The 2006 Conference That Advanced Molecular Simulation
Imagine watching a bicycle in motion rather than just seeing a static picture of it. This simple analogy, used by researchers in the field, captures the revolutionary power of molecular modeling and simulation 7 .
This transformative approach to understanding nature at its most fundamental level took center stage at the Third Foundations of Molecular Modeling and Simulation Conference (FOMMS 2006), held from July 9-14 at the Semiahmoo Resort in Blaine, Washington 1 .
July 9-14, 2006
Semiahmoo Resort, Blaine, Washington
Special issues in Molecular Physics and Molecular Simulation
Molecular simulations function as a computational microscope that allows scientists to observe the intricate dance of atoms and molecules over time. These simulations predict how every atom in a protein or molecular system will move, based on physics-based models of interatomic interactions 7 .
Simulations provide two crucial advantages that complement traditional laboratory experiments. First, experimental measurements typically produce averages over both space and time. Second, the number of measurable properties is generally much smaller than the number of degrees of freedom in molecular systems 4 .
Provide static snapshots and averaged measurements
Generate dynamic movies and conformational distributions
Powerful combination for interpreting experimental data at atomic resolution 4
A notable theme at FOMMS 2006 was the focus on education and knowledge transfer. With molecular simulation becoming increasingly cross-disciplinary, educators faced the challenge of teaching these complex methods to students with widely varying backgrounds 8 .
Michael P. Allen, in his presentation "Educational Aspects of Molecular Simulation," highlighted practical approaches to this challenge. Successful courses balanced theoretical knowledge with hands-on activity, navigating between treating simulation software as a "black box" and becoming bogged down in programming details 8 .
With the increasing availability of notebook computers and free, portable software, access to computational power was no longer the major limitation it had once been 8 .
Among the research presented at FOMMS 2006, one compelling study demonstrated how molecular simulation aided in solving a puzzling experimental phenomenon: the unpredictable appearance of spiky nanostructures during the continuous flow synthesis of silver "patchy particles" .
Silver nitrate, formaldehyde, and silica particles were mixed with aqueous ammonia solution
The outlet from the first mixer flowed directly into a second mixer where ammonia solution of higher concentration was added
The mixed solution then passed through a residence loop before being collected
Systematic investigation revealed an unexpected culprit: the age of the ammonia solutions. When researchers used freshly prepared ammonia, they observed spiky protrusions growing from the silver patches .
As the ammonia solution aged, these spiky structures became less prominent, disappearing completely after approximately 24 hours of ageing .
The researchers determined that carbon dioxide absorption from ambient air was gradually converting ammonia to ammonium carbonate, effectively changing the reagent's chemical composition .
This ageing process altered the balance between complexed and free silver ions, which in turn affected both nucleation and growth morphology .
The patchy particle synthesis study illustrates how carefully selected reagents enable advanced materials fabrication.
| Reagent | Function in the Experiment |
|---|---|
| Silver Nitrate | Silver ion source for patch formation through reduction to metallic silver |
| Formaldehyde | Reducing agent that converts silver ions to metallic silver in the Tollens-like process |
| Aqueous Ammonia | Complexes with silver ions to form $[Ag(NH_3)_2]^+$, controlling redox potential and growth morphology |
| Colloidal Silica | Dielectric core particles serving as substrates for heterogeneous nucleation of silver |
| Ammonium Carbonate | Additive identified to stabilize reagent behavior and prevent spiky growth morphologies |
The presentations at FOMMS 2006 showcased molecular modeling's expanding applications across chemistry, biology, and materials science. The conference featured invited talks on topics ranging from water transport in nanotubes to industrial fluid properties and protein aggregation relevant to neurodegenerative diseases 1 .
This broad applicability stemmed from major technological advancements that made molecular dynamics simulations more powerful and accessible. The introduction of graphics processing units (GPUs) for simulation allowed researchers to run powerful computations locally at modest cost, while improved physical models increased accuracy 7 .
Top downloaded papers from FOMMS 2003
Special journal issues
Proceedings from FOMMS 2006 were published in special issues of Molecular Physics and Molecular Simulation, creating a valuable scientific resource 1 .
FOMMS 2006 captured molecular modeling at a tipping point—transforming from a specialized niche to an essential tool across scientific disciplines. The conference highlighted how simulations had become crucial for interpreting experimental data, understanding biological mechanisms, and designing novel materials.
The insights gained from both the presentations and formal proceedings continue to influence scientific progress, demonstrating how foundational research in molecular modeling enables innovation across chemistry, materials science, and biology 1 3 .