Related papers: Reaction Coordinates for Conformational Transition…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics is characterized by rare or slow transition events. In a recent publication, precise defining…
We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space.…
Contemporary materials science research is heavily conducted in silico, involving massive simulations of the atomic-scale evolution of materials. Cataloging basic patterns in the atomic displacements is key to understanding and predicting…
The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above…
Deflection of atoms in \Lambda-type configuration passing through two crossed standing light waves is proposed for probing and visualization of atomic superposition states. For this goal, we use both the large-dispersive and Raman-resonant…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…
Biochemical and environmental modeling typically relies on reaction networks to represent complex transformations. While the Linkage Class Decomposition (LCD) partitions networks based on visual standard connectivity, it often misaligns…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
A study of the $\lambda$- and $N$-atomic configurations under dipolar interaction with $2$ modes of electromagnetic radiation is presented. The corresponding quantum phase diagrams are obtained by means of a variational procedure. Both…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
Adapting large language models (LLMs) trained on broad organic chemistry to smaller, domain-specific reaction datasets is a key challenge in chemical and pharmaceutical R&D. Effective specialisation requires learning new reaction knowledge…
Identifying reaction coordinates(RCs) is an active area of research, given the crucial role RCs play in determining the progress of a chemical reaction. The choice of the reaction coordinate is often based on heuristic knowledge. However,…
A supervised machine learning algorithm, called locally adaptive discriminant analysis (LADA), has been developed to locate boundaries between identifiable image features that have varying intensities. LADA is an adaptation of image…
The reaction-coordinate mapping is a useful technique to study complex quantum dissipative dynamics into structured environments. In essence, it aims to mimic the original problem by means of an 'augmented system', which includes a suitably…
We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve…
Mass-conserving reaction-diffusion (MCRD) systems are widely used to model phase separation and pattern formation in cell polarity, biomolecular condensates, and ecological systems. Numerical simulations and formal asymptotic analysis…
We calculate the electronic structure of several atoms and small molecules by direct minimization of the Self-Interaction Corrected Local Density Approximation (SIC-LDA) functional. To do this we first derive an expression for the gradient…