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Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle…
Aqueous lithium chloride solutions up to very high concentrations were investigated in classical molecular dynamics simulations. Various force fields based on the 12-6 Lennard-Jones model, parametrized for non-polarizable water solvent…
Several surfactant molecules self-assemble in solution to form long, flexible wormlike micelles which get entangled with each other, leading to viscoelastic gel phases. We discuss our recent work on the rheology of such a gel formed in the…
The self assembly of linear surfactants into reverse micelles (RMs) in nonpolar solvents and their efficiency in reducing the interfacial tension is studied using dissipative particle dynamics simulations. Given the importance of RMs as…
Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows…
There is a growing interest since the 1990s to understand the squeezing and shear behaviors of liquid films at nanometer scale by the atomic force microscope (AFM) measurement. We carry out all-atom contact-mode AFM simulations in a…
We use plasmon rulers to follow the conformational dynamics of a single protein for up to 24 h at a video rate. The plasmon ruler consists of two gold nanospheres connected by a single protein linker. In our experiment, we follow the…
The orientational dynamics of supercooled glycerol using molecular dynamics simulations for temperatures ranging from 323 K to 253 K, is probed through correlation functions of first and second ranks of Legendre polynomials, pertaining…
In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $\delta t$ for integrating the equations of motion. Thus $\delta t = 2$ fs is often used in…
Large scale molecular dynamics simulations are used to investigate the structural and dynamical modifications of supercooled water when confined inside an hydrophilic nanopore. We then investigate the evolution of the auto-organization of…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
The linear viscoelastic response of flexible polymer solutions in the dilute and semidilute unentangled regimes is investigated using Brownian dynamics simulations. The relaxation modulus and dynamic moduli are computed over a wide range of…
More than twenty coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Employing X-ray photon correlation spectroscopy we measure the kinetics and dynamics of a pressure-induced liquid-liquid phase separation (LLPS) in a water-lysozyme solution. Scattering invariants and kinetic information provide evidence…
We report molecular dynamics simulation results for two-component fluid mixtures of Gaussian-core particles, focusing on how tracer diffusivities and static pair correlations depend on temperature, particle concentration, and composition.…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
By performing dynamic Monte Carlo simulations, we investigate the microrheology of isotropic suspensions of hard-core colloidal cuboids. In particular, we infer the local viscoelastic behaviour of these fluids by studying the dynamics of a…
A combined molecular docking and molecular structure in silico analysis on the substrate and product of leukotriene A4 hydrolase (LTA4H) was performed. The molecular structures of the substrate leukotriene A4 (LTA4) and product leukotirene…