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We present a new model-based interpolation procedure for satisfiability modulo theories (SMT). The procedure uses a new mode of interaction with the SMT solver that we call solving modulo a model. This either extends a given partial model…
The fast multipole method (FMM) has had great success in reducing the computational complexity of solving the boundary integral form of the Helmholtz equation. We present a formulation of the Helmholtz FMM that uses Fourier basis functions…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
For Finite State Machines (FSMs) a rich testing theory has been developed to discover aspects of their behavior and ensure their correct functioning. Although this theory is widely used, e.g., to check conformance of protocol…
The Isochronous Mass Spectrometry (IMS) based on storage rings is a powerful technique for mass measurement of short-lived exotic nuclei. The transition energy $\gamma_t$ of the storage ring is a vital parameter of the IMS technique. It is…
We propose a construction for joint feature learning and clustering of multichannel extracellular electrophysiological data across multiple recording periods for action potential detection and discrimination ("spike sorting"). Our…
We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…
This paper presents eigensolution and non-modal analyses for immersed boundary methods (IBMs) based on volume penalization for the linear advection equation. This approach is used to analyze the behavior of flux reconstruction (FR)…
The efficient simulation of fluid-structure interactions at zero Reynolds number requires the use of fast summation techniques in order to rapidly compute the long-ranged hydrodynamic interactions between the structures. One approach for…
We develop a Gaussian process regression enhanced line integral string method to accelerate ring polymer instanton calculations of tunneling rates and tunneling splittings in molecular proton transfer reactions. By exploiting uncertainty…
The Isochronous Mass Spectrometry (IMS) is a powerful technique developed in heavy-ion storage rings for measuring masses of very short-lived exotic nuclei. The IMS is based on the isochronous setting of the ring. One of the main parameters…
Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around…
Identifying transition states (TSs), the high-energy configurations that molecules pass through during chemical reactions, is essential for understanding and designing chemical processes. However, accurately and efficiently identifying…
Interpolation and internal painting are one of the basic approaches in image internal painting, which is used to eliminate undesirable parts that occur in digital images or to enhance faulty parts. This study was designed to compare the…
We discuss an interferometric approach to the estimation of quantum mechanical damping. We study specific classes of entangled and separable probe states consisting of superpositions of coherent states. Based on the assumption of limited…
We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of…
Barrier certificates, a form of state invariants, provide an automated approach to the verification of the safety of dynamical systems. Similarly to barrier certificates, recent works explore the notion of closure certificates, a form of…
We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much…
Time delay estimation has long been an active area of research. In this work, we show that compressive sensing with interpolation may be used to achieve good estimation precision while lowering the sampling frequency. We propose an…
This paper presents a method to interpolate a periodic band-limited signal from its samples lying at nonuniform positions in a regular grid, which is based on the FFT and has the same complexity order as this last algorithm. This kind of…