Variance Reduction Result for a Projected Adaptive Biasing Force Method

This paper is committed to investigate an extension of the classical adaptive biasing force method, which is used to compute the free energy related to the Boltzmann-Gibbs measure and a reaction coordinate function. The issue of this technique is that the approximated gradient of the free energy, called biasing force, is not a gradient. The commitment to this field is to project the estimated biasing force on a gradient using the Helmholtz decomposition. The variance of the biasing force is reduced using this technique, which makes the algorithm more efficient than the standard ABF method. We prove exponential convergence to equilibrium of the estimated free energy, with a precise rate of convergence in function of Logarithmic Sobolev inequality constants

Proceedings of US - PRC international TOGA symposium

A series of 12 meridional transect along longitude 165°E in the Western Equatorial Pacific ocean were made between mid-1986 and mi-1988 : a time interval spanning an El Nino/Southern Oscillation (ENSO) event. Data collected on these cruises provide a detailed (albeit temporally sparse) view of the oceanic changes which occur in the Western Pacific during an ENSO event. The present work focuses on the evolution of the upper ocean thermohaline and zona velocity fields as revealed by high resolution hydrographic casts and direct near surface velocity measurements. (D'après résumé d'auteur

A dose-escalation study of indisulam in combination with capecitabine (Xeloda) in patients with solid tumours

This dose escalation study was designed to determine the recommended dose of the multi-targeted cell cycle inhibitor indisulam in combination with capecitabine in patients with solid tumours and to evaluate the pharmacokinetics of the combination. Thirty-five patients were treated with indisulam on day 1 of each 21-day cycle. Capecitabine was administered two times daily (BID) on days 1–14. Plasma concentrations of indisulam, capecitabine and its three metabolites were determined for pharmacokinetic analysis. The main dose-limiting toxicity was myelosuppression. Hand/foot syndrome and stomatitis were the major non-haematological toxicities. The recommended dose was initially established at indisulam 700 mg m−2 and capecitabine 1250 mg m−2 BID. However, during cycle 2 the recommended dose was poorly tolerated in three patients. A dose of indisulam 500 mg m−2 and capecitabine 1250 mg m−2 BID proved to be safe at cycle 1 and 2 in nine additional patients. Indisulam pharmacokinetics during cycle 1 were consistent with pharmacokinetic data from phase I mono-therapy studies. However, exposure to indisulam was remarkably increased at cycle 2 due to a drug–drug interaction between capecitabine and indisulam. Partial response was confirmed in two patients, one with colon carcinoma and the other with pancreatic carcinoma. Seventeen patients had stable disease. Indisulam (700 mg m−2) in combination with capecitabine (1250 mg m−2 BID) was well tolerated during the first cycle. A dose of indisulam 500 mg m−2 and capecitabine 1250 mg m−2 BID was considered safe in multiple treatment cycles. The higher incidence of toxicities observed during cycle 2 can be explained by a time-dependent pharmacokinetic drug–drug interaction

Gating of a pH-Sensitive K2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter

K+ channels share common selectivity characteristics but exhibit a wide diversity in how they are gated open. Leak K2P K+ channels TASK-2, TALK-1 and TALK-2 are gated open by extracellular alkalinization. The mechanism for this alkalinization-dependent gating has been proposed to be the neutralization of the side chain of a single arginine (lysine in TALK-2) residue near the pore of TASK-2, which occurs with the unusual pKa of 8.0. We now corroborate this hypothesis by transplanting the TASK-2 extracellular pH (pHo) sensor in the background of a pHo-insensitive TASK-3 channel, which leads to the restitution of pHo-gating. Using a concatenated channel approach, we also demonstrate that for TASK-2 to open, pHo sensors must be neutralized in each of the two subunits forming these dimeric channels with no apparent cross-talk between the sensors. These results are consistent with adaptive biasing force analysis of K+ permeation using a model selectivity filter in wild-type and mutated channels. The underlying free-energy profiles confirm that either a doubly or a singly charged pHo sensor is sufficient to abolish ion flow. Atomic detail of the associated mechanism reveals that, rather than a collapse of the pore, as proposed for other K2P channels gated at the selectivity filter, an increased height of the energetic barriers for ion translocation accounts for channel blockade at acid pHo. Our data, therefore, strongly suggest that a cycle of protonation/deprotonation of pHo-sensing arginine 224 side chain gates the TASK-2 channel by electrostatically tuning the conformational stability of its selectivity filter

Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets

A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations

Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics

© 2018, Springer Nature Switzerland AG. We present a new coarse-grained (CG) model of cholesterol (CHOL) for the electrostatic-based ELBA force field. A distinguishing feature of our CHOL model is that the electrostatics is modeled by an explicit point dipole which interacts through an ideal vacuum permittivity. The CHOL model parameters were optimized in a systematic fashion, reproducing the electrostatic and nonpolar partitioning free energies of CHOL in lipid/water mixtures predicted by full-detailed atomistic molecular dynamics simulations. The CHOL model has been validated by comparison to structural, dynamic and thermodynamic properties with experimental and atomistic simulation reference data. The simulation of binary DPPC/cholesterol mixtures covering the relevant biological content of CHOL in mammalian membranes is shown to correctly predict the main lipid behavior as observed experimentally

Root growth and crop performance of soybean under chemical, physical, and biological changes after subsoiling.

Chemical, physical and biological soil attributes can facilitate soybean root growth in greater volume and depth in the soil, which can minimize yield reduction caused by water deficit. Soil management can contribute positively or negatively to these soil attributes. The aim of this work was to evaluate the root growth and crop performance of soybean, in response to chemical, physical and biological changes after subsoiling at different depths. At the R5 phenological stage, trenches were made for sampling and soil collection for chemical, physical and biological analysis and root growth was carried out. At V5, V7, R2 and R5 stages, plants were collected to evaluate height, leaf area and dry mass. At V5, stage number and dry mass of the nodules were evaluated. Subsoiling increased pH and Ca, and decreased Al in the soil, resulted in higher relative density and did not affect in mechanical penetration resistance compared to non-subsoiled soil. Basal respiration and soybean nodulation were higher in the subsoiled soil. Up to 15 cm depth, there were 87.91% of the total root dry mass and 78.79% of the total root volume. Initial and final plant growth were the same in subsoiled and non-subsoiled soil. Number of nodules in the subsoiled soil was 28% higher than in the non-subsoiled soil. Under these study conditions, subsoiling provides lower root growth but benefits grain yield