Related papers: A coarse-grained model with implicit salt for RNAs…
We present the Stagger-grid, a comprehensive grid of time-dependent, 3D hydrodynamic model atmospheres for late-type stars with realistic treatment of radiative transfer, covering a wide range in stellar parameters. This grid of 3D models…
Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited…
The effect of polyvalent molecular cations, such as spermine, on the condensation of DNA into very well-defined toroidal shapes have been well studied and understood. However, a great effort has been made trying to obtain similar condensed…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Carbon fiber and graphene-based nanostructures such as carbon nanotubes (CNTs) and defective structures have extraordinary potential as strong and lightweight materials. A longstanding bottleneck has been lack of understanding and…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Context. The surface structures and dynamics of cool stars are characterized by the presence of convective motions and turbulent flows which shape the emergent spectrum. Aims. We used realistic three-dimensional radiative hydrodynamical…
The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD)…
We present a local and transferable machine learning approach capable of predicting the real-space density response of both molecules and periodic systems to external homogeneous electric fields. The new method, SALTER, builds on the…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Full 3D modelling of time-domain electromagnetic data requires tremendous computational resources. Consequently, simplified physics models prevail in geophysics, using a much faster but approximate (1D) forward model. We propose to join the…
Stellar evolution codes play a major role in present-day astrophysics, yet they share common simplifications related to the outer layers of stars. We seek to improve on this by the use of results from realistic and highly detailed 3D…
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix…
LiF-NaF-ZrF4 multicomponent molten salts are promising candidate coolants for advanced clean energy systems owing to their desirable thermophysical and transport properties. However, the complex structures enabling these properties, and…
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…
General circulation models (GCMs) typically have a grid size of 25--200 km. Parametrizations are used to represent diabatic processes such as radiative transfer and cloud microphysics and account for sub-grid-scale motions and variability.…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of…