Towards accurate solvation free energies of large biological systems

Continuum solvation models like PCM or COSMO are the standard tool to calculate solvation free energies in a quantum level, but have been typically limited to small biological molecules due to its large computational cost. Recently, a new implementation of COSMO based on a domain decomposition strategy (ddCOSMO) [1] has been presented, which speeds up calculations by several orders of magnitude, thus paving the way for its application to very large systems. Here, we report the parameterization of ddCOSMO to the prediction of hydration free energies based on the MST solvation model developed in Barcelona, [2][3]. The parameterization is based on the PM6 semi-empirical Hamiltonian, on a set of over 200 experimental hydration free energies. The new model opens the way to the accurate prediction of hydration free energies of very large biomolecules, thus going beyond the usual classical MM-PBSA or MM-GBSA approaches

Investigation of high frequency coupling between probe tips and wafer surface

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Three-Terminal Junctions operating as mixers, frequency doublers and detectors: A broad-band frequency numerical and experimental study at room temperature

The frequency response of nanometric T- and Y-shaped three-terminal junctions (TTJs) is investigated experimentally and numerically. In virtue of the parabolic down-bending of the output voltage of the central branch obtained at room temperature under a push-pull fashion input, we analyze: the low-frequency performance (<1 MHz) of TTJs operating as mixers, their RF capability as doublers up to 4 GHz and detection at 94 GHz. Special attention is paid to the impedance matching and cut-off frequency of the measurement set-up. The numerical study is done by means of Monte Carlo simulations. We illustrate the intrinsic functionality of the device as frequency doubler or rectifier up to THz. The role of the width of the central branch on the highfrequency response is also explored, finding different cut-off frequencies for doubling and detection as a consequence of the diverse working principles of both mechanisms and the particular geometry of the TTJs.ROOTHz (FP7-243845

Particle-unstable nuclei in the Hartree-Fock theory

Ground state energies and decay widths of particle unstable nuclei are calculated within the Hartree-Fock approximation by performing a complex scaling of the many-body Hamiltonian. Through this transformation, the wave functions of the resonant states become square integrable. The method is implemented with Skyrme effective interactions. Several Skyrme parametrizations are tested on four unstable nuclei: 10He, 12O, 26O and 28O.Comment: 5 pages, LaTeX, submitted to Phys. Rev. Let

Ab-Initio Calculation of Molecular Aggregation Effects: a Coumarin-343 Case Study

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules in order to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers, and to the coupling predicted by the transition density cube (TDC) method. We determine the accuracy of the dipole-dipole approximation and TDC with respect to the separation distance and orientation of the dimers. In particular, we investigate the effects of including Coulomb coupling terms ignored in the typical tight-binding effective Hamiltonian. We also examine effects of orbital relaxation which cannot be captured by either of these models

Continuum solvation models: Dissecting the free energy of solvation

The most usual self-consistent reaction field (SCRF) continuum models for the description of solvation within the quantum mechanical (QM) framework are reviewed, trying to emphasize their common roots as well as the inherent approximations assumed in the calculation of the free energy of solvation. Particular attention is also paid to the specific features involved in the development of current state-of-the-art QM SCRF continuum models. This is used to discuss the need to maintain a close correspondence between each SCRF formalism and the specific details entailing its parametrization, as well as the need to be cautious in analyzing the balance between electrostatic and non-electrostatic contributions to the solvation free energy between different SCRF models. Finally, special emphasis is given to the post-processing of the free energy of solvation to derive parameters providing a compact picture of the ability of a molecule to interact with different solvents, which can be of particular interest in biopharmaceutical studies

Reduced dielectric screening and enhanced energy transfer in single and few-layer MoS2

We report highly efficient non-radiative energy transfer from cadmium selenide (CdSe) quantum dots to monolayer and few-layer molybdenum disulfide (MoS2). The quenching of the donor quantum dot photoluminescence increases as the MoS2 flake thickness decreases, with the highest efficiency (>95%) observed for monolayer MoS2. This counterintuitive result arises from reduced dielectric screening in thin layer semiconductors having unusually large permittivity and a strong in-plane transition dipole moment, as found in MoS2. Excitonic energy transfer between a 0D emitter and a 2D absorber is fundamentally interesting and enables a wide range of applications including broadband optical down-conversion, optical detection, photovoltaic sensitization, and color shifting in light-emitting devices.Comment: 14 pages, 4 figure

Evaluation of National Surgical Practice for Lateral Lymph Nodes in Rectal Cancer in an Untrained Setting

Background: Involved lateral lymph nodes (LLNs) have been associated with increased local recurrence (LR) and ipsi-lateral LR (LLR) rates. However, consensus regarding the indication and type of surgical treatment for suspicious LLNs is lacking. This study evaluated the surgical treatment of LLNs in an untrained setting at a national level. Methods: Patients who underwent additional LLN surgery were selected from a national cross-sectional cohort study regarding patients undergoing rectal cancer surgery in 69 Dutch hospitals in 2016. LLN surgery consisted of either ‘node-picking’ (the removal of an individual LLN) or ‘partial regional node dissection’ (PRND; an incomplete resection of the LLN area). For all patients with primarily enlarged (≥7 mm) LLNs, those undergoing rectal surgery with an additional LLN procedure were compared to those undergoing only rectal resection. Results: Out of 3057 patients, 64 underwent additional LLN surgery, with 4-year LR and LLR rates of 26% and 15%, respectively. Forty-eight patients (75%) had enlarged LLNs, with corresponding recurrence rates of 26% and 19%, respectively. Node-picking (n = 40) resulted in a 20% 4-year LLR, and a 14% LLR after PRND (n = 8; p = 0.677). Multivariable analysis of 158 patients with enlarged LLNs undergoing additional LLN surgery (n = 48) or rectal resection alone (n = 110) showed no significant association of LLN surgery with 4-year LR or LLR, but suggested higher recurrence risks after LLN surgery (LR: hazard ratio [HR] 1.5, 95% confidence interval [CI] 0.7–3.2, p = 0.264; LLR: HR 1.9, 95% CI 0.2–2.5, p = 0.874). Conclusion: Evaluation of Dutch practice in 2016 revealed that approximately one-third of patients with primarily enlarged LLNs underwent surgical treatment, mostly consisting of node-picking. Recurrence rates were not significantly affected by LLN surgery, but did suggest worse outcomes. Outcomes of LLN surgery after adequate training requires further research.</p