Related papers: Simultaneous Fragment Docking for Geometrically Li…
In this paper, we consider the computational protein design (CPD) problem, which is usually modeled as a 0/1 programming and is extremely challenging due to its combinatorial properties. We propose an efficient algorithm for solving it.…
Fragment-Based Drug Discovery (FBDD) is a popular approach in early drug development, but designing effective linkers to combine disconnected molecular fragments into chemically and pharmacologically viable candidates remains challenging.…
This two-part paper develops novel methodologies for using fractional programming (FP) techniques to design and optimize communication systems. Part I of this paper proposes a new quadratic transform for FP and treats its application for…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…
In this paper we give a unified treatment of two different definitions of complementarity partition of multifold conic programs introduced independently in [J. F. Bonnans and H. Ram\'irez C., Math. Program. 104 (2005), no. 2-3, Ser. B,…
The peptide-protein docking problem is an important problem in structural biology that facilitates rational and efficient drug design. In this work, we explore modeling and solving this problem with the quantum-amenable quadratic…
Molecular docking (MD) is a crucial task in drug design, which predicts the position, orientation, and conformation of the ligand when bound to a target protein. It can be interpreted as a combinatorial optimization problem, where quantum…
In this paper, we present a new method to solve a certain type of Semidefinite Programming (SDP) problems. These types of SDPs naturally arise in the Quadratic Convex Reformulation (QCR) method and can be used to obtain dual bounds of…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Many computer vision problems can be formulated as binary quadratic programs (BQPs). Two classic relaxation methods are widely used for solving BQPs, namely, spectral methods and semidefinite programming (SDP), each with their own…
Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of classical algorithms have been developed to carry out…
In the presence of dynamic insertions and deletions into a partially reconfigurable FPGA, fragmentation is unavoidable. This poses the challenge of developing efficient approaches to dynamic defragmentation and reallocation. One key aspect…
Numerous problems in signal processing and imaging, statistical learning and data mining, or computer vision can be formulated as optimization problems which consist in minimizing a sum of convex functions, not necessarily differentiable,…
An accurate description of strong correlation is quintessential for the exploration of emerging chemical phenomena. While near-term variational quantum algorithms provide a theoretically scalable framework for quantum chemical problems, the…
We study an inverse design problem for the linear multiple fragmentation equation arising in particle dynamics. Our objective is to reconstruct an unknown initial size distribution that evolves, under a prescribed fragmentation law, into a…
In this paper, we define and study the new problem Simultaneous PQ-Ordering. Its input consists of a set of PQ-trees, which represent sets of circular orders of their leaves, together with a set of child-parent relations between these…
Two kinds of approximation algorithms exist for the k-BALANCED PARTITIONING problem: those that are fast but compute unsatisfying approximation ratios, and those that guarantee high quality ratios but are slow. In this paper we prove that…
Maximum bipartite matching is a fundamental algorithmic problem which can be solved in polynomial time. We consider a natural variant in which there is a separation constraint: the vertices on one side lie on a path or a grid, and two…
This paper improves the algorithms based on supporting halfspaces and quadratic programming for convex set intersection problems in our earlier paper in several directions. First, we give conditions so that much smaller quadratic programs…
Chordal and factor-width decomposition methods for semidefinite programming and polynomial optimization have recently enabled the analysis and control of large-scale linear systems and medium-scale nonlinear systems. Chordal decomposition…