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In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, Choline Chloride (ChCl) and urea, in 1:2 molar ratio form a deep eutectic mixture, a liquid at room temperature and…
We report the first measurements of the dynamics of liquid germanium (l-Ge) by quasi-elastic neutron scattering on time-of-flight and triple-axis spectrometers. These results are compared with simulation data of the structure and dynamics…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas,…
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Binary mixtures of water with lower alcohols display non-linear phase behaviour upon mixing which are attributed to potential cluster formation at molecular level. Unravelling such elusive structures requires the investigation of…
We review exact formalisms for describing the dynamics of liquids in terms of static parameters. We discuss how these formalisms are prone to suffer from imposing restrictions that appear to adhere to common sense but which are overly…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the…
We investigate how shear influences the dynamics of active particles in dilute to concentrated suspensions. Using apolar active suspensions of squirmers as model systems, we show how their long-time diffusive dynamics can surprisingly slow…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…