Related papers: Using Partial Structure R1 to Do Molecular Replace…
This paper demonstrates how pre-knowledge of a crystal structure, including the constituent fragments, the atomic connectivity, and the approximate bond lengths, etc., can be utilized in the partial-structure R1 (pR1) and the single-atom R1…
This paper explores the lowest data resolution at which the partial structure R1 (pR1) method can determine a small-molecule crystal structure. Three specific structures have been studied. For a structure having 4 S atoms out of total 32…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
As originally designed [Zhang & Donahue (2024), Acta Cryst. A80, 2370248.], after one cycle of calculation, the single-atom R1 (sR1) method required a user to intelligently determine a partial structure to start the next cycle. In this…
A new method for solving small X-ray structures with up to couple of hundreds of atoms in the unit cell has been developed. The method works by locating atoms one-by-one via global minimization of a newly defined single-atom R1 factor in…
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…
The prediction of material structure from chemical composition has been a long-standing challenge in natural science. Although there have been various methodological developments and successes with computer simulations, the prediction of…
Rapid determination of molecular structures can greatly accelerate workflows across many chemical disciplines. However, elucidating structure using only one-dimensional (1D) NMR spectra, the most readily accessible data, remains an…
The visual information in V1 is processed by an array of modules called orientation preference columns. In some species including humans, orientation columns are radially arranged around singular points like the spokes of a wheel, that are…
One-dimensional NMR spectroscopy is one of the most widely used techniques for the characterization of organic compounds and natural products. For molecules with up to 36 non-hydrogen atoms, the number of possible structures has been…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
Partial Reconfiguration (PR) is a technique that allows reconfiguring the FPGA chip at runtime. However, current design support tools require manual floorplanning of the partial modules. Several approaches have been proposed in this field,…
Let $P$ be a set of $n$ labeled points in the plane. The radial system of $P$ describes, for each $p\in P$, the order in which a ray that rotates around $p$ encounters the points in $P \setminus \{p\}$. This notion is related to the order…
In this paper, we propose an orbital iteration based parallel approach for electronic structure calculations. This approach is based on our understanding of the single-particle equations of independent particles that move in an effective…
We study the problems of covering or partitioning a polygon $P$ (possibly with holes) using a minimum number of small pieces, where a small piece is a connected sub-polygon contained in an axis-aligned unit square. For covering, we seek to…
We propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm Iteratively suggests Rotated…
Search is a major technique for planning. It amounts to exploring a state space of planning domains typically modeled as a directed graph. However, prohibitively large sizes of the search space make search expensive. Developing better…
Many random growth models have the property that the set of discovered sites, scaled properly, converges to some deterministic set as time grows. Such results are known as shape theorems. Typically, not much is known about the shapes. For…
Multivariate data is often visualized using linear projections, produced by techniques such as principal component analysis, linear discriminant analysis, and projection pursuit. A problem with projections is that they obscure low and high…
We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of…