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We briefly summarize the kernel regression approach, as used recently in materials modelling, to fitting functions, particularly potential energy surfaces, and highlight how the linear algebra framework can be used to both predict and train…
Adsorbed atoms and molecules play an important role in controlling and tuning the functional properties of two-dimensional (2D) materials. Understanding and predicting this process from theory is challenging because of the need to capture…
Protein amyloidosis is a cytopathological process characterized by the formation of highly beta-sheet-rich fibrils. How this process occurs and how to prevent/treat the associated diseases are not completely understood. Here, we carry out a…
Surface interaction is extremely important to both fundamental research and practical application. Physisorption can induce shape and structural distortion (i.e. conformational changes) in macromolecular and biomolecular adsorbates, but…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
Orientational ordering driven by mechanical distortion of soft substrates plays a major role in material transformation processes such as elastocapillarity and surface anchoring. We present a theoretical model of the orientational response…
Amphiphilic molecules spontaneously form self-assembly structures based on physical conditions such as molecular structure, concentration, and temperature. These structures exhibit various useful functions according to their morphology. The…
The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the $C_{\alpha}$-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
Using field theoretic renormalization, an MBE-type growth process with an obliquely incident influx of atoms is examined. The projection of the beam on the substrate plane selects a "parallel" direction, with rotational invariance…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
We examine the ordering properties of rectangular hard rods with length L and diameter D at a single planar wall and between two parallel hard walls using the second-virial density functional theory. The theory is implemented in the…
Collagen fibres play an important role in the mechanical behaviour of many soft tissues. Modelling of such tissues now often incorporates a collagen fibre distribution. However, the availability of accurate structural data has so far lagged…
Due to their architecture and how they are trained, artificial neural networks are typically not robust toward pruning or shuffling layers at test time. However, such properties would be desirable for different applications, such as…
The shape of biological shells, such as cell nuclei, membranes, and vesicles, often deviates from a perfect sphere due to an interplay of complex interactions with a myriad of molecular structures. In particular, semiflexible biopolymers…
The Random Sequential Adsorption (RSA) problem holds crucial theoretical and practical significance, serving as a pivotal framework for understanding and optimizing particle packing in various scientific and technological applications. Here…
Intermolecular interactions are crucial in determining the morphology of solution-processed semiconducting polymer thin films. However, these random interactions often lead to disordered or short-range ordered structures. Achieving…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…