Related papers: A Modular and Extensible CHARMM-Compatible Model f…
Converting peptide sequences into useful representations for downstream analysis is a common step in computational modeling and cheminformatics. Furthermore, peptide drugs (e.g., Semaglutide, Degarelix) often take advantage of the diverse…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
The recently proposed generalized epidemic modeling framework (GEMF) \cite{sahneh2013generalized} lays the groundwork for systematically constructing a broad spectrum of stochastic spreading processes over complex networks. This article…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…
In this work, a coarse-grained (CG) model of carbon nanotube (CNT) reinforced polymer matrix composites is developed. A distinguishing feature of the CG model is the ability to capture interactions between polymer chains and nanotubes. The…
Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…
NpT ensemble Monte Carlo simulations were performed for fully flexible Lennard-Jones chains in the solid phase. The bond length between monomers within the chains is fixed to $L=\sigma$ and the molecule is free to adopt any configuration.…
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving…
In the field of pharmacokinetics and pharmacodynamics (PKPD) modeling, which plays a pivotal role in the drug development process, traditional models frequently encounter difficulties in fully encapsulating the complexities of drug…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
A generalized-ensemble technique, multicanonical sampling, is used to study the folding of a 34-residue human parathyroid hormone fragment. An all-atom model of the peptide is employed and the protein-solvent interactions are approximated…
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided…
Coarse-grained model for saturated (DCPC, DLPC, DMPC, DPPC, DSPC) and unsaturated (POPC, DOPC) phospholipids is introduced within the Single Chain Mean Field theory. A single set of parameters adjusted for DMPC bilayers gives an adequate…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
Diffusion and flow matching models have recently emerged as promising approaches for peptide binder design. Despite their progress, these models still face two major challenges. First, categorical sampling of discrete residue types…
Tandem Mass Spectrometry is a cornerstone technique for identifying unknown small molecules in fields such as metabolomics, natural product discovery and environmental analysis. However, certain aspects, such as the probabilistic…
We extend the phase field crystal (PFC) framework to quantitative modeling of polycrystalline graphene. PFC modeling is a powerful multiscale method for finding the ground state configurations of large realistic samples that can be further…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…