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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…
We present a newly developed approach for the calculation of interfacial stiffness and contact area evolution between two rough bodies exhibiting self affine surface structures. Using spline assisted discretization to define localised…
The science of fractography revolves around the correlation between topographic characteristics of the fracture surface and the mechanisms and external conditions leading to their creation. While being a topic of investigation for…
In this article, microscopic understanding of the surface tension are provided, which needs basic knowledge of thermodynamics, statistical mechanics as well as continuum mechanics. By introducing the intermolecular interaction potential and…
The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. Above all nuclear scattering and reactions, which require the solution of the…
The friction and adhesion between elastic bodies are strongly influenced by the roughness of the surfaces in contact. Here we develop a multiscale molecular dynamics approach to contact mechanics, which can be used also when the surfaces…
X-ray photoemission and x-ray absorption spectroscopy are important techniques to characterize chemical bonding at surfaces and are often used to identify the strength and nature of adsorbate-substrate interactions. In this study, we judge…
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein--ligand interaction energies, enzymatic reaction energies, or spectroscopic…
Split-pulse x-ray photon correlation spectroscopy has been proposed as one of the unique capabilities made possible with the x-ray free electron lasers. It enables characterization of atomic scale structural dynamics that dictates the…
In this perspective article, we discuss the challenges of imaging assemblies of particles in three dimensions. Starting from a brief motivation for the investigation of particulate materials, we provide an overview of experimental…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Small-angle scattering (SAS) of X-rays, neutrons or light from ensembles of randomly oriented and placed deterministic fractal structures are studied theoretically. In the standard analysis, a very few parameters can be determined from SAS…
We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy…
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
The process of nuclear multifragmentation has been implemented, together with evaporation and fission channels of the disintegration of excited remnants in nucleus-nucleus collisions using percolation theory and the intranuclear cascade…
Large scale molecular dynamics simulations are used to study drying suspensions of a binary mixture of large and small particles in explicit and implicit solvents. The solvent is first modeled explicitly and then mapped to a uniform viscous…
Small-angle X-ray or neutron scattering (SAXS/SANS/SAS) is widely used to obtain structural information on biomolecules or soft-matter complexes in solution. Deriving a molecular interpretation of the scattering signals requires methods for…