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A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design.…
Chemical, mechanical, thermal and/or electronic properties of bulk or low-dimensional materials can be engineered by introducing structural defects to form novel functionalities. When using particles irradiation, these defects can be…
We introduce the idea that the electronic band structure of a charge density wave system may mimic the electronic structure of graphene. In that case a class of materials quite different from graphene might be opened up to exploit…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
In this paper we first apply the general analysis described in our first paper to a binary mixture of cyclohexane and $n$-hexane. We use the square gradient model for the continuous description of a non-equilibrium surface and obtain…
First-principles calculations are used to investigate the electronic properties of neutral and negatively charged n-pyrrole oligomers with n= 2-18. Chains of neutral oligomers are bent while the negatively charged oligomers become almost…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We investigate the complexation of a highly charged sphere with a long flexible polyelectrolyte, \textit{both negatively charged} in salt free environment. Electroneutrality is insured by the presence of divalent counterions. Using…
The grain boundary (GB) energy is a quantity of fundamental importance for understanding several key properties of graphene. Here we present a comprehensive theoretical and numerical study of the entire space of symmetric and asymmetric…
We predict the nature (attractive or repulsive) and range (exponentially screened or long-range power law) of the electrostatic interactions of oppositely charged and planar plates as a function of the salt concentration and surface charge…
How accurate is pair additivity in describing interactions between soft polymer-based nanoparticles? Using numerical simulations we compute the free energy cost required to overlap multiple chains in the same region of space, and provide a…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
The problem of charged polymer chains (polyelectrolytes) as they adsorb on a planar surface is addressed theoretically. We review the basic mechanisms and theory underlying polyelectrolyte adsorption on a single surface in two situations:…
N-\alpha structures of light nuclei with axial symmetry are studied using relativistic Hartree approximation. Metastable excited states are searched in a configuration space which allows linear alpha chain structures. As a result, it is…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
We present a new multiphase-field theory for describing pattern formation in multi-domain and/or multi-component systems. The construction of the free energy functional and the dynamic equations is based on criteria that ensure mathematical…
The structure and electrical properties of a two-dimensional (2D) sheet of silicon on a graphene substrate are studied using first-principles calculations. A new corrugated rectangular structure of silicon is proposed to be the most…
Phosphorene, a 2D allotrope of phosphorus, is technologically very appealing because of its semiconducting properties and narrow band gap. Further reduction of the phosphorene dimensionality may spawn exotic properties of its electronic…
The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable…
Graphene quantum dots (GQDs) represent single layers up to dozens of graphene layers smaller than 30 nm. GQDs are newish molecules that have aroused great interest in research because of their exceptional and manageable optical, electrical,…