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A fundamental step in the rational design of vascular targeted particles is the firm adhesion at the blood vessel walls. Here, a combined Lattice Boltzmann Immersed Boundary model is presented for predicting the near wall dynamics of…
Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse…
Peptides are recognized for their varied self-assembly behaviors, forming a wide array of structures and geometries, such as spheres, fibers, and hydrogels, each presenting a unique set of material properties. The functionalities of these…
Understanding interactions between microparticles and lipid membranes is of increasing importance, especially for unraveling the influence of microplastics on our health and environment. Here, we study how a short-ranged adhesive force…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
The evolution of drug-resistant microbial species is one of the major challenges to global health. The development of new antimicrobial treatments such as antimicrobial peptides needs to be accelerated to combat this threat. However, the…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
We use Markov state models (MSMs) to analyze the dynamics of a $\beta$-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin…
Microswimmers such as E. Coli bacteria accumulate and exhibit an intriguing dynamics near walls, governed by hydrodynamic and steric interactions. Insight into the underlying mechanisms and predominant interactions demand a detailed…
Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
Recently, Antimicrobial peptides (AMPs) have been an area of interest in the researches, as the first line of defense against the bacteria. They are raising attention as an efficient way of fighting multidrug resistance. Discovering and…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and…
An efficient method is reported for rapid identification of bacterial or mycobacterial infection in a suspected clinical/biological sample. The method is based on the fact that the ring methylene protons of cyclic fatty acids (constituting…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…