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Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials

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Thermomechanical properties of honeycomb lattices from internal-coordinates potentials: the case of graphene and hexagonal boron nitride

Nicola Marzari, Francesco Libbi

Lattice dynamics in low-dimensional materials and, in particular, the quadratic behaviour of the flexural acoustic modes play a fundamental role in their thermomechanical properties. A first-principles evaluation of these can be very demanding, and can be ...

IOP PUBLISHING LTD2021

The role of NH3 and DMA in new particle formation from ambient measurements, bias exchange metadynamics and reactive MD simulations

Athanasios Nenes, Satoshi Takahama, Spyros Pandis, Mária Lbadaoui-Darvas

Ammonia (NH3) and organic amines (dimethyl amine, DMA) play an important role in the heteromolecular nucleation of sulfuric acid (H2SO4) and water. Nucleation rates depend on their concentrations. Extremely low amine concentrations can increase nucleation ...

2021

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in ...

2021

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High-Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi-threading and distributed computing) used in all the natural sciences, including molecular bi ...

WILEY-V C H VERLAG GMBH2020

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This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium-size organic molecules at high ab initio level. We offer a modular envir ...

AMER CHEMICAL SOC2020

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We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computatio ...

2019

The redox potential of molecular species is largely modulated by its molecular environment so that a change of the environment will lead to a different redox potential. However, a detailed molecular picture of reorganization of the environment upon reducti ...

AMER CHEMICAL SOC2019

The predictive simulation of molecular liquids requires potential energy surface (PES) models that are not only accurate but also computationally efficient enough to handle the large systems and long time scales required for reliable prediction of macrosco ...

AMER CHEMICAL SOC2019

Metal cations often play an important role in shaping the three-dimensional structure of peptides. As an example, the model system AcPheAla5LysH+ is investigated in order to fully understand the forces that stabilize its helical structure. In particular, t ...

EPFL2018

Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as a statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the mo ...

Amer Chemical Soc2017