Related papers: PIPER: An FFT-based Protein Docking Program with P…

Identifying reliable domain-domain interactions (DDIs) will increase our ability to predict novel protein-protein interactions (PPIs), to unravel interactions in protein complexes, and thus gain more information about the function and…

We present a feature functional theory - binding predictor (FFT-BP) for the protein-ligand binding affinity prediction. The underpinning assumptions of FFT-BP are as follows: i) representability: there exists a microscopic feature vector…

Linear scaling density functional theory approaches to electronic structure are often based on the tendency of electrons to localize even in large atomic and molecular systems. However, in many cases of actual interest, for example in…

Computational high-throughput virtual screening is essential for identifying redox-active molecules for sustainable applications such as electrochemical carbon capture. A primary challenge in this approach is the high computational cost…

Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing challenges for…

The Fokker-Planck (FP) equation is a linear partial differential equation which governs the temporal and spatial evolution of the probability density function (PDF) associated with the response of stochastic dynamical systems. An exact…

The structure of proteins is the basis for studying protein function and drug design. The emergence of AlphaFold 2 has greatly promoted the prediction of protein 3D structures, and it is of great significance to give an overall and accurate…

With the tremendous success of large transformer models in natural language understanding, down-sizing them for cost-effective deployments has become critical. Recent studies have explored the low-rank weight factorization techniques which…

Fourier and related transforms is a family of algorithms widely employed in diverse areas of computational science, notoriously difficult to scale on high-performance parallel computers with large number of processing elements (cores). This…

We study a distributed antenna system where $L$ antenna terminals (ATs) are connected to a Central Processor (CP) via digital error-free links of finite capacity $R_0$, and serve $K$ user terminals (UTs). We contribute to the subject in the…

In this article we present an algorithm to efficiently evaluate the exchange matrix in periodic systems when Gaussian basis set with pseudopotentials are used. The usual algorithm for evaluating exchange matrix scales cubically with the…

Affine Frequency Division Multiplexing (AFDM), a new chirp-based multicarrier waveform for high mobility communications, is introduced here. AFDM is based on discrete affine Fourier transform (DAFT), a generalization of discrete Fourier…

Multicomponent density functional theory (DFT) enables the consistent quantum mechanical treatment of both electrons and protons. A major challenge has been the design of electron-proton correlation functionals that produce even…

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability…

Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary…

Density functional theory (DFT) remains the most widely used electronic structure method. Although exact in principle, in practice, it relies on approximations to the exchange-correlation (XC) functional, which is known to be a unique…

Parameter Recombination (PR) methods aim to efficiently compose the weights of a neural network for applications like Parameter-Efficient FineTuning (PEFT) and Model Compression (MC), among others. Most methods typically focus on one…

This paper proposes an anti-interference affine frequency division multiplexing (AFDM) system to ensure reliability and resource efficiency under malicious high-power interference originating from adversarial devices in high-mobility…

The feedback particle filter (FPF) is an innovative, control-oriented and resampling-free adaptation of the traditional particle filter (PF). In the FPF, individual particles are regulated via a feedback gain, and the corresponding gain…

Parameter Efficient Fine-Tuning (PEFT) is a key technique for adapting a large pretrained model to downstream tasks by fine-tuning only a small number of parameters. Recent methods based on Fourier transforms have further reduced the…