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Review
During the eighties, molecular modeling became a promising application in the pharmaceutical industry. In the nineties, biotechnology, automation and robotics have increased the speed for experimental screenings and out-ranked the tedious calculations of computer simulations for drug candidates. Meanwhile, the scientific focus in computational chemistry improved methodologies, models and simulation to better accuracy. Computational power helps to simulate ever more processes at an atomistic or molecular level in bigger systems. What cost millions in the nineties you're desktop personal computer now sports inside. xirrus simulation is ready to use nowadays power for your molecular problems to solve. | |
Applied Atomistic and Molecular Dynamics:
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The big picture - Bottom-UpIn recent decades, your industry stepped top-down below microscopic applications towards nano-scale technologies. We predict within your SME you can profit from our bottom-up approach, that leads beyond molecular modeling and atomistic simulation to provide insight at the nanoscale. This technology leap will help improve top-down R&D with molecular-based bottom-up knowledge. |
xirrus simulation offersxirrus addresses SME managers and researchers, who ask themselves: How to compete with industrial key players but use knowledge from recent research? If your application and your problem is defined molecular, you may ask xirrus simulation.Don't hesitate - innovate!With xirrus simulation, you're driving atomistic simulation to nano-scale applying Molecular Dynamics. Instead of a top-down approach used to construct in macroscopic dimensions down to the nano-technology level, xirrus simulation is used to apply a bottom-up approach and starts with setting up atoms and molecules and scales systems and results up to the systems interactions at nano-scale. This method becomes available for Small and Medium Enterprises (SME) that do not possess capabilities in their own research groups to establish this particular approach, but are as well interested in atomistic details of their research at the heart of nano-technologies, material science, physical chemistry, biological systems or life science.Industrial realworld reference - made anonymousFor the manufacturer of a human implant it is important that his implant shall not be recognised as a foreign entity by the immuno-system, it shall be applicable in surgery and it shall fulfill its function for its expected lifetime. Many of these implications have their origin in molecular interactions with the organism. xirrus simulation has applied as a partner in a research project initiated by a medical-implant manufacturer to improve the interface between target cells and the implant surface and evaluate drug delivery on the nano-scale.Consult xirrus simulation or simulate in-house?Although many commercial and freely available software packages and models do exist, the right choice of parameter sets, appropriate methods and numerical simulation algorithms is not an easy task - lacking the experience for the newer technologies. xirrus partners have worked for years in molecular simulation and keep track of recent method developments, applications and research papers.Atomistic simulation does consider the simulation of molecules as physical entities that should obey physical laws even if some unphysical simplifications or introduced numerical inaccuracies counteract this intention. Our expertise in molecular simulation can interprete the interplay of different components and involved difficulties by heart. It may overcome difficulties that occur in simulations by interpretation and experience. A newcomer tends to struggle with the numerous choices he should wisely decide and may use up computational resources for weeks or months without producing serious results. Therefore, if you decide for in-house solutions you should at least let educate your people in the field or by people from the field. You can always choose to consult xirrus simulation to become your assistance for building up your own research team for molecular simulation. But this makes only sense if your needs for modeling and simulation are large enough to reason its own researchers. What can be achieved?Macroscopic properties are used to fit the molecular models to physical observables measured in experiments. After this essential parametrisation that model may as well predict some of the molecular properties that experiments can not measure well or experiments are not able to distinguish the reasons for deviations.
Current exampleIn many industrial applications, barriers like polymer membranes are involved, that cannot be easily characterised in detail by experiment. In simulation, the transfer of individual molecules through the membrane can be comprehensivly studied and proofs of better suitable substances, properties and conditions may be derived.
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Atomistic SimulationOrganic chemists and material scientists take a close atomistic look at their synthetical molecules or structures by quantum mechanical ab initio or semi-empirical calculations. It helps them better understand key properties of their chemical compounds, or let them investigate possible reaction pathways and products.Molecular ModelingPharmaceutical industries have a long tradition for rational drug design and molecular modeling. They investigate their target and drug molecules with different computational methods to find desirable key qualities for new medical applications.Molecular Simulation (Molecular Dynamics)For larger structures, Molecular Dynamics (MD), Monte Carlo (MC) or e.g. Brownian Dynamics (BD) are applied, that neglect chemical reactions but focuse on structural interactions between molecules based on empirical force fields.This is where xirrus simulation steps in with expertise. When empirical force-fields are used, it is important to understand their limitations and key qualities and gain most out of the limited system set-ups that are computationally feasible. The main advantage of empirical force-fields is their faster computation allows larger nano-scale systems to investigate. Mesoscale SimulationCoarse grained models allow to define even larger systems such as polymers.Due to model simplification computational power is available for larger systems. Simpler models though need more careful calibration to become realistic and keep real properties. Macroscopic SimulationFinite Element Methods (FEM) and Computational Fluid Dynamics (CFD) are used for engineering and design of new powerful shapes, machines and constructions. xirrus will help its CFD partner to combine fluid dynamics of combustions with chemical reactions and particle based systems.Multi-Scale SimulationThe combination of different levels of simulation keeps the bigger systems while investigation of atomic details at points of interest becomes possible.Industrial key playersBig research and market players are equipped with large computational clusters and can afford atomistic simulation of growth reactions, molecular simulations of molten and reorienting compounds, and much more to study their newest applications in e.g. chip design or catalysts.Research at universities and institutesNaturally, every group has its preferred target. Some develop new methodologies and models, many support investigations of existing experiments of their preferred chemistry by computer simulation. Usually computational power is shared, but not the least. The careful research undertaken is more basic and profound. Usually it leads to applications ten years later. | ||
Recommendationxirrus simulation is highly recommended for additional investigations about molecular interactions of your nano-scale systems which help you enhance your systems efficiency and help getting better results in the market place for long-term innovations.Just contact us for further information without obligation.
Dr. Lukas Schuler | |||
Dr. Lukas Schuler is scientist and owner of a didactic certificate of ETH Zürich. He simulated various lipid aggregates on a molecular level and significantly improved the available molecular model.
Replication allowed only with written agreement with xirrus
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