Related papers: Molassembler: Molecular graph construction, modifi…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
Recent advances in machine learning (ML) have expedited materials discovery and design. One significant challenge faced in ML for materials is the expansive combinatorial space of potential materials formed by diverse constituents and their…
It is well known that Drug Design is often a costly process both in terms of time and economic effort. While good Quantitative Structure-Activity Relationship models (QSAR) can help predicting molecular properties without the need to…
While stabilizer tableaus have proven exceptionally useful as a descriptive tool for additive quantum codes, they offer little guidance for concrete constructions or coding algorithm analysis. We introduce a representation of stabilizer…
Molecular optimization in drug discovery aims to discover molecules with improved target properties, but practical lead optimization often requires more than high predicted scores. A useful candidate should also be actionable: it should be…
Invariant theory provides more efficient tools, such as Molien generating functions and integrity bases, than basic group theory, that relies on projector techniques for the construction of symmetry--adapted polynomials in the symmetry…
I show how to construct Monte Carlo algorithms (programs), prove that they are correct and document them. Complicated algorithms are build using a handful of elementary methods. This construction process is transparently illustrated using…
This paper investigates given an assembly graph, find the possible micronuclear sequences in terms of MDSs and IESs; which represent Hamiltonian polygonal paths. We will consider the orientations of the assembly graph and Hamiltonian…
A novel two-phase molecule inference framework, mol-infer, has recently been developed to infer chemical graphs with prescribed abstract structures and desired property values through mixed integer linear programming (MILP) under the…
Graphs can be leveraged to model polyphonic multitrack symbolic music, where notes, chords and entire sections may be linked at different levels of the musical hierarchy by tonal and rhythmic relationships. Nonetheless, there is a lack of…
We propose a new approach, named PolyMapper, to circumvent the conventional pixel-wise segmentation of (aerial) images and predict objects in a vector representation directly. PolyMapper directly extracts the topological map of a city from…
Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
Molecular editing aims to modify a given molecule to optimize desired chemical properties while preserving structural similarity. However, current approaches typically rely on string-based or continuous representations, which fail to…
Multiblock copolymer chains in implicit nonselective solvents are studied by Monte Carlo method which employs a parallel tempering algorithm. Chains consisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct microarchitectures:…
The Mapper algorithm is a popular tool for visualization and data exploration in topological data analysis. We investigate an inverse problem for the Mapper algorithm: Given a dataset $X$ and a graph $G$, does there exist a set of Mapper…
Identifying local structural motifs and packing patterns of molecular solids is a challenging task for both simulation and experiment. We demonstrate two novel approaches to characterize local environments in different polymorphs of…
Construction of non-isomorphic cospectral graphs is a nontrivial problem in spectral graph theory specially for large graphs. In this paper, we establish that graph theoretical partial transpose of a graph is a potential tool to create…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
Reticular materials, including metal-organic frameworks and covalent organic frameworks, combine relative ease of synthesis and an impressive range of applications in various fields, from gas storage to biomedicine. Diverse properties arise…