Related papers: Design of Geometric Molecular Bonds
Molecules with versatile functionalities and well-defined structures, can serve as building blocks for extreme nanoscale devices. This requires their precise integration into functional heterojunctions, most commonly in the form of…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
Our curiosity-driven desire to "see" chemical bonds dates back at least one-hundred years, perhaps to antiquity. Sweeping improvements in the accuracy of measured and predicted electron charge densities, alongside our largely bondcentric…
We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
A two-dimensional grid with dots is called a \emph{configuration with distinct differences} if any two lines which connect two dots are distinct either in their length or in their slope. These configurations are known to have many…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
By folding into particular 3D structures, proteins play a key role in living beings. To learn meaningful representation from a protein structure for downstream tasks, not only the global backbone topology but the local fine-grained…
Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these…
Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy (STM) images of structures formed on Au(111)…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
In this work, the geometric relation between space time block code design for the coherent channel and its non-coherent counterpart is exploited to get an analogue of the information theoretic inequality $I(X;S)\le I((X,H);S)$ in terms of…