Related papers: A symmetry-adapted algebraic approach to molecular…
The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…
The analysis of nonlinear spectroscopy, widely used to study the dynamics and structures of condensed-phase matter, typically employs a perturbative approach noticing the weak interaction between the laser and the matter of interest.…
A universal formula for an action associated with a noncommutative geometry, defined by a spectal triple $(\Ac ,\Hc ,D)$, is proposed. It is based on the spectrum of the Dirac operator and is a geometric invariant. The new symmetry…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into…
Intermolecular correlations in liquid acetonitrile (CH3CN) have been revisited by calculating orientational correlation functions. In the present approach, hydrogen atoms are included, so that a concept applicable for molecules of (nearly)…
We consider the problem of localizing relevant subsets of non-rigid geometric shapes given only a partial 3D query as the input. Such problems arise in several challenging tasks in 3D vision and graphics, including partial shape similarity,…
Despite its simplicity, the single-trajectory thawed Gaussian approximation has proven useful for calculating vibrationally resolved electronic spectra of molecules with weakly anharmonic potential energy surfaces. Here, we show that the…
We report on a new approach to ease the computational overhead of ab initio on-the-fly semiclassical dynamics simulations for vibrational spectroscopy. The well known bottleneck of such computations lies in the necessity to estimate the…
The computation of the nuclear quantum dynamics of molecules is challenging, requiring both accuracy and efficiency to be applicable to systems of interest. Recently, theories have been developed for employing time-dependent basis functions…
This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…
Benchmarks of molecular machine learning models often treat the molecular representation as a neutral input format, yet the representation defines the syntax of validity, edit operations, and invariances that models implicitly learn. We…
Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT…
A general machine learning architecture is introduced that uses wavelet scattering coefficients of an inputted three dimensional signal as features. Solid harmonic wavelet scattering transforms of three dimensional signals were previously…
The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact…
Observations and theoretical calculations have shown the importance of non-spherically symmetric structures in supernovae. Thus, the interpretation of observed supernova spectra requires the ability to solve the transfer equation in 3-D…
In this article we formulate and solve the problem of molecular beam diffraction when each molecule consists of two interacting bodies. Then, using our results, we present the diffraction patterns for various molecular sizes employing the…
We investigate a new algebra-based approach of finding Grassmannian formulas for scattering amplitudes. Our prime motivation is massive amplitudes of 4D $\mathcal{N}=4$ SYM, and therefore we consider a 6D Grassmannian formula, where we can…
Studies of quantum thermal effects on molecular excitation dynamics have often relied on oversimplified models, such as energy eigenstates or low-dimensional potentials, which fail to capture the complexity of real chemical systems. In…
There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular…