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An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
Adaptive precision molecular dynamics simulations have developed along energy- and force-coupling approaches, which allow for a continuous transition between different particle descriptions or interaction potentials. Most approaches…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
The calcium (Ca$^{2+}$) signalling system is important for many cellular processes within the human body. Signals are transmitted within the cell by releasing Ca$^{2+}$ from the endoplasmic reticulum (ER) into the cytosol via clusters of…
Post-Translational Modifications (PTMs) are known to play a critical role in the regulation of the protein functions. Their impact on protein structures, and their link to disorder regions have already been spotted on the past decade.…
Periodic crystals repeatedly instantiate similar local coordination motifs across translated cells and chemically related structures, but current equivariant atomistic models usually encode these patterns only implicitly in dense edge…
As photonic systems progress toward enhanced miniaturization, dynamic reconfigurability, and improved energy efficiency, a central challenge endures: the accurate and independent control of optical losses and resonant properties on…
Plasma electrolytic oxidation (PEO) processing of EV 31 magnesium alloy has been carried out in fluoride containing electrolyte under bipolar pulse current regime. Unusual PEO cathodic micro-discharges have been observed and investigated.…
We survey the current state of phase change memory (PCM), a non-volatile solid-state memory technology built around the large electrical contrast between the highly-resistive amorphous and highly-conductive crystalline states in so-called…
Conducting Polymer Dendrites (CPD) can engrave sophisticated patterns of electrical interconnects in their morphology with low-voltage spikes and few resources: they may unlock in operando manufacturing functionalities for electronics using…
The paper addresses a common assumption of elastoplastic modeling: that the recoverable, elastic strain increment is unaffected by alterations of the elastic moduli that accompany loading. This assumption is found to be false for a granular…
We compare the predicted phase behaviour of lead (Pb) using three different interatomic potential models, including an embedded atom method (EAM), a modified embedded atom method (MEAM), and a neural network-based machine-learned model in…
The crystal plasticity finite element method (CPFEM) is a widely used technique for resolving macroscopic stress and strain onto the physically relevant length scales of grains and slip systems in ductile crystalline materials like…
The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…
Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work, we show that the enzyme can interact with the lipid membrane and further alter its mechanical properties. Vesicle fluctuation spectroscopy is…
Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…
Simple cubic (SC) phase has been long experimentally determined as the high-pressure phase III of elemental calcium (Ca) since 1984. However, recent density functional calculations within semi-local approximation showed that this SC phase…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…
Phase Change Memory (PCM) is an attractive candidate for main memory as it offers non-volatility and zero leakage power, while providing higher cell densities, longer data retention time, and higher capacity scaling compared to DRAM. In…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…