Related papers: A contact map method to capture the features of kn…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
We report on numerical simulations of the two-dimensional Blume-Capel ferromagnet embedded in the triangular lattice. The model is studied in both its first- and second-order phase transition regime for several values of the crystal field…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
We study geometrical aspects of entanglement, with the Hilbert--Schmidt norm defining the metric on the set of density matrices. We focus first on the simplest case of two two-level systems and show that a ``relativistic'' formulation leads…
Knot theory provides a powerful tool for the understanding of topological matters in biology, chemistry, and physics. Here knot theory is introduced to describe topological phases in the quantum spin system. Exactly solvable models with…
Polymer systems in slab geometries are studied on the basis of the recently presented Gaussian Ellipsoid Model [J. Chem. Phys. 114, 7655 (2001)].The potential of the confining walls has an exponential shape. For homogeneous systems in…
Simulated configurations of flexible knotted rings confined inside a spherical cavity are fed into long-short term memory neural networks (LSTM NNs) designed to distinguish knot types. The results show that they perform well in knot…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
Geometric mechanics provides valuable insights into how biological and robotic systems use changes in shape to move by mechanically interacting with their environment. In high-friction environments it provides that the entire interaction is…
A simple statistical mechanical approach for studying multilayer adsorption of interacting polyatomic adsorbates (k-mers) has been presented. The new theoretical framework has been developed on a generalization in the spirit of the…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
We develop Monte Carlo simulations for uniformly charged polymers and machine learning algorithm to interpret the intra-polymer structure factor of the charged polymer system, which can be obtained from small-angle scattering experiments.…
Representations of planar triangulations as contact graphs of a set of internally disjoint homothetic triangles or of a set of internally disjoint homothetic squares have received quite some attention in recent years. In this paper we…
(Rephrased) Non-conformance decision-making processes in high-precision manufacturing of engineering structures are often delayed due to numerical simulations that are needed for analyzing the defective parts and assemblies. Interfaces…
We consider the statistical mechanics of a system of topologically linked polymers, such as for instance a dense solution of polymer rings. If the possible topological states of the system are distinguished using the Gauss linking number as…
The knowledge of transitions between regular, laminar or chaotic behavior is essential to understand the underlying mechanisms behind complex systems. While several linear approaches are often insufficient to describe such processes, there…
In this work, we build on our method for manipulating unknown objects via contact configuration regulation: the estimation and control of the location, geometry, and mode of all contacts between the robot, object, and environment. We…
We introduce a framework for adsorption of a single polymer in which the topology of the polymer is quenched before adsorption, in contrast to more standard adsorption models having annealed topology. Our "topology" refers either to the…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…