相关论文: A Central Partition of Molecular Conformational Sp…

It is well known that not every combinatorial configuration admits a geometric realization with points and lines. Moreover, some of them do not even admit realizations with pseudoline arrangements, i.e., they are not topological. In this…

This paper aims to undertake an exploration of the behavior of the moduli space of line arrangements while establishing its combinatorial interplay with the incidence structure of the arrangement. In the first part, we investigate…

Membrane particles such as proteins and lipids organize into zones that perform unique functions. Here, I introduce a topological and category-theoretic framework to represent particle and zone intra-scale interactions and inter-scale…

Using a uniform partitioning of cubic cells, we cover the total volume of a $\Lambda$CDM cosmological simulation based on particles. We define a visualisation cell as a spatial extension of the cubic cell, so that we collect all simulation…

We examine, using molecular dynamics simulation, the structure and thermodynamics of the (100) and (111) disordered face-centered cubic (FCC) crystal/melt interfaces for a binary hard-sphere system. This study is an extension of our…

The rapid advances in 3D scanning and acquisition techniques have given rise to the explosive increase of volumetric digital models in recent years. This dissertation systematically trailblazes a novel volumetric modeling framework to…

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…

The continuous 1D defects of an isotropic homogeneous material in a flat 3D space are classified by the Volterra process construction method. We employ the same method to classify the continuous 2D defects of a vacuum in a 4D maximally…

This paper introduces a new shape-matching methodology, combinative matching, to combine interlocking parts for geometric shape assembly. Previous methods for geometric assembly typically rely on aligning parts by finding identical surfaces…

The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…

From a scalar field defined at the corner of a cube, an isosurface can be extracted using the Marching Cube algorithm. The isosurface separates the cell into two or more partial cells. A similar situation arises when an material interface…

We describe the equations of motion of elastodynamic bounded bodies in 3-space, and their linearizations at a stationary point. Using the latter as an approximation to model small motions, we develop a scheme to find numerical solutions of…

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used…

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…

In the core accretion model of planet formation, envelope cooling regulates the accretion of material and ultimately sets the timescale to form a giant planet. Given the diversity of planet-forming environments, opacity uncertainties, and…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the…