NanoHive@home

NanoHive@Home is a distributed computing system used for large-scale nanotech systems simulation and analysis. The goal of NanoHive@Home is to perform large-scale nanosystems simulation and analysis that is otherwise too intensive to be calculated via normal means, and thereby enable further scientific study in the field of nanotechnology.

NanoHive@home project URL; http://www.nanohive-1.org/atHome/

About NanoHive@home

NanoHive@home

Getting started

Participants

Community

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Information

Here are some key points about the NanoHive@Home project:

Completely open-source and free
Not-for-profit, and with all results made available to the public domain, free and clear
Benefits humanity by advancing our knowledge and understanding of nanotechnology
Calculations are performed with state-of-the-art simulation software making the most use of your donated computing power
Attention to security and safety so that you can run our software without worrying that it will damage your computer
Interesting and interactive graphics and screensaver that shows more of the simulation results as they become available
Uses the popular Berkeley Open Infrastructure for Network Computing (BOINC) platform so you can contribute via a familiar interface

Benefits to Humanity

The video is the result of a simulation designed to test various distributed computing mechanisms. While just a test, it's still an interesting simulation to watch. Three carbon nanotubes are anchored at their ends, and a diamondoid carbon "knife" is pushed down on the nanotubes with a 5 nanonewton force. Will the knife cut through the nanotubes? Watch the video for some nanotube-fu.

Nanotechnology is the understanding and manipulation of matter at the molecular scale. At this scale, the physical and chemical properties of materials are fundamentally different from material at micrometer or larger scales. It is that fundamental difference which is both the cause of amazing challenge and potentially amazing benefit to humanity.

As we increase our understanding of nanotechnology and our ability to manipulate matter at this scale, a broad range of vital industries and applications begin to benefit. Here are some examples:

Medicine: New pharmaceuticals, therapeutics, drug delivery methods, skin care and protection, anti-viral coatings, biocompatible materials, nerve and tissue repair, cancer treatments, and diagnostic methods
Energy: Development of efficient, inexpensive catalysts for hydrogen production and storage
Computing: Molecular circuitry will enable significant advances in processor speed, energy efficiency, parallelization, data transfer speeds, ultra-dense storage capacity, and quantum computing.
Materials: New composites with significantly improved properties compared to traditional materials
Security: Ultra-sensitive chemical sensors

Accompanying the targeted benefits of nanotechnology are potential risks. For example, there are concerns over the toxicity of nanoscale devices. This emphasizes the importance of developing our understanding of nanoscale phenomenon so as to reduce the potential risks.

Screensaver Graphics

Here's a screenshot of the NanoHive@Home screensaver graphics.

NanoHive@Home screensaver graphics

NanoHive@Home

Nanohive@home Fine Motion Controller One limitation of nanoscale computer simulation is the size of system that can be simulated. Small systems of hundreds or perhaps thousands of atoms can be simulated with a high level of quantum mechanical accuracy on single computing clusters, but systems of hundreds of thousands, or millions of atoms are prohibitively large for calculation with in-house computing hardware.

Another limitation is the number of analyses that can be performed in a timely manner. Quantum mechanical optimization of a single molecular structure can take several hours. A search for alternative minimum energy structures could involve thousands of optimizations consuming several thousand hours - years of computation.

The goal of NanoHive@Home is to perform large-scale nanosystems simulation and analysis that is otherwise too intensive to be calculated via normal means, and thereby enable further scientific study in the field of nanotechnology.

NanoHive@Home works with scientists developing large nanosystems to understand what simulations will result in publications that would have the biggest impact in the field. For example, our first production simulations are for the testing and development of a series of nanofactory mechanisms. Nanofactories, also called assemblers, are seen as one of the most important (potential) milestones in the field of nanotechnology. They are machines that build products using direct molecular manipulation. An illustrative movie of the nanofactory in operation is at the bottom of this article.

Nanoscale Simulation

Before we can productively assemble, or orchestrate the assembly of nanoscale devices and systems, we must understand them. Computer simulation of nanosystems is critical to testing and exploring our theories and ideas about nanotechnology.

Simulation enables us to perform experiments with nanosystems that we can not yet build.
It is a key part of research and development in terms of economy. Simulation can take significantly less money than owning or renting the equipment and expertise necessary to build and instrument real nanodevices
It enables us to perform experiments that may be too hazardous to perform otherwise

Screenshot of the simulation software

Simulation Software

At its core, NanoHive@Home uses the NanoHive-1 Nanospace Simulator to calculate the simulations. NanoHive-1 is a modular simulator used for modeling the physical world at a nanometer scale. Two important issues that NanoHive-1 was designed to handle are

The number and complexity of factors that play a part in simulating nanospace
The computational intensity required to calculate those factors for each atom per time and space quantum

To that end, the architecture of the simulator provides a plugin framework for key simulation functions such as the physical interactions between atomic and molecular entities, and the traversal of atomic and molecular entities in time and space. A detailed description is available here. The BOINC platform is integrated with NanoHive-1 via two plugins:

BOINC_PIC_Control plugin. This plugin interfaces the master NanoHive-1 instance with the BOINC server components to generate, and re-assimilate work units. PIC stands for Physical Interaction Calculator, which essentially represents a computer running NanoHive-1 (although it could also be a cluster of computers sharing the same memory).
BOINC_ClientControl plugin. This plugin interfaces the Main Program with the slave NanoHive-1 instance running on the participant.s computer. The Main Program orchestrates the process of un-zipping and executing the graphics/screensaver program and NanoHive-1 simulator, monitoring simulation progress, and finally communicating claimed credit via the BOINC Manager.

This diagram shows how all the components are coordinated:

The Q-SMAKAS Tooltip Failure Mode Search Project

Nanohive haveland schematic The project scope (and the reason behind the Q-SMAKAS project) is best introduced in the context of the nanofactory movie, which you can view at the bottom of this article. As a quantum chemist, the business end of the movie to my mind occurs between 1 min. 47 sec. and 2 min. 34 sec., the region between which the molecular tooltip binds an acetylene feedstock, a second tooltip dehydrogenates the acetylene (which is another interesting project to think about simulating as well!), and the now highly strained carbon dimer (C2) finds itself deposited onto a workspace (in the movie a block of diamond, which is ALSO an interesting project to think about simulating). I refer to this part of the movie as the quantum chemical "business end" because the act of making and breaking chemical bonds (as shown) is something that precious few molecular mechanics programs (the common "ball and spring" molecular simulations) are capable of simulating (and those that can are still under active development). Quantum chemistry is the route by which such changes to electronic structure are best handled.

The intent of Q-SMAKAS as a general simulation protocol is to diagnose defect structures from among a selection of tooltips as a means to predicting which ones are more or less likely to behave correctly in this mechanosynthetic context (to weed out the field of candidate structures).

Sourcecode

NanoHive@Home is open-source. Specifically, all the green hexagonal programs in the above illustration that make up NanoHive@Home are available via Sourceforge.net CVS (browse).

Cool movie showing a nanofactory in operation

This is an illustrative movie of the nanofactory in operation. A slideshow is available here, and this same movie is avalable in hi-res for download here [86.1 Mb Quicktime]. See the NanoFactory project page for technical information and details about the simulations.