Moscow University Supercomputing Center

Computer simulations of amyloid-like fibrils

Shaitan Aleksey
Moscow State Uiversity

DRIVER: Understanding structure and properties of artificial amyloid-like fibrils for bionanotechnology applications

STRATEGY: Employ multiscale atomistic computer simulations based on molecular dynamics simulations

OBJECTIVE: Determine the structure and properties of specific amyloid-like fibrils used to enhance retroviral transfection.

IMPACT: Understanding the structure and mechanisms of action of the fibrils

USAGE: Biotechnology, genetic engineering

AREA: Physicochemical Biology, High Molecular Weight Compounds

Investigation of the properties of ultrathin organic films on solid surfaces

Komarov Pavel
Tver State University

DRIVER: Design of new materials based on the multiscale computer simulations

STRATEGY: Using multiscale simulation methods to study the properties of polymer matrix and organic liquids on solid substrates and containing nanoparticles

OBJECTIVE: A fundamental understanding of a mechanism of the formation and stabilization conditions of ultra-thin organic films and filled polymer matrix

IMPACT: New functional materials

USAGE: formation of nanoscale structures, protective coatings

AREA: High Molecular Weight Compounds

Branched polymer system based on the dendritic structures

Darinsky Anatoly
Institute of Macromolecular Compounds of RAS

DRIVER: The establishment of Conformational and dynamic properties of the branched polymer systems containing dendritic structure

STRATEGY: Modeling with coarse-grained models to establish the universal properties of the systems studied

OBJECTIVE: Establish a correlation structure-properties for branched polymer systems based on dendrites to manage their properties

IMPACT: The possibility of predicting the properties of the branched polymer systems based on knowledge of their chemical and spatial structure

USAGE: Branched polymer systems: dendrimers , molecular brushes may find the use in nanotechnologies and biomedicine

AREA: High Molecular Weight Compounds

Computer Simulation of Hypercrosslinked Polystyrene

Lazutin Aleksey
Nesmeyanov Institute of Organoelement Compounds of RAS

DRIVER: Investigation of formation of hypercrosslinked polymer networks. Investigation of the structure of hypercrosslinked polymer networks

STRATEGY: Multi-scale computer simulation

OBJECTIVE: Determination of structural properties of hypercrosslinked polymer networks

IMPACT: Knowledge of formation of hypercrosslinked polymer networks and their structure

USAGE: Development of theory of polymer networks

AREA: Structure and Dynamics of Atomic-Molecular Systems, High Molecular Weight Compounds

Structure and dynamic properites of polymer nanocomposites

Liulin Sergey
Institute of Macromolecular Compounds of RAS

DRIVER: Study and prediction of structure and dynamic properties of polymer nanocomposites

STRATEGY: Development of nanocomposite models, further computer simulation of their structure and dynamic properties on the base of quantum mechanics and full-atomic molecular dynamics

OBJECTIVE: Virtual design and testing of advanced polymer nanocomposites, including development of nanocomposite models, further computer simulation of their structure and dynamic properties, study of reinforcement mechanisms

IMPACT: Methodology of calculation and prediction of polymer nanocomposites properties

USAGE: Development of new polymer nanocomposites

AREA: High Molecular Weight Compounds

Computer simulation of stiffness copolymers with different stiffness along the chain

Martemianova Yulia
Moscow State Uiversity

DRIVER: To make a phase diagrams for copolymers with different stiffness along the chain

STRATEGY: We use a coarse-grained model and Monte carlo method.

OBJECTIVE: To study a phase diagram

IMPACT: We will define a main states of the system on phase diagram and describe main structures.

USAGE: display technology, processor technology, medicine

AREA: High Molecular Weight Compounds

Investigation of complexes of peptide dendrimer with biological macromolecules

Neelov Igor
Institute of Macromolecular Compounds of RAS

DRIVER: Investigation of interaction of peptide dendrimer with biological macromolecules

STRATEGY: Use of a method of full atomic molecular dynamics for modeling of dendrimers and biomolecules in water

OBJECTIVE: To get structure and dynamical properties of peptide dedrimers, biological molecules and their complexes

IMPACT: Modification of properties of biomacromolecules by means of formation of complexes with dendrimers

USAGE: Possible use in biomedicine as new biocompatible materials, and also for targeted delivery of drugs and a genetic material

AREA: High Molecular Weight Compounds

Development of new ways to control the nanostructure in thin block copolymer films

Rudov Andrey
Moscow State Uiversity

DRIVER: Modeling of thin films based on both grafted and non-grafted block copolymers. Investigation of structural rearrangements in thin block-copolymer films caused by solvent uptake.

STRATEGY: Using the coarse-grained method like dissipative particle dynamics will significantly reduce the simulation time

OBJECTIVE: 1. Investigation of the morphology of nanostructured polymer films based on graft, as well as star-shaped block copolymers. 2. Investigation of the influence of of condensation processes of non-selective solvent vapor on the structure of the block copolymer films

IMPACT: Creation of high-performance solar cells and membranes with improved characteristics, etc.

USAGE: Medicine, Energetics

AREA: High Molecular Weight Compounds

The effect of nanofiller's surface modification on the structure and properties of nanocomposite polymer materials.

Rudov Andrey
Moscow State Uiversity

DRIVER: It is well known that the properties of the nanocomposite material depend on interaction between nanofiller and the matrix, distribution and orientation of the nanoparticles (fibers nanoplates) in the matrix. Typically, to produce a high quality material, it is necessary to create a highly dispersed distribution of the filler nanoparticles in a polymer matrix. For that reason, as in the case of colloidal suspensions, the steric stabilization of particles is frequently used: the surface of the particles is modified by a polymer which is compatible with the matrix, but prevented the aggregation of the particles. The aim of the project is detailed investigation of the influence of modification of the filler particle surface by the polymers on the properties of the nanocomposites in two cases: l) polymers are adsorbed on the surface (physical crosslinking) and ll) polymers are chemically attached to the particles. Moreover modification conditions will be maximally close to the experimental one.

STRATEGY: To achieve the objectives of the project the following methods of computer simulation will be used: a dissipative particle dynamics (DPD) and molecular dynamics (MD). These methods are based on the numerical solution of Newton's equations with a certain form of interaction potentials. To implement high-performance computing on parallel systems, we will use the program written by the staff of our department and also freeware packet for the classical molecular dynamics such as Lammps.

OBJECTIVE: To begin with we plan to investigate the adsorption process of the amphiphilic macromolecules onto the surface of filler particles in solution. Factors affecting on the adsorption of the polymers such as the shape of the particles, the quality of the solvent and others will be identified. Then modified particles will be placed in a polymer matrix, and their distribution will be determined. In case of chemical modification, various types of polymerization reaction of chains in the shell will be modeled. In particular, we plan to model the process of attaching already prepared chains to the filler particle ("grafting onto" method) and the process of growth of chains occurring by polymerization of the active sites located on the particle surface ("grafting from" method).

IMPACT: Expected scientific effect is related to the development principally new method manufacturing nanocomposites by preliminary surface modification of nanofillers. From a practical perspective, this approach will enable the preparation of nanocomposites with a uniform distribution of filler particles in the polymer matrix, resulting in the creation of new materials with improved characteristics and high mechanical properties.

USAGE: Automotive, aviation and aerospace industry. Medicine.

AREA: High Molecular Weight Compounds

Computer modeling of supramolecular complexes of polyelectrolytes with biological membranes

Gurtovenko Andrey
Institute of Macromolecular Compounds of RAS

DRIVER: The project focuses on molecular mechanisms behind interactions between natural and synthetic polyelectrolytes with biological membranes. Such interactions are important for bionanotechnology as well as for biological processes in cell nuclei. In particular, synthetic polycations are widely used for modulating the structure of biomembranes. Lipid bilayer membranes are of increasing interest due to their potential to serve as delivery vectors for DNA strands which are essentially natural polyanions. Despite the importance of the polyelectrolyte-membrane interactions the molecular mechanisms of such interactions and the microscopic structure of supramolecular polyelectrolyte-membrane complexes remain largely unknown mostly due to limitations of existing experimental techniques. In this project we will employ the state-of-the-art computer modeling along with computational models of high (atomistic) resolution to get insight into the interactions of anionic DNA molecules and synthetic cationic polymers with model phospholipid membranes.

STRATEGY: In order to unlock molecular mechanisms of the polyelectrolyte-membrane interactions, we will use the state-of-the-art computer simulations. In particular, the molecular dynamics techniques will be used; this method is nowadays one of the standard tools for studying complex biomolecular and polymer systems. To describe polyelectrolytes (synthetic cationic polymers and native polyanionic DNA molecules) and phospholipid model membranes we will employ computational models of high (atomistic) resolution, in which the chemical structure of compounds is explicitly accounted for. This allows us to obtain microscopic details of adsorption processes, the details that are not accessible for most experimental methods. The usage of atomistic models and relatively large size of the polyelectrolyte-membrane systems will require considerable multi-CPU computational resources. It should be emphasized that the project leader has extensive experience of computer modeling of biomolecular and polymer systems, which can be seen through high scientific impact of his publications (1500 citations, H-index 24).

OBJECTIVE: The project focuses on a systematic study of adsorption of various types of polyelectrolytes on biomembranes. DNA polyanions and synthetic polycations (such as polyethylenimine and poly-L-lysine) will be considered as polyelectrolytes. The main objective of the project is to establish possible mechanisms behind a controlled manipulation of permeability of biomembranes due to adsorption of polyelectrolytes. The structure and stability of supramolecular complexes "DNA-lipids" which are used for gene delivery will be also of special interest.

IMPACT: The supramolecular complexes of natural and synthetic polyelectrolytes with biological membranes play a crucial role in biotechnology, medicine and biology, thereby making the present research project timely and important. The results will stimulate further development novel, antibacterial agents as well as new effective liposome-based vehicles for DNA delivery. Most of the problems mentioned in the project have not been handled yet with the use of atomic-scale computer modeling. Therefore, a successful implementation of the project will produce a number of pioneering contributions into the very promising area of biological and biomedical research.

USAGE: The results of the project can be used in medicine, biotechnology, pharmacy, and biology.

AREA: High Molecular Weight Compounds, Physical Chemistry, Physicochemical Biology