Computational Chemical Physics Group

Exploring Nature With Computer Simulations

August 20, 2016
by Danilo Roccatano

Molecular Properties of Astaxanthin in Water/Ethanol Solutions from Computer Simulations

Khadga Jung KarkiSusruta Samanta, and Danilo Roccatano*

J. Phys. Chem. B, August 2016

DOI: 10.1021/acs.jpcb.6b06055

Astaxanthin (AXT) is a reference model of xanthophyll carotenoids, which is used in medicine and food industry, and has potential applications in nanotechnology. Because of its importance, there is a great interest in understanding its molecular properties and aggregation mechanism in water and mixed solvents. In this paper, we report a novel model of AXT for molecular dynamics simulation.

The model is used to estimate different properties of the molecule in pure solutions and in water/ethanol mixtures. The calculated diffusion coefficients of AXT in pure water and ethanol are (3.22 +/- 0.01) 10-6 cm2s-1 and (2.7+/-0.4) 10-6 cm2s-1, respectively. Our simulations also show that the content of water plays a clear effect on the morphology of the AXT aggregation in water/ethanol mixture. In up to 75% (v/v) water concentration, loosely connected network of dimers and trimers, and two-dimensional array structures are observed. At higher water concentrations, AXT molecules form more compact three-dimensional structures that are preferentially solvated by the ethanol molecules. The ethanol preferential binding and the formation of a well connected hydrogen bonding network on these AXT clusters, suggest that such preferential solvation can play an important role in controlling the aggregate structure.


April 5, 2016
by Danilo Roccatano

Strings-to-Rings Transition and Anti-parallel Dipole Alignment in Two-Dimensional Methanols

Ronen Zangi and Danilo Roccatano

Nano Lett. 2016, DOI: 10.1021/acs.nanolett.6b00460


Structural order emerging in the liquid state necessitates a critical degree of anisotropy of the molecules. For example, liquid crystals and Langmuir monolayers require rod/disc-shaped and long chain amphiphilic molecules, respectively, to break the isotropic symmetry of liquids. In this paper, we present results from molecular dynamics simulations demonstrating that in two-dimensional liquids, a significantly smaller degree of anisotropy is sufficient to allow structural organization. In fact, the condensed phase of the smallest amphiphilic molecule, methanol, confined between two or adsorbed on, graphene sheets form a monolayer characterized by long chains of molecules. Intra-chain interactions are dominated by hydrogen bonds, whereas inter-chain interactions are dispersive. Upon a decrease in density toward a gas-like state, these strings are transformed into rings. The two-dimensional liquid phase of methanol undergoes another transition upon cooling; in this case, the order-disorder transition is characterized by a low-temperature phase in which the hydrogen bond dipoles of neighboring strings adopt anti-parallel orientation.

February 3, 2016
by Danilo Roccatano

Invited Seminar at Norwich

On 3rd February 2016, Danilo Roccatano visited the School of Computing Science of the University of East Anglia in Norwich hosted by Dr Steven Hayward. He gave the invited seminar:

Study of Interaction Mechanisms of Block Copolymers with Biological Interfaces


Polyethylene oxide and polypropylene oxide homopolymers, as well as block copolymers based on them (Poloxamers or Pluronics®) have many applications in biotechnology and in pharmacology. This versatility is due to their biocompatibility and tuneable properties. Still, the molecular mechanisms of their interactions with biological systems remain not fully investigated. A powerful and versatile approach to study these processes is the Molecular Dynamics (MD) simulation method that allows exploring these systems on scale of a different order of magnitude in length and time. In the last years, we have developed for these purpose full atoms and coarse-grained models of these polymers that have been successfully tested against several experimental data in solution, and at the interface with lipid bilayers. Using a recently proposed and developedSelf-Consistent density Field MD method, we also accomplished to perform large-scale simulations study of polymeric micelles formation and their interaction with lipid bilayers. These results have unrevealed possible mechanisms of single polymer and micelle interaction with lipid bilayers. In this talk, I will summarize the main achievements and future directions of these studies.


December 16, 2015
by Danilo Roccatano

Physics Christmas Lecture 2015

Exploring the Molecular Machines within: a Fantastic Voyage

DrDanilo Roccatano

Lincoln School of Mathematics and Physics

Wednesday 16th December 2015

at 3.30 pm

EMMTEC Lecture Theatre, Brayford Pool Campus, University of Lincoln


To see a World in a Grain of Sand

And a Heaven in a Wild Flower,

Hold Infinity in the palm of your hand

And Eternity in an hour.

William Blake, Auguries of Innocence

Roccatano 2015















Nature is a great source of inspiration and emulation for scientist and engineering, and the continuous advance in the knowledge of the complex machinery of life is producing profound impacts in the modern societies. Life, in the form that we know, definitively exploited what we now call “nanotechnology” to emerge. Living cells are crowded of fascinating molecular machines with a large variety of functions not yet completely explored. Nature as a blind and patient engineer builds these machines without a blueprint but using the evolution. However, in the last 50 years, thanks to the continuous accumulation of knowledge, we have also learnt how to produce new nanosized engineering marvels.

The story plot of the 1966 SF movie A fantastic voyage, popularized with the novel written by the polymath science fiction writer Isaac Asimov, is based on the exploration of the human body with a cell sized submarine. In this talk, we will take a next step in this fantastic voyage to explore the nuts and bolts of our cell. We will use as submarine powerful computers and our imagination. In this voyage, we will discover that machines similar to those used in our day-life experience are within us and their functions is nowadays studied using the same basic physical laws discovered 350 years ago by the universal genius Isaac Newton. Therefore, the same principles that describe the motion of stars in our galaxy is helping us to unravel the complex machinery of life.