Related papers: Determining Molecular Complexity using Assembly Th…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
We build a comprehensive methodology for the fast computation of entropy across both solid and liquid phases. The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
Spectral densities encode non-perturbative information that enters the calculation of a plethora of physical observables in strongly coupled field theories. Phenomenological applications encompass aspects of standard-model hadronic physics,…
The opportunities of the application of the recently proposed approach in optical emission spectroscopy of non-equilibrium plasmas have been studied. The approach consists of several methods of the determination of {\em absolute} particle…
The field of astrochemistry has seen major advances triggered by the completion of new powerful radio telescopes, with gains in sensitivity of receivers and in bandwidth. To date, about 330 molecular species are detected, in interstellar…
Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence…
Raman spectroscopy is a powerful experimental technique for characterizing molecules and materials that is used in many laboratories. First-principles theoretical calculations of Raman spectra are important because they elucidate the…
Nuclear magnetic resonance spectroscopy (MRS) allows for the determination of atomic structures and concentrations of different chemicals in a biochemical sample of interest. MRS is used in vivo clinically to aid in the diagnosis of several…
Inside living cells are complex mixtures of thousands of components. It is hopeless to try to characterise all the individual interactions in these mixtures. Thus, we develop a statistical approach to approximating them, and examine the…
The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…
To obtain an electron-density map from a macromolecular crystal the phase-problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitantly the determination of the heavy atom substructure. This is…
An accurate assessment of a model's complexity is crucial for topics such as interpretation, generalization, and model selection. However, most existing complexity measures either rely on heuristic assumptions or are computationally…
Assembly theory (AT) quantifies selection using the assembly equation and identifies complex objects that occur in abundance based on two measurements, assembly index and copy number, where the assembly index is the minimum number of…
This article covers few selected aspects of quantum theory of molecular rotations and vibrations. Triatomic molecules are the simplest systems, which show qualitative characteristics of larger polyatomic molecules. On the minimal example of…
One-dimensional nuclear magnetic resonance (NMR) spectroscopy is essential for molecular structure elucidation in organic synthesis, drug discovery, natural product characterization, and metabolomics, yet its interpretation remains heavily…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
We present a new method for assessing the intrinsic 3D shape of prestellar cores from molecular column densities. We have employed hydrodynamic simulations of contracting, isothermal cores considering three intrinsic geometries: spherical,…
We explore the sensitivity of several core-level spectroscopic methods to the underlying atomistic structure by using the water molecule as our test system. We first define a metric that measures the magnitude of spectral change as a…