Brownian dynamics simulation of DNA condensation.

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

Toll-like receptor 3 is necessary for dsRNA adjuvant effects.

Toll-like receptors (TLR) recognize pathogen associated molecular patterns, and the binding of their specific ligands triggers a proinflammatory response that helps to fight invading microorganisms, and can be harnessed to increase vaccine efficiency. The present study demonstrates that double-stranded RNA is a promising vaccine adjuvant able to increase both proliferation and activation of antigen-specific CD8(+) T cells. Importantly, TLR3 is required for this adjuvant effect, as TLR3 deficient recipients failed to enhance proliferation of adoptively transferred TCR transgenic CD8(+) T cells in the presence of double-stranded RNA. Finally, this study also shows that, in contrast to previous reports in humans, TLR3 does not exert direct costimulatory activity on CD8(+) T cells in mice.

Entropy Production In Thermodynamic Climate Models

We present a non-equilibrium theory in a system with heat and radiative fluxes. The obtained expression for the entropy production is applied to a simple one-dimensional climate model based on the first law of thermodynamics. In the model, the dissipative fluxes are assumed to be independent variables, following the criteria of the Extended Irreversible Thermodynamics (BIT) that enlarges, in reference to the classical expression, the applicability of a macroscopic thermodynamic theory for systems far from equilibrium. We analyze the second differential of the classical and the generalized entropy as a criteria of stability of the steady states. Finally, the extreme state is obtained using variational techniques and observing that the system is close to the maximum dissipation rate

Periodic Solutions in Low-Dimensional Climatic Models

Classic climatic models use constitutive laws without any response time. A more realistic approach to the natural processes governing climate dynamics must introduce response time for heat and radiation fluxes. Extended irreversible thermodynamics (EIT) is a good thermodynamical framework for introducing nonclassical constitutive laws. In the present study EIT has been used to analyze a Budyko–Sellers one-dimensional energybalance model developed by G. R. North. The results present self-sustained periodic oscillations when the response time is greater than a critical value. The high-frequency (few kiloyears) damped and nondamped oscillations obtained can be related to abrupt climatic changes without any variation in the external forcing of the system

Second differential of the entropy as a criterion for the stability in low-dimensional climate models

The second differential of the entropy is used for analysing the stability of a thermodynamic climatic model. A delay time for the heat flux is introduced whereby it becomes an independent variable. Two different expressions for the second differential of the entropy are used: one follows classical irreversible thermodynamics theory; the second is related to the introduction of response time and is due to the extended irreversible thermodynamics theory. the second differential of the classical entropy leads to unstable solutions for high values of delay times. the extended expression always implies stable states for an ice-free earth. When the ice-albedo feedback is included, a discontinuous distribution of stable states is found for high response times. Following the thermodynamic analysis of the model, the maximum rates of entropy production at the steady state are obtained. A latitudinally isothermal earth produces the extremum in global entropy production. the material contribution to entropy production (by which we mean the production of entropy by material transport of heat) is a maximum when the latitudinal distribution of temperatures becomes less homogeneous than present values

Extremal climatic states simulated by a 2-dimensional model Part I: Sensitivity of the model and present state

The criterion, based on the thermodynamics theory, that the climatic system tends to extremizesome function has suggested several studies. In particular, special attention has been devoted to the possibility that the climate reaches an extremal rate of planetary entropy production.Due to both radiative and material effects contribute to total planetary entropy production,climatic simulations obtained at the extremal rates of total, radiative or material entropy production appear to be of interest in order to elucidate which of the three extremal assumptions behaves more similar to current data. In the present paper, these results have been obtainedby applying a 2-dimensional (2-Dim) horizontal energy balance box-model, with a few independent variables (surface temperature, cloud-cover and material heat fluxes). In addition, climatic simulations for current conditions by assuming a fixed cloud-cover have been obtained. Finally,sensitivity analyses for both variable and fixed cloud models have been carried out

DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting.

Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What is the physical basis of this organization? Here we show evidence from stochastic simulation techniques that suggests that a key element is the tendency of contacting DNA strands to order, as in cholesteric liquid crystals. This interaction favors their preferential juxtaposition at a small twist angle, thus promoting an approximately nematic (and apolar) local order. The ordering effect dramatically impacts the geometry and topology of DNA inside phages. Accounting for this local potential allows us to reproduce the main experimental data on DNA organization in phages, including the cryo-EM observations and detailed features of the spectrum of DNA knots formed inside viral capsids. The DNA knots we observe are strongly delocalized and, intriguingly, this is shown not to interfere with genome ejection out of the phage.

Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

Protein-ligand docking has made important progress during the last decade and has become a powerful tool for drug development, opening the way to virtual high throughput screening and in silico structure-based ligand design. Despite the flattering picture that has been drawn, recent publications have shown that the docking problem is far from being solved, and that more developments are still needed to achieve high successful prediction rates and accuracy. Introducing an accurate description of the solvation effect upon binding is thought to be essential to achieve this goal. In particular, EADock uses the Generalized Born Molecular Volume 2 (GBMV2) solvent model, which has been shown to reproduce accurately the desolvation energies calculated by solving the Poisson equation. Here, the implementation of the Fast Analytical Continuum Treatment of Solvation (FACTS) as an implicit solvation model in small molecules docking calculations has been assessed using the EADock docking program. Our results strongly support the use of FACTS for docking. The success rates of EADock/FACTS and EADock/GBMV2 are similar, i.e. around 75% for local docking and 65% for blind docking. However, these results come at a much lower computational cost: FACTS is 10 times faster than GBMV2 in calculating the total electrostatic energy, and allows a speed up of EADock by a factor of 4. This study also supports the EADock development strategy relying on the CHARMM package for energy calculations, which enables straightforward implementation and testing of the latest developments in the field of Molecular Modeling.

Estudio termodinámico sobre la mineralogénesis de la Galena en la mina de Cierco (Alta Ribagorza)

Se efectúa un estudio de la mineralogénesis de la galena en la mina de Cierco (Alta Riborgaza). Se determina a partir de cálculos termodinamicos la solubilidad de la galena en una solución hidrotermal a 150ºC y 3 molal de NaCl y se estudian 10s efectos de los diferentes posibles agentes precipitantes. A partir de las mineralizaciones que acompañan a la galena, del conocimiento que se dispone de las inclusiones presentes en las mineralizaciones se efectúan posibles hipótesis sobre la formación del yacimiento.

Stochastic resonance in noisy nondynamical systems

We have analyzed the effects of the addition of external noise to nondynamical systems displaying intrinsic noise, and established general conditions under which stochastic resonance appears. The criterion we have found may be applied to a wide class of nondynamical systems, covering situations of different nature. Some particular examples are discussed in detail.

Asymptotic analysis of the Gunn effect with realistic boundary conditions

A general asymptotic analysis of the Gunn effect in n-type GaAs under general boundary conditions for metal-semiconductor contacts is presented. Depending on the parameter values in the boundary condition of the injecting contact, different types of waves mediate the Gunn effect. The periodic current oscillation typical of the Gunn effect may be caused by moving charge-monopole accumulation or depletion layers, or by low- or high-field charge-dipole solitary waves. A new instability caused by multiple shedding of (low-field) dipole waves is found. In all cases the shape of the current oscillation is described in detail: we show the direct relationship between its major features (maxima, minima, plateaus, etc.) and several critical currents (which depend on the values of the contact parameters). Our results open the possibility of measuring contact parameters from the analysis of the shape of the current oscillation.

Stationary states and phase diagram for a model of the Gunn effect under realistic boundary conditions

A general formulation of boundary conditions for semiconductor-metal contacts follows from a phenomenological procedure sketched here. The resulting boundary conditions, which incorporate only physically well-defined parameters, are used to study the classical unipolar drift-diffusion model for the Gunn effect. The analysis of its stationary solutions reveals the presence of bistability and hysteresis for a certain range of contact parameters. Several types of Gunn effect are predicted to occur in the model, when no stable stationary solution exists, depending on the value of the parameters of the injecting contact appearing in the boundary condition. In this way, the critical role played by contacts in the Gunn effect is clearly established.

Entropy change of martensitic transformations in Cu-based shape-memory alloys

We have investigated the different contributions to the entropy change at the martensitic transition of different families of Cu-based shape-memory alloys. The total entropy change has been obtained through calorimetric measurements. By measuring the evolution of the magnetic susceptibility with temperature, the entropy change associated with conduction electrons has been evaluated. The contribution of the anharmonic vibrations of the lattice has also been estimated using various parameters associated with the anharmonic behavior of these alloys, collected from the literature. The results found in the present work have been compared to values published for the martensitic transition of group-IV metals. For Cu-based alloys, both electron and anharmonic contributions have been shown to be much smaller than the overall entropy change. This finding demonstrates that the harmonic vibrations of the lattice are the most relevant contribution to the stability of the bcc phase in Cu-based alloys.