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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…
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field based classical molecular dynamics simulations are a fundamental tool to characterize biomolecular dynamics and their…
Machine learning continues to emerge as an important tool to be utilised within structural engineering and structural health monitoring, due to its ability to accurately and quickly perform both regression and classification tasks. However,…
Modeling and analysis of spectroscopy data is an active area of research with applications to chemistry and biology. This paper focuses on analyzing Raman spectra obtained from a bone fracture healing experiment, although the functional…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
The relative balance between physics and data within any physics-informed machine learner is an important modelling consideration to ensure that the benefits of both physics and data-based approaches are maximised. An over reliance on…
Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized…
Composite fabrication technologies now provide the means for producing high-strength, low-weight panels, plates, spars and other structural components which use embedded fiber optic sensors and piezoelectric transducers. These materials,…
Current protein forcefields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the forcefields do not take into account the use of hydrogen bonds which are important for secondary…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…
Friction is one of the fundamental issues in physics, mechanics and material science with lots of practical applications. However, the understanding of macroscopic friction phenomena from microscopic aspect is still on the way. In this…
Biomolecular thermodynamics and spectroscopy depend on relative conformer energies, local curvatures, and collective dipole fluctuations on the potential-energy surface. Conventional molecular mechanics force fields enable large-scale…
The interpretation of the experimental data collected by testing systems across input datasets and model parameters is of strategic importance for system design and implementation. In particular, finding relationships between variables and…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Measures of discrepancy between probability distributions (statistical distance) are widely used in the fields of artificial intelligence and machine learning. We describe how certain measures of statistical distance can be implemented as…
Process mining techniques can help organizations to improve their operational processes. Organizations can benefit from process mining techniques in finding and amending the root causes of performance or compliance problems. Considering the…
Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel…
With the rise in high resolution remote sensing technologies there has been an explosion in the amount of data available for forest monitoring, and an accompanying growth in artificial intelligence applications to automatically derive…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…