Related papers: An efficient algorithm to compute the minimum free…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
The finite element method is a well-established method for the numerical solution of partial differential equations (PDEs), both linear and nonlinear. However, the repeated reassemblage of finite element matrices for nonlinear PDEs is…
The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
Computational modeling is an integral part of catalysis research. With it, new methodologies are being developed and implemented to improve the accuracy of simulations while reducing the computational cost. In particular, specific…
We study the completion of approximately low rank matrices with entries missing not at random (MNAR). In the context of typical large-dimensional statistical settings, we establish a framework for the performance analysis of the nuclear…
Throughout many fields, practitioners often rely on differential equations to model systems. Yet, for many applications, the theoretical derivation of such equations and/or accurate resolution of their solutions may be intractable. Instead,…
Motivated by applications in clustering and synthetic data generation, we consider the problem of releasing a minimum spanning tree (MST) under edge-weight differential privacy constraints where a graph topology $G=(V,E)$ with $n$ vertices…
Submodular function minimization (SFM) is a fundamental discrete optimization problem which generalizes many well known problems, has applications in various fields, and can be solved in polynomial time. Owing to applications in computer…
For identification of systems embedded in dynamic networks, applying the prediction error method (PEM) to a correct tailor-made parametrization of the complete network provided asymptotically efficient estimates. However, the network…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
In the minimum spanning tree (MST) interdiction problem, we are given a graph $G=(V,E)$ with edge weights, and want to find some $X\subseteq E$ satisfying a knapsack constraint such that the MST weight in $(V,E\setminus X)$ is maximized.…
Motivated by the increasing need to understand the algorithmic foundations of distributed large-scale graph computations, we study a number of fundamental graph problems in a message-passing model for distributed computing where $k \geq 2$…
Physics-informed neural networks (PINNs) are capable of finding the solution for a given boundary value problem. We employ several ideas from the finite element method (FEM) to enhance the performance of existing PINNs in engineering…
Miller et al. \cite{MPVX15} devised a distributed\footnote{They actually showed a PRAM algorithm. The distributed algorithm with these properties is implicit in \cite{MPVX15}.} algorithm in the CONGEST model, that given a parameter $k =…
Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct…
We present a new divergence-free and well-balanced hybrid FV/FE scheme for the incompressible viscous and resistive MHD equations on unstructured mixed-element meshes in 2 and 3 space dimensions. The equations are split into subsystems. The…
We present the novel algorithmically regularised integration method MSTAR for high accuracy ($|\Delta E/E| \gtrsim 10^{-14}$) integrations of N-body systems using minimum spanning tree coordinates. The two-fold parallelisation of the…
The problem of finding a nontrivial factor of a polynomial f(x) over a finite field F_q has many known efficient, but randomized, algorithms. The deterministic complexity of this problem is a famous open question even assuming the…
A neural ordinary differential equations network (ODE-Net)-enabled reachability method (Neuro-Reachability) is devised for the dynamic verification of networked microgrids (NMs) with unidentified subsystems and heterogeneous uncertainties.…