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Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
Determining the structure and following the structural evolution of molecules undergoing chemical reactions is one of the key goals of ultrafast molecular physics and chemistry. Recently, Coulomb explosion imaging has emerged as a promising…
Interpreting spectroscopy data is a critical bottleneck in automating chemical research and industrial characterization. Particularly within infrared (IR) spectroscopy, identifying compounds in complex, liquid-phase chemical mixtures…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Backward elastic electron scattering from odd-A nuclear targets is characterized by magnetic form factors containing precise information on the nuclear structure. We study the sensitivity of the magnetic form factors to structural effects…
Machine Learning Interatomic Potentials play a fundamental role in computational chemistry and materials science, enabling applications from molecular dynamics simulations to drug design and materials discovery. While recent approaches can…
Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…
Nuclear magnetic resonance (NMR) has been widely used in the graphene oxide (GO) structure study. However, the detailed relationship between its spectroscopic features and the GO structural configuration has remained elusive. Based on first…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Electronic transitions involving core-level orbitals offer a localized, atomic-site and element specific peek window into statistical systems such as molecular liquids. Although formally understood, the complex relation between structure…
In this paper, we propose a map which connects nucleons bound in nuclei and Ising spins in Ising model. This proposal is based on the fact that the description of states of nucleons and Ising spins could share the same type of observables.…
Coarse-grained (CG) modeling enables molecular simulations to reach time and length scales inaccessible to fully atomistic methods. For classical CG models, the choice of mapping, that is, how atoms are grouped into CG sites, is a major…
X-ray as well as electron diffraction are powerful tools for structure determination of molecules. Studies on randomly oriented molecules in the gas-phase address cases in which molecular crystals cannot be generated or the interaction-free…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
We introduce a number of techniques in quantitative convergent-beam electron diffraction under development by our group and discuss the basis for measuring interatomic electrostatic potentials (and therefore also electron densities),…
The study of molecule-target interaction is quite important for drug discovery in terms of target identification, hit identification, pathway study, drug-drug interaction, etc. Most existing methodologies utilize either biomedical network…
The aim of our work is to study the effect of geometry variation on nucleation times and to address its role in the context of eukaryotic chemotaxis (i.e. the process which allows cells to identify and follow a gradient of chemical…