Related papers: Embedding protein 3D-structures in a cubic lattice…
The present research is developed into the realm of industrial design engineering and additive manufacturing by introducing a parametric design model and adaptive mechanical analysis for a new lattice structure, with a focus on 3D additive…
The notion of multidimensional quadrilateral lattice is introduced. It is shown that such a lattice is characterized by a system of integrable discrete nonlinear equations. Different useful formulations of the system are given. The…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
We show that every finite semilattice can be represented as an atomized semilattice, an algebraic structure with additional elements (atoms) that extend the semilattice's partial order. Each atom maps to one subdirectly irreducible…
Quantum heuristics have shown promise in solving various optimization problems, including lattice protein folding. Equally relevant is the inverse problem, protein design, where one seeks sequences that fold to a given target structure. The…
The simulation of large nonlinear dynamical systems, including systems generated by discretization of hyperbolic partial differential equations, can be computationally demanding. Such systems are important in both fluid and kinetic…
Optical lattices with one atom on each site and interacting via cold controlled collisions provide an efficient way to entangle a large number of qubits with high fidelity. It has already been demonstrated experimentally that this approach…
Lattice structures have great potential for several application fields ranging from medical and tissue engineering to aeronautical one. Their development is further speeded up by the continuing advances in additive manufacturing…
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano…
Ultracold atoms are crucial for unlocking truly precise and accurate quantum metrology, and provide an essential platform for quantum computing, communication and memories. One of the largest ongoing challenges is the miniaturization of…
Adiabatic quantum programming defines the time-dependent mapping of a quantum algorithm into an underlying hardware or logical fabric. An essential step is embedding problem-specific information into the quantum logical fabric. We present…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
We review algorithms for protein design in general. Although these algorithms have a rich combinatorial, geometric, and mathematical structure, they are almost never covered in computer science classes. Furthermore, many of these algorithms…
Lattice structures have been widely used in various applications of additive manufacturing due to its superior physical properties. If modeled by triangular meshes, a lattice structure with huge number of struts would consume massive…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
State-of-the-art lattice QCD simulations enable the evaluation of nucleon form factors and Mellin moments with controlled systematics, yielding results with unprecedented accuracy. At the same time, new theoretical approaches are allowing…
We propose two protocols to encode a logical qubit into physical qubits relying on common types of qubit-qubit interactions in as simple forms as possible. We comment on its experimental implementation in several quantum computing…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
Geometric deep learning has recently achieved great success in non-Euclidean domains, and learning on 3D structures of large biomolecules is emerging as a distinct research area. However, its efficacy is largely constrained due to the…