Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields

Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding can be extremely difficult, due to the size of the systems and the small energy differences. In many cases, one has to resort to computational methods to calculate such properties. In this work, we used molecular dynamics simulations in conjunction with metadynamics to calculate the free energy of dimerization of small aromatic rings, and compared three models from popular online servers for atomistic force fields, namely G54a7, CHARMM36 and OPLS. We show that, regardless of the force field, the profiles for the dimerization free energy of these compounds are very similar. However, significant care needs to be taken when studying larger molecules, since the deviations from the trends increase with the size of the molecules, resulting in force field dependent preferred stacking modes; for example, in the cases of pyrene and tetracene. Our results provide a useful background study for using topology builders to model systems which rely on stacking of aromatic moieties, and are relevant in areas ranging from drug design to supramolecular assembly

Financial regimes and uncertainty shocks

Financial markets are central to the transmission of uncertainty shocks. This paper documents a new aspect of the interaction between the two by showing that uncertainty shocks have radically di¤erent macroeconomic implications depending on the state finan- cial markets are in when they occur. Using monthly US data, we estimate a nonlinear VAR where economic uncertainty is proxied by the (unobserved) volatility of the struc- tural shocks, and a regime change occurs whenever credit conditions cross a critical threshold. An exogenous increase in uncertainty has recessionary e¤ects in both good and bad credit regimes, but its impact on output is estimated to be five times larger when the economy is experiencing financial distress. Accounting for this nonlinearity, uncertainty accounts for about 1% of the peak fall in industrial production observed in the 2007-2009 recession

Recurrence and algorithmic information

In this paper we initiate a somewhat detailed investigation of the relationships between quantitative recurrence indicators and algorithmic complexity of orbits in weakly chaotic dynamical systems. We mainly focus on examples.Comment: 26 pages, no figure

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high efficiency devices. However, no method currently available can predict morphologies for a novel donor:acceptor blend. An approach which allows to reach relevant length scales, retain chemical specificity, mimic experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT):phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but for any other solution-processed soft matter device.</p

Resolving Donor-Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains

Organic semiconductors consisting of molecules bearing polar side chains have been proposed as potential candidates to overcome the limitations of organic photovoltaics owing to their enhanced dielectric constant. However, introducing such polar molecules in photovoltaic devices has not yet resulted in higher efficiencies. A microscopic understanding of the impact of polar side chains on electronic and structural properties of organic semiconductors is paramount to rationalize their effect. Here, the impact of such side chains on bulk heterojunction overall morphology, molecular configurations at donor-acceptor (DA) interfaces, and charge carrier energy levels is investigated. The multiscale modeling approach used allows to resolve DA interfaces with atomistic resolution while taking into account the large-scale self-organization process which takes place during the processing of an organic thin film. The polar fullerene-based blends are compared to the well-studied reference system, poly(3-hexyl-thiophene) (P3HT):phenyl-C-61-butyric acid methyl ester (PCBM). Introduction of polar side chains on a similar molecular scaffold does not affect molecular orientations at the DA interfaces; such orientations are, however, found to be affected by processing conditions and polymer molecular weight. Polar side chains, instead, are found to impact considerably the charge carrier energy levels of the organic blend, causing electrostatic-induced broadening of these levels

Pitfalls of the Martini Model

R.A. thanks The Netherlands Organisation for Scientific Research NWO (Graduate Programme Advanced Materials, No. 022.005.006) for financial support. S.T. thanks the European Commission for financial support via a Marie Skłodowska-Curie Actions Individual Fellowship (MicroMod-PSII, grant agreement 748895).The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current computational modeling landscape. Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of applications without the need to reparametrize the force field each time. However, there are certain inherent limitations to this approach, which we investigate in detail in this work. We first study the consequences of the absence of specific cross Lennard-Jones parameters between different particle sizes. We show that this lack may lead to artificially high free energy barriers in dimerization profiles. We then look at the effect of deviating too far from the standard bonded parameters, both in terms of solute partitioning behavior and solvent properties. Moreover, we show that too weak bonded force constants entail the risk of artificially inducing clustering, which has to be taken into account when designing elastic network models for proteins. These results have implications for the current use of the Martini CG model and provide clear directions for the reparametrization of the Martini model. Moreover, our findings are generally relevant for the parametrization of any other building block based force field.publishersversionpublishe

State estimation using a network of distributed observers with switching communication topology

State estimation of linear time-invariant (LTI) systems by using a network of distributed observers is studied in this paper. We assume that each observer has access to a local measurement which may be insufficient to provide the observability of the system, but the ensemble of all measurements in the network guarantees the observability. In this condition, the objective is to design a distributed state estimation approach such that, while the observers can exchange their estimated state vectors under a communication network, the estimated state vector of each observer converges to the state vector of the system. We consider a scenario when the communication links may fail and rebuild over time and the communication network does not stay connected constantly. Accordingly, the main contribution of the paper is to propose a distributed approach (with guarantees on the feasibility of the design) such that the state vector of the system is estimated by each observer if the union/joint of communication links in bounded intervals of time makes the network communication graph connected. Moreover, we also consider a scenario when the LTI system is subject to external disturbances and measurement noise. In this case, we derive sufficient conditions on the proposed approach such that if the communication topology stays connected during links failure, a desired performance to attenuate the effect of external disturbances and measurement noise on estimation errors is guaranteed. Simulation results show the effectiveness of the proposed estimation approach

A Critical Ear: Analysis of Value Judgments in Reviews of Beethoven's Piano Sonata Recordings

What sets a great music performance apart? In this study we addressed this question through an examination of value judgements in written criticism of recorded performance. One hundred reviews of recordings of Beethoven’s piano sonatas, published in the Gramophone between 1934 and 2010, were analyzed through a three-step qualitative analysis that identified the valence (positive/negative) expressed by critics’ statements and the evaluation criteria that underpinned their judgements. The outcome is a model of the main evaluation criteria used by professional critics: aesthetic properties, including intensity, coherence, and complexity, and achievement-related properties, including sureness, comprehension, and endeavor. The model also emphasizes how critics consider the suitability and balance of these properties across the musical and cultural context of the performance. The findings relate directly to current discourses on the role of evaluation in music criticism and the generalizability of aesthetic principles. In particular, the perceived achievement of the performer stands out as a factor that drives appreciation of a recording

Rational approximation and arithmetic progressions

A reasonably complete theory of the approximation of an irrational by rational fractions whose numerators and denominators lie in prescribed arithmetic progressions is developed in this paper. Results are both, on the one hand, from a metrical and a non-metrical point of view and, on the other hand, from an asymptotic and also a uniform point of view. The principal novelty is a Khintchine type theorem for uniform approximation in this context. Some applications of this theory are also discussed