Anticooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents and apply it to the encounter reaction between an antibody and its antigen. We reduce the problem to the solution of dual series relations, which can be solved iteratively, yielding the exact solution for the encounter rate constant at any desired order of accuracy. We quantify the encounter effectiveness by means of a simple indicator and show that the two binding centers systematically behave in an anticooperative fashion. However, we demonstrate that a reduction of the binding active sites allows the composite molecule to recover binding effectiveness, in spite of the overall reduction of the rate constant. In addition, we provide a simple formula that enables one to calculate the anticooperativity as a function of the size of the binding site for any values of the separation between the two active lobes and of the antigen size. Finally, some biological implications of our results are discusse

An AT-barrier mechanically controls DNA reannealing under tension

Regulation of genomic activity occurs through the manipulation of DNA by competent mechanoenzymes. Force-clamp optical tweezers that allow the structural dynamics of the DNA molecule to be measured were used here to investigate the kinetics of mechanically-driven strand reannealing. When the force on the torsionally unconstrained lambda-phage DNA is decreased stepwise from above to below the overstretching transition, reannealing occurs via discrete shortening steps separated by exponentially distributed time intervals. Kinetic analysis reveals a transition barrier 0.58 nm along the reaction coordinate and an average reannealing-step size of approximately 750 bp, consistent with the average bp interval separating segments of more than 10 consecutive AT bases. In an AT-rich DNA construct, in which the distance between segments of more than 10 consecutive AT is reduced to approximately 210 bps, the reannealing step reduces accordingly without changes in the position of the transition barrier. Thus, the transition barrier for reannealing is determined by the presence of segments of more than 10 consecutive AT bps independent of changes in sequence composition, while the length of the reannealing strand changes according to the distance between poly-AT segments at least 10 bps long

Geometry of the energy landscape of the self-gravitating ring

We study the global geometry of the energy landscape of a simple model of a self-gravitating system, the self-gravitating ring (SGR). This is done by endowing the configuration space with a metric such that the dynamical trajectories are identified with geodesics. The average curvature and curvature fluctuations of the energy landscape are computed by means of Monte Carlo simulations and, when possible, of a mean-field method, showing that these global geometric quantities provide a clear geometric characterization of the collapse phase transition occurring in the SGR as the transition from a flat landscape at high energies to a landscape with mainly positive but fluctuating curvature in the collapsed phase. Moreover, curvature fluctuations show a maximum in correspondence with the energy of a possible further transition, occurring at lower energies than the collapse one, whose existence had been previously conjectured on the basis of a local analysis of the energy landscape and whose effect on the usual thermodynamic quantities, if any, is extremely weak. We also estimate the largest Lyapunov exponent $\lambda$ of the SGR using the geometric observables. The geometric estimate always gives the correct order of magnitude of $\lambda$ and is also quantitatively correct at small energy densities and, in the limit $N\to\infty$, in the whole homogeneous phase.Comment: 20 pages, 12 figure

Frequency map analysis of resonances in a nonlinear lattice with space charge

Abstract In storage rings for heavy ion fusion beam losses must be minimized. During bunch compression high space charge is reached and the reciprocal effects between the collective modes of the beam and the single particle lattice nonlinearities must be considered to understand the problem of resonance crossing and halo formation. We show that the frequency map analysis of particle in core models gives an adequate description of the resonance network and of the chaotic regions where the halo particles can diffuse

Anti-cooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents and apply it to the encounter reaction between an antibody and its antigen. We reduce the problem to the solution of dual series relations, which can be solved iteratively, yielding the exact solution for the encounter rate constant at any desired order of accuracy. We quantify the encounter effectiveness by means of a simple indicator and show that the two binding centers systematically behave in an anti-cooperative fashion. However, we demonstrate that a reduction of the binding active sites allows the composite molecule to recover binding effectiveness, in spite of the overall reduction of the rate constant. In addition, we provide a simple formula that enables one to calculate the anti-cooperativity as a function of the size of the binding site for any values of the separation between the two active lobes and of the antigen size. Finally, some biological implications of our results are discussed

Subsea Compression Applications - Panel Session

TutorialThe use of Subsea gas compression technology for subsea re-injection and/or gas transport boosting represents a new and exciting application for rotating equipment, which will allow new gas/condensate field production opportunities, enhanced recovery of existing gas/condensate fields and cost effective production from marginal gas fields. This panel session includes short presentations on the benefits of subsea compression, an overview of currently ongoing projects, and recent advances and technologies that are available and/or under development for subsea gas compression. The panel session includes presentations from STATOIL, INTECSEA, MAN DIESEL & TURBO, GE OIL & GAS and DRESSER-RAND. The respective presentation titles are: DATUM I Compressor for Subsea Applications: Update on Qualification Efforts- Dresser-Rand; HOFIMTM Type Compressors for Subsea Applications – MAN Diesel & Turbo; Improving Recovery with Subsea Compression – INTECSEA; GE Oil & Gas Experience in Subsea Gas Compression technology Development – GE Oil & Gas; Realization of Subsea Gas Compression – Statoil

Dynamics of market correlations: Taxonomy and portfolio analysis

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the ``asset tree'' have been studied to reflect the economic taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer (MOL). During crashes the strong global correlation in the market manifests itself by a low value of MOL. The tree seems to have a scale free structure where the scaling exponent of the degree distribution is different for `business as usual' and `crash' periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects like the window size dependence of the investigated quantities are also discussed.Comment: 13 pages including 12 figures. Uses REVTe

Competing risk analysis on outcome after hepatic resection of hepatocellular carcinoma in cirrhotic patients

To investigate death for liver failure and for tumor recurrence as competing events after hepatectomy of hepatocellular carcinoma. METHODS Data from 864 cirrhotic Child-Pugh class A consecutive patients, submitted to curative hepatectomy (1997-2013) at two tertiary referral hospitals, were used for competing-risk analysis through the Fine and Gray method, aimed at assessing in which circumstances the oncological benefit from tumour removal is greater than the risk of dying from hepatic decompensation. To accomplish this task, the average risk of these two competing events, over 5 years of follow-up, was calculated through the integral of each cumulative incidence function, and represented the main comparison parameter. RESULTS Within a median follow-up of 5.6 years, death was attributable to tumor recurrence in 63.5%, and to liver failure in 21.2% of cases. In the first 16 mo, the risk of dying due to liver failure exceeded that of dying due to tumor relapse. Tumor stage only affects death from recurrence; whereas hepatitis C infection, Model for End-stage Liver Disease score, extent of hepatectomy and portal hypertension influence death from liver failure (P < 0.05 in all cases). The combination of these clinical and tumoral features identifies those patients in whom the risk of dying from liver failure did not exceed the tumour-related mortality, representing optimal surgical candidates. It also identifies those clinical circumstances where the oncological benefit would be borderline or even where the surgery would be harmful. CONCLUSION Having knowledge of these competing events can be used to weigh the risks and benefits of hepatic resection in each clinical circumstance, separating optimal from non-optimal surgical candidates