Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Cosmological perturbations from stochastic gravity

In inflationary cosmological models driven by an inflaton field the origin of the primordial inhomogeneities which are responsible for large-scale structure formation are the quantum fluctuations of the inflaton field. These are usually calculated using the standard theory of cosmological perturbations, where both the gravitational and the inflaton fields are linearly perturbed and quantized. The correlation functions for the primordial metric fluctuations and their power spectrum are then computed. Here we introduce an alternative procedure for calculating the metric correlations based on the Einstein-Langevin equation which emerges in the framework of stochastic semiclassical gravity. We show that the correlation functions for the metric perturbations that follow from the Einstein-Langevin formalism coincide with those obtained with the usual quantization procedures when the scalar field perturbations are linearized. This method is explicitly applied to a simple model of chaotic inflation consisting of a Robertson-Walker background, which undergoes a quasi-de Sitter expansion, minimally coupled to a free massive quantum scalar field. The technique based on the Einstein-Langevin equation can, however, deal naturally with the perturbations of the scalar field even beyond the linear approximation, as is actually required in inflationary models which are not driven by an inflaton field, such as Starobinsky¿s trace-anomaly driven inflation or when calculating corrections due to nonlinear quantum effects in the usual inflaton driven models.

Dislocation jamming and Andrade creep

We simulate the glide motion of an assembly of interacting dislocations under the action of an external shear stress and show that the associated plastic creep relaxation follows Andrades law. Our results indicate that Andrade creep in plastically deforming crystals involves the correlated motion of dislocation structures near a dynamic transition separating a flowing from a jammed phase. Simulations in the presence of dislocation multiplication and noise confirm the robustness of this finding and highlight the importance of metastable structure formation for the relaxation process.

Coalition formation in a contest game with three heterogeneous players

We analyze the incentives for cooperation of three players differing in their efficiency of effort in a contest game. We concentrate on the non-cooperative bargaining foundation of coalition formation, and therefore, we adopt a two-stage model. In the first stage, individuals form coalitions following a bargaining protocol similar to the one proposed by Gul (1989). Afterwards, coalitions play the contest game of Esteban and Ray (1999) within the resulting coalition structure of the first stage. We find that the grand coalition forms whenever the distribution of the bargaining power in the coalition formation game is equal to the distribution of the relative efficiency of effort. Finally, we use the case of equal bargaining power for all individuals to show that other types of coalition structures may be observed as well.

When does universal peace prevail? Secession and group formation in rent seeking contests and policy conflicts

This paper analyzes secession and group formation in a general model of contest inspired by Esteban and Ray (1999). This model encompasses as special cases rent seeking contests and policy conflicts, where agents lobby over the choice of a policy in a one-dimensional policy space. We show that in both models the grand coalition is the efficient coalition structure and agents are always better off in the grand coalition than in a symmetric coalition structure. Individual agents (in the rent seeking contest) and extremists (in the policy conflict) only have an incentive to secede when they anticipate that their secession will not be followed by additional secessions. Incentives to secede are lower when agents cooperate inside groups. The grand coalition emerges as the unique subgame perfect equilibrium outcome of a sequential game of coalition formation in rent seeking contests.

Entrepreneurial structure of the mercantile company in pre-industrial Catalonia

The mercantile company was the basic form of enterprise in pre-industrial Catalonia. The aim of this paper is to study the formation and development of the mercantile companies in Barcelona whose end was the wholesale and retail sale of textiles in the botigues de teles (textile retail shops) throughout the eighteenth century. These firms were officially registered before a notary and their deeds reveal how these establishments were administered and managed.The study covers a sample of 121 mercantile companies, and the articles and documentation that were put into effect by 32 notaries who were active in Barcelona in the 18th century have been consulted in their entirety. From an initial selection of documentation, a total of 228 deeds registering companies have been found, 107 of which (47%) relate to the creation of companies whose various activities were centred in taverns, textile manufacturing, braiding.... While the 121 companies, which make up our sample and which account for 53% of the deeds registered with the notaries mentioned above, focused exclusively on the management of textile retail shops located in the commercial heart of the city. Thus one point of interest that the documentation reveals is that the majority of the mercantile companies registered by Barcelona notaries throughout the 18th century were establishments which traded in textiles. The first part of the article focuses on the structural characteristics of these enterprises, the number and socio-professional status of the partners and the extent of each partner s involvement in the administration and management. The second part of the article examines the capital investment made by each partner, their rights and obligations agreed on, the sharing out of profits and possible losses and the duration of the companies. The final aim of the paper is to highlight the evolution of these companies through one specific case.

The Coordinated Radio and Infrared Survey for High-Mass Star Formation (The CORNISH Survey). I. Survey Design

We describe the motivation, design, and implementation of the CORNISH survey, an arcsecondresolution radio continuum survey of the inner galactic plane at 5 GHz using the Very Large Array (VLA). It is a blind survey coordinated with the northern SpitzerGLIMPSE I region covering 10° formation. A sensitivity around 2 mJy will allow the automatic distinction between radio-loud and radio-quiet midIR sources found in the Spitzersurveys. This survey has many legacy applications beyond star formation, including evolved stars, active stars and binaries, and extragalactic sources. The CORNISH survey for compact ionized sources complements other Galactic plane surveys that target diffuse and nonthermal sources, as well as atomic and molecular phases to build up a complete picture of the interstellar medium in the Galaxy.

Pattern formation during mesophase growth in a homologous series

Remarkable differences in the shape of the nematic-smectic-B interface in a quasi-two-dimensional geometry have been experimentally observed in three liquid crystals of very similar molecular structure, i.e., neighboring members of a homologous series. In the thermal equilibrium of the two mesophases a faceted rectanglelike shape was observed with considerably different shape anisotropies for the three homologs. Various morphologies such as dendritic, dendriticlike, and faceted shapes of the rapidly growing smectic-B germ were also observed for the three substances. Experimental results were compared with computer simulations based on the phase field model. The pattern forming behavior of a binary mixture of two homologs was also studied.

Atomic structure of the nanocrystalline Si particles appearing in nanostructured Si thin films produced in low-temperature radiofrequency plasmas

Nanostructured Si thin films, also referred as polymorphous, were grown by plasma-enhanced chemical vapor deposition. The term "polymorphous" is used to define silicon material that consists of a two-phase mixture of amorphous and ordered Si. The plasma conditions were set to obtain Si thin films from the simultaneous deposition of radical and ordered nanoparticles. Here, a careful analysis by electron transmission microscopy and electron diffraction is reported with the aim to clarify the specific atomic structure of the nanocrystalline particles embedded in the films. Whatever the plasma conditions, the electron diffraction images always revealed the existence of a well-defined crystalline structure different from the diamondlike structure of Si. The formation of nanocrystallinelike films at low temperature is discussed. A Si face-cubic-centered structure is demonstrated here in nanocrystalline particles produced in low-pressure silane plasma at room temperature.

Self-similar community structure in a network of human interactions

We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar. This suggests that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.

Dynamics of transient pattern formation in nematic liquid crystals

We analyze the dynamics of a transient pattern formation in the Fréedericksz transition corresponding to a twist geometry. We present a calculation of the time-dependent structure factor based on a dynamical model which incorporates consistently the coupling of the director field with the velocity flow and also the effect of fluctuations. The appearance and development of a characteristic periodicity is described in terms of the time dependence of the maximum of the structure factor. We find a well-defined time for the appearance of the pattern and a subsequent stage of pattern development in which the characteristic periodicity tends to an asymptotic value.

Nonlinear effects in the dynamics of transient pattern formation in nematics

A nonlinear calculation of the dynamics of transient pattern formation in the Fréedericksz transition is presented. A Gaussian decoupling is used to calculate the time dependence of the structure factor. The calculation confirms the range of validity of linear calculations argued in earlier work. In addition, it describes the decay of the transient pattern.

Electronic structure of a neutral oxygen vacancy in SrTiO3

The electronic structure of an isolated oxygen vacancy in SrTiO3 has been investigated with a variety of ab initio quantum mechanical approaches. In particular we compared pure density functional theory (DFT) approaches with the Hartree-Fock method, and with hybrid methods where the exchange term is treated in a mixed way. Both local cluster models and periodic calculations with large supercells containing up to 80 atoms have been performed. Both diamagnetic (singlet state) and paramagnetic (triplet state) solutions have been considered. We found that the formation of an O vacancy is accompanied by the transfer of two electrons to the 3d(z2) orbitals of the two Ti atoms along the Ti-Vac-Ti axis. The two electrons are spin coupled and the ground state is diamagnetic. New states associated with the defect center appear in the gap just below the conduction band edge. The formation energy computed with respect to an isolated oxygen atom in the triplet state is 9.4 eV.

Ab initio study of the charge order and Zener polaron formation in half-doped manganites

The character of the electronic ground state of La0.5Ca0.5MnO3 has been addressed with quantum chemical calculations on large embedded clusters. We find a charge ordered state for the crystal structure reported by Radaelli et al. [Phys. Rev. B 55, 3015 (1997)] and Zener polaron formation in the crystal structure with equivalent Mn sites proposed by Daoud-Aladine et al. [Phys. Rev. Lett. 89, 097205 (2002)]. Important O to Mn charge transfer effects are observed for the Zener polaron.