Related papers: Dynamic polarizability of macromolecules for singl…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
We study slow dynamics of particles moving in a matrix of immobile obstacles using molecular dynamics simulations. The glass transition point decreases drastically as the obstacle density increases. At higher obstacle densities, the…
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently,…
The polarization of light conveys crucial information about the spatial ordering and optical properties of a specimen. However, precise polarization measurement in challenging conditions, including constrained spaces, low light levels, and…
Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Inducing and controlling the ultrafast molecular rotational dynamics using shaped laser fields is essential in numerous applications. Several approaches exist that allow following the coherent molecular motion in real-time, including…
Single molecule detection has revolutionised the fields of chemistry and biology by offering powerful ways to study individual molecules under different scenarios. Nanophotonic structures, including plasmonic antennas, significantly…
An analysis on the discrete versus continuous views of kinetics of macromolecules is presented. It is shown that the discrete approach traditional to biochemistry is insufficient for understanding the dynamics of protein molecules in…
Molecular dynamics calculations were preformed on organic crystals 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium tosylate (DAST) and 4-N,N-dimethylamino-4'-N'-methylstilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS). Vibrational modes of…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
A multi-time extension of a density correlation function is introduced to reveal temporal information about dynamical heterogeneity in glass-forming liquids. We utilize a multi-time correlation function that is analogous to the higher-order…
Motor proteins drive persistent motion and self-organisation of cytoskeletal filaments. However, state-of-the-art microscopy techniques and continuum modelling approaches focus on large length and time scales. Here, we perform…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of…
Coupled-cluster calculations of static electronic dipole polarizabilities for 145 organic molecules are performed to create a reference data set. The molecules are composed from carbon, hydrogen, nitrogen, oxygen, fluorine, sulfur,…
A cell is polarised when it has developed a main axis of organisation through the reorganisation of its cytosqueleton and its intracellular organelles. Polarisation can occur spontaneously or be triggered by external signals, like gradients…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
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…