Unfolding designable structures

Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are unusually stable, a property called the designability principle. In this paper we use the 2D hydrophobic-polar lattice model to classify structures according to their designability, and Langevin dynamics to account for their time evolution in the presence of shear flow. We demonstrate that, among all possible folds, the more designable ones are easier to unfold due to their large number of surface-core bonds.     

Small polaron migration in LixMn2O4: From first principles calculations

Migration of small polarons in λ-MnO₂, Li_0.5Mn₂O₄ and LiMn₂O₄ is studied via first principles calculations. Migration energy barriers of single small polaron migrations in λ-MnO₂, Li_0.5Mn₂O₄ and LiMn₂O₄ are 0.22 eV, 0.45 eV and 0.35 eV, respectively. The energy level changes of Mn-3d states along the polaron migration path are analyzed in detail. Results indicate that the activation energy barrier of polaron migration is strongly associated with the energy level shift of Mn-3dz² orbital, which is dependent on the short range structural arrangement of Mn³⁺/Mn⁴⁺ in the crystal. The electrical conduction properties of Li_xMn₂O₄ at room temperature are then discussed.     

Conduction transition of nano-scaled molecular wires driven by environment coupling

We propose a hybridization model to simulate a molecular wire coupling with the environmental molecules. Results reveal that the conduction transition from conducting to semiconducting depends on the coupling strength. In our simulations, the non-equilibrium Green's function method is employed to calculate the current-voltage relationship for the molecular wire through metallic contacts. Our calculations show that the band gap can be manipulated from the outside molecules coupling. Temperature dependence of the conductivity is represented in our results with strong dependence in high temperature range, which is qualitatively comparable with the experimental results of DNA. In our results, with small coupling, the current is enhanced by the exchange. On the contrary, too large a coupling results in localization of the transport carriers, leading to a semiconducting like property. We try to associate this study with the conducting property of DNA, which can be manipulated by environmental modulation.     

Effects of population mixing on the spread of SIR epidemics

We study dynamics of spread of epidemics of SIR type in a realistic spatially-explicit geographical region, Southern and Central Ontario, using census data obtained from Statistics Canada, and examine the role of population mixing in epidemic processes. Our model incorporates the random nature of disease transmission, the discreteness and heterogeneity of distribution of host population.We find that introduction of a long-range interaction destroys spatial correlations very easily if neighbourhood sizes are homogeneous. For inhomogeneous neighbourhoods, very strong long-range coupling is required to achieve a similar effect. Our work applies to the spread of influenza during a single season.     

Strategies for the separation of polyelectrolytes based on non-linear dynamics and entropic ratchets in a simple microfluidic device

We perform Monte Carlo simulations of an existing electrophoretic microchannel device used for the size separation of large DNA fragments. This device is normally operated with a constant (dc) driving field. In contrast, we consider the case of a varying (ac) driving field, in the zero-frequency limit. We find that a time-asymmetric pulse can yield interesting migration regimes, in particular bidirectional transport for different molecular sizes. We also study a spatially asymmetric version of the device and show that it can rectify unbiased but non-equilibrium molecular motion, in agreement with previous predictions for entropic ratchets. Finally, at finite frequency we uncover a resonance for the molecular velocity in the channel which could lead to improved performance. Received: 16 November 2001 / Accepted: 11 February 2002 / Published online: 22 April 2002     

Scaling regimes for second layer nucleation

Nucleation on top of two-dimensional islands with step edge barriers is investigated using scaling arguments. The nucleation rate is expressed in terms of three basic time scales: the time interval between deposition events, the residence time of atoms on the island, and the encounter time required for atoms forming a stable nucleus to meet. Application to the problem of second layer nucleation on growing first layer islands yields a sequence of scaling regimes with different scaling exponents relating the critical island size, at which nucleation takes place, to the diffusion and deposition rates. Second layer nucleation is fluctuation-dominated, in the sense that the typical number of atoms on the island is small compared to , when the first layer island density exponent satisfies . The upper critical nucleus size, above which the conventional mean field theory of second layer nucleation is valid, increases with decreasing dimensionality. In the related case of nucleation on top of multilayer mounds fluctuation-dominated and mean field like regimes coexist for arbitrary values of the critical nucleus size . Received 4 September 2000     

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs

Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.     

Chromatin physics: Replacing multiple, representation-centered descriptions at discrete scales by a continuous, function-dependent self-scaled model

This commentary on the inspiring works and ideas by Langowski, Mangeol et al., Lee et al., Bundschuh and Gerland, Schiessel, Vaillant et al., Lesne and Victor, Claudet and Bednar, Fuks, Allemand et al., and Blossey, all appearing in this issue (Eur. Phys. J. E 19 (2006)), expresses our felt need of novel approaches to chromatin modeling.     

Vectorial representation of single- and multi-domain protein folds

We discuss a vectorial representation applicable to both single- and multi-domain protein folds. This generalized vectorial representation is essentially identical to the previously described vectorial representation for single-domain proteins folds when applied to these, but allows for the additional consistent representation of multi-domain structures. We show that the generalized vectorial representation enables the accurate analytical prediction of site-specific amino acid distributions for both single- and multi-domain protein folds, similarly as the previously described vectorial representation does for single-domain folds.