) 103, 19033-19038 (2006).

[2] N. S. Holter, M. Mitra, A. Maritan, M. Cieplak, J. R. Banavar, and N. V. Fedoroff, Fundamental patterns underlying gene expression profiles: simplicity from
complexity, Proc. Natl. Acad. Sci. USA 97, 8409-8414 (2000).

[3] N. S. Holter, A. Maritan, M. Cieplak, N. V. Fedoroff, and J. R. Banavar, Dynamic modeling of gene expression data, Proc. Natl. Acad. Sci. USA 98, 1693-1698 (2001).

Dr. Muyoung Heo

Center for Proteome Biophysics, Pusan National University, Korea

E-mail: mheo@pusan.ac.kr

A First-Principle Model of a Living Cell Reveals Evolutionary Relationships among Physical-Chemical Properties of Proteins

  How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and  binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein–protein interaction (PPI) subnetworks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical–chemical properties of protein interactions and their abundances due to a “frustration” effect: Strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. On the basis of these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture–mass spectroscopy experiments can detect functional interactions with high fidelity only for high-abundance proteins while missing most interactions for low-abundance proteins.
　

Prof. Michal Hnatič

Institute of Experimental Physics Slovak Academy of Sciences, Košice, Slovakia

E-mail: hnatic@sors.com

Field-Theoretic Approach to the Kinetics of Reaction Processes: Role of Density and Velocity  Fluctuations

  The irreversible annihilation reaction of two identical particles  is a fundamental model of non-equilibrium physics. The reacting particles perform chaotic motion due to diffusion or some external advection field such as atmospheric eddy and may react after the mutual collision with constant microscopic probability  per unit time. Implicitly it is assumed that resulting molecule is inert, i.e. chemically inactive, and has no influence on the movement of the reacting particles. Many reactions of this type are observed in diverse chemical, biological or physical systems.

  The usual approach to this kind of problems is based on the use of the kinetic rate equation (KRE). It leads to a self-consistent description analogous to the mean-field approximation in the theory of critical phenomena. This equation predicts a long-time asymptotic decay of the mean particle number  proportional to $ t^{-1}$ and the decay exponent does not depend on the space dimension. This is a common situation observed in the mean field theory.

 However, it turns out  that in lower space dimensions $d\leq 2$ the assumption of spatially uniform density, or equivalently of negligible density fluctuations of reacting particles, is not appropriate, and we are challenged to construct new appropriate theoretical tools .

  A typical reaction occurs in liquid or gaseous environment. Thermal fluctuations of this underlying environment cause additional advection of the reacting particles. Therefore, it is interesting to study the influence of the advection field on the annihilation process.

  I am going to analyze  the advection of reactive scalar using random velocity field generated by the stochastic Navier-Stokes equation, which is used for production   a velocity field corresponding to thermal fluctuations  and/or  a turbulent velocity field with the Kolmogorov scaling behavior [1-4]. The aim  is to examine the long-time (infrared = IR) behavior of the annihilation process under the influence of advecting velocity fluctuations and to determine its stability. Using mapping procedure based on the Doi formalism an effective field-theoretic model for the annihilation process is constructed. A powerful tool for analyzing asymptotic behavior of stochastic systems is provided by the renormalization-group (RG) method. It allows to determine IR asymptotic regimes of the system and also is very efficient tool for calculation of various universal physical quantities, e.g. critical exponents.

  Actually, RG method is applied on the model and within the two-parameter expansion the renormalization constants and fixed points of the renormalization group are determined in the two-loop approximation.

The non-linear integro-differential equation, which includes first non-trivial corrections to the KRE, is obtained for the mean particle number and it is shown how the information about IR asymptotics can be extracted from it. 

References:

[1] Hnatich M., Honkonen J., Velocity -fluctuation-induced anomalous kinetics of the A+A -> 0 reaction, Phys. Rev. E 61, 3904-3911(2000).

[2] M.Hnatich, J.Honkonen, T.Lucivjansky, Field theory approach in kinetic reaction: Role of random souces and sinks, Theor. and Math.  Physics 169 (1) 1489  –1498 (2011).

[3] M.Hnatich, J.Honkonen, T.Lucivjansky, Study of anomalous kinetics of annihilation reaction A+ A -> 0, Theoretical and Matnematical Physics 169 (1) 1481 -1488 (2011).

[4] Field-theoretic study of the reaction process A+ A -> 0, submitted to  PRE

Prof. Peter Kopčanský

Institute of Experimental Physics, Slovak Academy of Sciences, Wastonova 47, Košice, Slovakia

E-mail:

Structuralization Phenomena in Complex Systems Containing Nanosized Magnetic Particles

  The presence of very low concentration of magnetic nanoparticles (with volume fraction 10^-3) can significantly influence structuralization effects in composite systems. In this lecture two composite systems will be presented. The first one is the system with liquid crystal i.e. so called ferronematic, ferrosmectic or ferrocholesteric, respectively. The addition of nanosized magnetic particles to liquid crystal matrix can change the sensitivity of these materials to application of magnetic field due to increasing to magnetic susceptibility of complex systems. The influence of sensitivity to magnetic fields on the shape of magnetic nanoparticles will be discussed as well as structural Fredericksz transitions. The presence of magnetic nanoparticles can induce isotropic-nematic transition in magnetic field which are 10 times lower than in pure liquid crystals. The addition of magnetic nanoparticles can influence also sensitivity to very low magnetic fields. This is promising for the constructions of magnetovision camera like thermovision camera for mapping of external magnetic fields [1– 3]. The second presented system in which presence of magnetic particles change the properties will be amyloid structures which are responsible for neurodegenerative diseases as Alzheimer, Parkinson, Huntington and/or Diabetes Mellitus II. Inhibition and depolymerization effects in two systems of amyloid aggregates as Hen Egg White Lysozyme (HEWL) [4] and Insuline [5] will be presented.

References:

[1] TOMAŠOVIČOVÁ, N. - KOPČANSKÝ, P. - KONERACKÁ, M. - TOMČO, L. - ZÁVIŠOVÁ, V. - TIMKO, Milan - ÉBER, N. - FODOR-CSORBA, K. - TÓTH-KATONA, T. - VAJDA, A. - JADZYN, J. The structural transitions in 6CHBT-based ferronematic droplets. Journal of Physics : Condensed Matter., 20, no. 20, 204123-1-5 (2008).

[2] KOPČANSKÝ, P. - TOMAŠOVIČOVÁ, N. - KONERACKÁ, M. - ZÁVIŠOVÁ, V. - TIMKO, M. - DŽAROVÁ, A. - ŠPRINCOVÁ, A. - ÉBER, N. - FODOR-CSORBA, K. - TÓTH-KATONA, T. - VAJDA, A. - JADZYN, Jan. Structural changes in the 6CHBT liquid crystal doped with spherical, rodlike, and chainlike magnetic particles. Physical Review E., 78, 011702-1-5 (2008).

[3] MITRÓOVÁ, Z. - TOMAŠOVIČOVÁ, N. - TIMKO, M. - KONERACKÁ, M. - KOVÁČ, J. - JADZYN, Jan - VÁVRA, I. - ÉBER, N. - TÓTH-KATONA, T. - BEAUGNON, E. - CHAUD, X. - KOPČANSKÝ, P. The sensitivity of liquid crystal doped with functionalized carbon nanotubes to external magnetic fields. New Journal of Chemistry, 35, no. 6, 1260-1264 (2011).

[4] KONERACKÁ, M. - BELLOVÁ, A. - BYSTRENOVÁ, E. - KONERACKÁ, M. - KOPČANSKÝ, P. - VALLE, Francesco - TOMAŠOVIČOVÁ, N. - TIMKO, M. - BÁGEĽOVÁ, J. - BISCARINI, F. - GAŽOVÁ, Z. Effect of Fe3O4 magnetic nanoparticles on lysozyme amyloid aggregation. Nanotechnology, 21, no. 6, art. no. 065103 (2010).

[5] SIPOSOVA, K. - KUBOVCIKOVA, M. - BEDNARIKOVA, Z. - KONERACKA, M. - ZAVISOVA, V. - ANTOSOVA, A. - KOPCANSKY, P. - DAXNEROVA, Z. - GAZOVA, Z. Depolymerization of insulin amyloid fibrils by albumin-modified magnetic fluid. Nanotechnology 23, 2012 055101 (2012) .

Prof. Sasun Gevorgyan

Yerevan Physics Institute, Yerevan, Armenia

E-mail:gevorgyan@phys.sinica.edu.tw

The New Use of Light Pressure: A New Method for Studying the Mechanical Properties of Biopolymers in the Solid Phase

  To capture, translate, and manipulate microscopic particles, such as dielectric microspheres and cells, researchers use the optical trapping technique. Ashkin and co-workers demonstrated optical trap using a single beam. It was consequently called a single-beam gradient trap or optical tweezers [1-4]. In the single-beam gradient force trap, the beam is strongly focused on a diffraction-limited spot by a high-numerical-aperture objective. The relation of refractive index between the micro object and surrounding medium in this trapping system is critical factor for trapping [5]. No optical trap by the conventional trapping system was created at all because of the reflection of light, which gives rise to a scattering force. However, they could not levitate a micro object against the gravity. They tried to levitate a micro object by the laser beams emerging from plural optical fibers [6, 7].

  In this work, we demonstrate а new simple method to study the viscoelastic properties of biopolymers in the air. For the first time, that light pressure is used to deviate a sample from the equilibrium position, and the force of gravity is overcome by the elasticity of the sample. The advantages of the method have been demonstrated on the DNA fibers. Using the B-A transition  as an example process, the  sensitivity of the method to the intramolecular phase transformations has been shown.

References:

[1] A. Ashkin, Phys. Rev. Lett. 24, 156 (1970).

[2] A. Ashkin and J. M. Dziedzic, Appl. Phys. Lett. 19, 283 (1971).

[3] A. Ashkin and J. M. Dziedzic, Appl. Phys. Lett. 28, 333 (1976).

[4] A. Ashkin, J. M. Dziedzic, J. E. Bjorkholm, and S. Chu, Opt. Lett. 11, 288 (1986).

[5] Taguchi, K., Electron Lett., 33, pp.413-414 (1997).

[6] Taguchi, K., Optical and Quantum Electronics, 33, pp.99-106 (2001).

[7] Taguchi, K., Optics Communications, 194, pp.67-7 (2001).

Prof. Hisashi Okumura

Research Center for Computational Science, Institute for Molecular Science, Okazaki, Japan

E-mail: hokumura@ims.ac.jp

New Type of the Hamiltonian Replica-Exchange Molecular Dynamics Method

  Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics and Monte Carlo simulations in physical ensembles, such as the canonical and isobaric-isothermal ensemble, tend to get trapped in these local-minimum states. In order to avoid this difficulty, generalized-ensemble algorithms such as the multicanonical algorithm and replica-exchange method are frequently employed.

  We proposed a new type of the Hamiltonian replica-exchange method [1], where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution again and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical and replica-exchange methods.

References:

[1] S. G. Itoh, H. Okumura, Y.Okamoto: J. Chem. Phys. 132, 134105 (2010).

Dr. Jaroslav Skrivanek

Sors Research, Kosice, Slovakia

E-mail: skrivanek@sors.com

1.About Homogeneous Loop Closure in Polymers

  The loop closure in polymers via insertion of an arbitrary number of geometrically identical elements can be efficiently achieved using basic principles of spherical geometry. Described formalism does not work with a coordinate system. In this presentation the problem is concisely reduced to an equation of only one single unknown.

2.Prompt Evaluation of Covariance Matrix Forecasts

  We present a prompt method, which would allow to evaluate and compare various forecasts (m,H) of the mean vector and the covariance matrix of a random vector X. The proposed criterion can be additionally employed in the construction of an objective function when optimizing parameters of automatic forecast systems. This work was initialy motivated by the lack of appropriate expertise appraisals, promptly evaluating particular mean and covariance matrix forecasts, appreciating their adequacy and accuracy. Covariance matrix forecasts of financial asset returns are an important component of current practice in financial risk management. Even though there is a wide variety of models available for generating such forecasts, the ways to compare and evaluate them are not much developed by now.
　

Prof. Gwoing Yu

Department of Computer Science, Memorial University of Newfoundland, St John's, Canada 

E-mail: gwoing_yu@yahoo.com

Evolutionary Stable Strategies in Quantum Penny Flip Games

Prof. Bo Zheng

Department of Physics, Zhejiang University, Hangzhou, P.R. China

E-mail: bozheng@zju.edu.cn

Spatial and Temporal Structure in Financial Systems

  With the daily and minute-to-minute data of the American, German and Chinese stock markets, we compute the spatial and temporal correlation functions. Taking into account the signs of the components in the eigenvectors of the cross-correlation matrix, we explore the sector and subsector structure. Based on the cross-correlation decomposition, we study the temporal correlations and relevant dynamic characteristics.