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Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
This study investigates the spatial integration of agent-based models (ABMs) and compartmental models for infectious disease modeling, presenting a novel hybrid approach and examining its implications. ABMs offer detailed insights by…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
By leveraging quantum-mechanical properties like superposition, entanglement, and interference, quantum computing (QC) offers promising solutions for problems that classical computing has not been able to solve efficiently, such as drug…
Accurate identification of antiviral peptides (AVPs) is critical for accelerating novel drug development. However, current computational methods struggle to capture intricate sequence dependencies and effectively handle ambiguous,…
The reconfiguration of soft, deformable particles upon adsorption at the interface between two fluids underpins many aspects of their dynamics and interactions, ultimately controlling the macroscopic properties of particle monolayers of…
Large language models (LLMs) have shown remarkable advancements in chemistry and biomedical research, acting as versatile foundation models for various tasks. We introduce AMP-Designer, an LLM-based approach for swiftly designing novel…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…
Protein folding -- the problem of predicting the spatial structure of a protein given its sequence of amino-acids -- has attracted considerable research effort in biochemistry in recent decades. In this work, we explore the potential of…
Nanophotonic devices excel at confining light into intense hot spots of the electromagnetic near fields, creating unprecedented opportunities for light-matter coupling and surface-enhanced sensing. Recently, all-dielectric metasurfaces with…
Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized…
A stable added-mass partitioned (AMP) algorithm is developed for fluid-structure interaction (FSI) problems involving viscous incompressible flow and compressible elastic solids. Deforming composite grids are used to effectively handle the…
Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as limited controllability, lack of representations that efficiently model antimicrobial properties, and low experimental hit rates. To address these…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
Atomistic simulations of electrochemical interfaces remain challenging due to the long time scales required to adequately sample the structure of the electric double layer. The emergence of efficient, short-range machine learning…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…
Water-phospholipid interactions at the lipid bilayer/water interfaces are of essential importance for the dynamics, stability and function of biological membrane, and are also strongly associated with numerous biological processes at the…