26 research outputs found
Pulling a polymer out of a potential well and the mechanical unzipping of DNA
Motivated by the experiments on DNA under torsion, we consider the problem of
pulling a polymer out of a potential well by a force applied to one of its
ends. If the force is less than a critical value, then the process is activated
and has an activation energy proportinal to the length of the chain. Above this
critical value, the process is barrierless and will occur spontaneously. We use
the Rouse model for the description of the dynamics of the peeling out and
study the average behaviour of the chain, by replacing the random noise by its
mean. The resultant mean-field equation is a nonlinear diffusion equation and
hence rather difficult to analyze. We use physical arguments to convert this in
to a moving boundary value problem, which can then be solved exactly. The
result is that the time required to pull out a polymer of segments
scales like . For models other than the Rouse, we argue that Comment: 11 pages, 6 figures. To appear in PhysicalReview
Could we identify hot Ocean-Planets with CoRoT, Kepler and Doppler velocimetry?
Planets less massive than about 10 MEarth are expected to have no massive
H-He atmosphere and a cometary composition (50% rocks, 50% water, by mass)
provided they formed beyond the snowline of protoplanetary disks. Due to inward
migration, such planets could be found at any distance between their formation
site and the star. If migration stops within the habitable zone, this will
produce a new kind of planets, called Ocean-Planets. Ocean-planets typically
consist in a silicate core, surrounded by a thick ice mantle, itself covered by
a 100 km deep ocean. The existence of ocean-planets raises important
astrobiological questions: Can life originate on such body, in the absence of
continent and ocean-silicate interfaces? What would be the nature of the
atmosphere and the geochemical cycles ?
In this work, we address the fate of Hot Ocean-Planets produced when
migration ends at a closer distance. In this case the liquid/gas interface can
disappear, and the hot H2O envelope is made of a supercritical fluid. Although
we do not expect these bodies to harbor life, their detection and
identification as water-rich planets would give us insight as to the abundance
of hot and, by extrapolation, cool Ocean-Planets.Comment: 47 pages, 6 Fugures, regular paper. Submitted to Icaru
Theory of High-Force DNA Stretching and Overstretching
Single molecule experiments on single- and double stranded DNA have sparked a
renewed interest in the force-extension of polymers. The extensible Freely
Jointed Chain (FJC) model is frequently invoked to explain the observed
behavior of single-stranded DNA. We demonstrate that this model does not
satisfactorily describe recent high-force stretching data. We instead propose a
model (the Discrete Persistent Chain, or ``DPC'') that borrows features from
both the FJC and the Wormlike Chain, and show that it resembles the data more
closely. We find that most of the high-force behavior previously attributed to
stretch elasticity is really a feature of the corrected entropic elasticity;
the true stretch compliance of single-stranded DNA is several times smaller
than that found by previous authors. Next we elaborate our model to allow
coexistence of two conformational states of DNA, each with its own stretch and
bend elastic constants. Our model is computationally simple, and gives an
excellent fit through the entire overstretching transition of nicked,
double-stranded DNA. The fit gives the first values for the elastic constants
of the stretched state. In particular we find the effective bend stiffness for
DNA in this state to be about 10 nm*kbt, a value quite different from either
B-form or single-stranded DNAComment: 33 pages, 11 figures. High-quality figures available upon reques
Estado del arte de la quinua en el mundo en 2013
Alimento de base de las poblaciones andinas desde hace milenios, la quinua se ha convertido hoy en un producto apreciado en el mercado internacional de alimentos dietéticos, orgánicos y equitativos. Este cambio lo iniciaron los mismos productores del Altiplano Sur de Bolivia hace aproximadamente unos 40 años. En medio de un desierto de altura, ellos lograron desarrollar una floreciente producción agrícola de exportación. Aunque cuentan con lucrativos nichos de mercado, los productores de quinua no son agricultores especializados, ni residen de forma permanente en la zona de producción. Estas son algunas de las paradojas que caracterizan la producción de quinua en el Altiplano Sur de Bolivia. Después de describir el origen, la diversidad y los rasgos biológicos del ecotipo Quinua Real en el cual se basa la producción de esta zona, se plantea la importancia de la quinua en los agrosistemas locales y, más allá, en los sistemas de actividades agrícolas y no agrícolas manejados por las familias del Altiplano Sur. Movilidad geográfica y pluriactividad forman parte del modo de vida ancestral de estas poblaciones y determinan hasta hoy en día las condiciones de uso de los recursos territoriales y la organización de los productores en el contexto del auge comercial de la quinua. La producción actual de quinua en la región presenta rasgos de vulnerabilidad agroecológica y social, así como capacidades adaptativas para enfrentarlos. Se resaltan como puntos clave para la sostenibilidad de los agrosistemas locales : i) la concertación de reglas comunales e individuales para el acceso y uso de la tierra en agrosistemas socialmente equitativos y equilibrados entre cultivo y ganadería, ii) las normas internacionales para el reconocimiento de la Quinua Real en los mercados de exportación, iii) una actualización continua de las reglas y normas para mantener la adaptabilidad de los agrosistemas locales a los cambios imprevisibles del contexto socio-ecológico a varias escalas de espacio y de tiempo
Mesoscopic models for DNA stretching under force: new results and comparison to experiments
Single molecule experiments on B-DNA stretching have revealed one or two
structural transitions, when increasing the external force. They are
characterized by a sudden increase of DNA contour length and a decrease of the
bending rigidity. It has been proposed that the first transition, at forces of
60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA,
while the second one, at stronger forces, is a strand peeling resulting in
single stranded DNAs (ssDNA), similar to thermal denaturation. But due to
experimental conditions these two transitions can overlap, for instance for
poly(dA-dT). We derive analytical formula using a coupled discrete worm like
chain-Ising model. Our model takes into account bending rigidity, discreteness
of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit
of zero force, this model simplifies into a coupled model already developed by
us for studying thermal DNA melting, establishing a connexion with previous
fitting parameter values for denaturation profiles. We find that: (i) ssDNA is
fitted, using an analytical formula, over a nanoNewton range with only three
free parameters, the contour length, the bending modulus and the monomer size;
(ii) a surprisingly good fit on this force range is possible only by choosing a
monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase
length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss)
transitions; (iv) an analytical formula for fitting B to S transitions is
derived in the strong force approximation and for long DNAs, which is in
excellent agreement with exact transfer matrix calculations; (v) this formula
fits perfectly well poly(dG-dC) and -DNA force-extension curves with
consistent parameter values; (vi) a coherent picture, where S to ssDNA
transitions are much more sensitive to base-pair sequence than the B to S one,
emerges.Comment: 14 pages, 9 figure
EPIdemiology of Surgery-Associated Acute Kidney Injury (EPIS-AKI) : Study protocol for a multicentre, observational trial
More than 300 million surgical procedures are performed each year. Acute kidney injury (AKI) is a common complication after major surgery and is associated with adverse short-term and long-term outcomes. However, there is a large variation in the incidence of reported AKI rates. The establishment of an accurate epidemiology of surgery-associated AKI is important for healthcare policy, quality initiatives, clinical trials, as well as for improving guidelines. The objective of the Epidemiology of Surgery-associated Acute Kidney Injury (EPIS-AKI) trial is to prospectively evaluate the epidemiology of AKI after major surgery using the latest Kidney Disease: Improving Global Outcomes (KDIGO) consensus definition of AKI. EPIS-AKI is an international prospective, observational, multicentre cohort study including 10 000 patients undergoing major surgery who are subsequently admitted to the ICU or a similar high dependency unit. The primary endpoint is the incidence of AKI within 72 hours after surgery according to the KDIGO criteria. Secondary endpoints include use of renal replacement therapy (RRT), mortality during ICU and hospital stay, length of ICU and hospital stay and major adverse kidney events (combined endpoint consisting of persistent renal dysfunction, RRT and mortality) at day 90. Further, we will evaluate preoperative and intraoperative risk factors affecting the incidence of postoperative AKI. In an add-on analysis, we will assess urinary biomarkers for early detection of AKI. EPIS-AKI has been approved by the leading Ethics Committee of the Medical Council North Rhine-Westphalia, of the Westphalian Wilhelms-University Münster and the corresponding Ethics Committee at each participating site. Results will be disseminated widely and published in peer-reviewed journals, presented at conferences and used to design further AKI-related trials. Trial registration number NCT04165369