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Vibrational properties of molecular crystals are constantly used as structural fingerprints, in order to identify both the chemical nature and the structural arrangement of molecules. The simulation of these properties is typically very…
Recent Suzaku X-ray observations revealed that the observed entropy profile of the intracluster medium (ICM) deviates significantly from the prediction of hydrodynamical simulations of galaxy clusters. In this work, we show that gas…
Large-scale HI surveys and their cross-correlations with galaxy distributions have immense potential as cosmological probes. Interpreting these measurements requires theoretical models that must incorporate redshift-space distortions…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
A simple scaling theory for the sintering of fractal aerogels is presented. The densification at small scales is described by an increase of the lower cut-off length $a$ accompanied by a decrease of the upper cut-off length $\xi$, in order…
The structure of aqueous CsCl solutions was investigated by classical molecular dynamics simulations (MD) at three salt concentrations (1.5, 7.5, and 15 mol %). Thirty interatomic potential sets, based on the 12-6 Lennard-Jones model,…
The relaxed and unrelaxed formation energies of neutral antisites and interstitial defects in InP are calculated using ab initio density functional theory and simple cubic supercells of up to 512 atoms. The finite size errors in the…
The observation of scaling in processes in which a weakly interacting probe delivers large momentum ${\bf q}$ to a many-body system reflects the dominance of incoherent scattering off target constituents. While a suitably defined scaling…
Smoothed particle hydrodynamics (SPH) has been extensively studied in computer graphics to animate fluids with versatile effects. However, SPH still suffers from two numerical difficulties: the particle deficiency problem, which will…
Packings of macroscopic granular chains capture some of the essential aspects of molecular polymer systems and have been suggested as a paradigm to understand the physics on a molecular scale. However, here we demonstrate that the…
The folding and structure of biomacromolecules depend on the 3D distributions of their constituents, which ultimately controls their functionalities and interactions with other biomacromolecules. Atom probe tomography (APT) with its…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
This work investigates the prediction performance of the kriging predictors. We derive some error bounds for the prediction error in terms of non-asymptotic probability under the uniform metric and $L_p$ metrics when the spectral densities…
The proton structure function is re-deduced from the data of deep inelastic electron-proton scattering after enhanced correction that is made due to the multiple scattering effect. The Glauber approach is used to account for the multiple…
The prediction of material structure from chemical composition has been a long-standing challenge in natural science. Although there have been various methodological developments and successes with computer simulations, the prediction of…
The prospects for a determination of the strong coupling constant $\alpha_s$ via scaling violations of fragmentation functions in deeply inelastic scattering are studied. The statistical error in the case of an integrated luminosity of $250…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
We develop a coarse-grained protein model with a simplified amino acid interaction potential. We perform discrete molecular dynamics folding simulations of a small 20 residue protein - Trp-cage - from a fully extended conformation. We…
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…