Science of Atoms and Molecules

The Science of Atoms and MoleculesThe Science of Atoms and Molecules project offers 24 research-based, field-tested activities for physics, chemistry, and biology. We provide these all freely to teachers and students online. Through the SAM activities' interactive models and simulations, we involve students in active learning. Teachers can register online to receive Teacher Guides for each activity and to gain access reporting functions to track student progress.

SAM was designed to assist the realignment of high school science disciplines into a physics, chemistry and biology sequence. Funded by NSF from 2006-2010*, SAM activities provide critical atomic-scale science content that can enable and take advantage of the revised sequence. The atomic and molecular model-based activities facilitate not only the disciplinary order but also four thematic sequences: Motion and Energy, Charge, Atoms and Molecules, and Light.

This NSF-funded project has achieved its goal of providing the materials and professional development resources that schools need to implement high-quality secondary science curricula with a unifying theme of atoms and molecules. The SAM materials enable students to acquire a progressive understanding of the centrality of atomic-scale phenomena and their implications.

Biology, chemistry, and physics courses do not have to be entirely re-written to profit from the new sequences. In many cases, the needed new content can be substituted as an enhanced approach to traditional content. This atomic/molecular content, together with the revised order, makes it easier to reason causally about phenomena that lie at the heart of modern science and technology.

The target audience of the SAM project is students enrolled in grades 8 through 12. Some of the activities have been enhanced from previous National Science Foundation funded projects undertaken at the Concord Consortium, namely – Molecular Workbench, Molecular Logic and Molecular Literacy.

*The SAM Project was originally funded from 2006-2009 and was extended from 2009-2010 via NSF’s RAPID funding mechanism.

Principal Investigator

Frieda Reichsman

Project Inquiries

freichsman@concord.org

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This material is based upon work supported by the National Science Foundation under Grant No. DRL-0946582. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

How to cite this material.

Usage/Citation

The Concord Consortium (n.d.) Science of Atoms and Molecules. Retrieved 2014, December 20 from http://concord.org/projects/sam

Disclaimer: The Concord Consortium offers citation styles as a guide only. We cannot offer interpretations about citations as this is an automated procedure.

Connecting the Sciences

Overview: Why Teach the Science of Atoms and Molecules?

An excerpt from "The Science of Atoms and Molecules," published in @Concord, Spring 2007 vol. 11, no. 1.

The Science of Atoms and Molecules Computer ModelPhysics, chemistry, and biology have long been taught as separate subjects although there is very little subject matter that is exclusive to any one of them. However, students have little chance to recognize the connections because they are not made explicit. The Science of Atoms and Molecules (SAM) project emphasizes the connections between physics, chemistry, and biology by getting students to explore science at the atomic and molecular level.

The science of atoms and molecules is the fundamental basis of biology. Atoms and molecules are also central to modern chemistry, earth science, electronics, nanoscience, forensics, and all the interdisciplinary fields like biochemistry, space weather, and plasma dynamics.

The atomic world is very different from our macroscopic world. Indeed, many of the instincts you have developed about the way things work do not apply at the atomic scale. It is critically important to understand the science of atoms and molecules because it is at the heart of modern science and technology. “A concise summary of the last 100 years of science is that atoms and molecules are 85% of physics, 100% of chemistry, and 90% of modern molecular biology,“ claims Concord Consortium board member Leon Lederman.

Read more: "The Science of Atoms and Molecules."

How Do People Learn?

Learning Progressions Strengthen Understanding

An excerpt from "Why Are Progressions Important?," published in @Concord, Fall 2006.

"We must learn how to walk before we can run."
–French Proverb
"If you have a strong foundation, then you can build or rebuild anything on it. But if you've got a weak foundation you can't build anything."
–Jack Scalia

The Hows and Whys of Science

Diffusion, the tendency of atoms and molecules to spread out evenly, seems to be a simple concept; perfume sprayed in one corner of the room soon spreads out throughout the entire room. Dissolving salt into water seems like a similarly easy concept. They are phenomena that are common and easily accessible to students. But do students really understand them? If a student cannot explain why the perfume smell soon permeates the room and the salt dissolves into the water, then do they really understand the phenomena?

Physics, chemistry, and biology are full of complex interrelationships of atoms and molecules. Underneath it all, the goal of science is to explain the natural world around us. Using the power of models in Molecular Workbench, the SAM project gives students a firm footing in the Hows and Whys of science. Students first learn the basics:

From Diffusion, Osmosis & Active Transport1. Atomic Movement Never Stops.
Students start with a single molecule in a virtual container and gradually add molecules to the system. As they add heat energy, they observe increased frequency of molecular collisions. Students can select a single molecule and trace its path to see how its motion is affected by collisions with other molecules. By changing the amount of heat in the system, students can address issues of thermal motion, average kinetic energy of molecules, and temperature. This dynamic picture of matter composed of constantly moving and colliding molecules must be a foundation of students' mental models.

From Solubility2. It's a Sticky, Sticky Molecular World. 
Few students realize that all atoms attract one another. This fundamental idea is central to an understanding of the atomic scale. It is quite common for students to think that only opposite charged ions are attracted to each other. Our model allows them to experiment with systems that depict attractive forces, such as van der Waals and hydrogen bonds that exist between atoms and molecules.

With just these basic building blocks, students can explain the migrating perfume smell as perfume molecules randomly bumping into other molecules in the air and will be able to predict what will occur when the temperature is changed. Similarly, students can explain the dissolving salt as a combination of random molecular movements coupled with attractive forces between the polar water molecules and charged ions in salt.

Once students have mastered these building blocks, they have a strong foundation on which to build their understandings and explanations of more complex phenomena, such as chemical reactions, protein folding, and photosynthesis.

Read more of "Why Are Progressions Important?" describing a sequence of learning progressions used to teach about DNA and protein synthesis.

Models & Simulations

The SAM activities use the scientifically accurate models and simulations of the Molecular Workbench to assist students in visualizing and understanding the molecular level.

Models are used everywhere, from insuring the safety of the car you ride in to designing the next anti-cancer drug. Why are models so useful, and what are their limitations?

Models & Simulations Screen ShotUsing computational models of atoms and molecules, both scientists and students can...

  • experience an otherwise inaccessible world
  • construct mental models of how atoms and molecules interact
  • connect atomic-scale events with the macroscopic world
  • understand and predict macroscopic phenomena

The Molecular Workbench is designed with students in mind. There is a real distinction between the scientist's use of models and a student's use. Scientists are often searching for fine detail, performing extensive preparations, and using long runs of a model to get their results. On the other hand, students require short, repeatable experiments with the ability to change variables on the fly, allowing fundamental concepts to emerge quickly.

Modeling limitations help teach critical thinking

Of course, models are not perfect: models and reality are not identical. The limitations of models and simulations is as important for using them as an understanding of the phenomenon being modeled. Just check out the weather forecast to see the results of a model that is pretty good at telling you the weather over the next day or two, but not so good at telling you the weather a week from now. Teaching students to understand and anticipate the limitations of models is an example of building critical thinking skills. Students can come to understand that even with the limitations we learn enough from using models to improve our understanding and make more accurate predictions.

Butter & OilThe molecular dynamics engine in Molecular Workbench simulates the motion of atoms and molecules by (1) calculating the interaction forces among them (including bonded and non-bonded interactions) and then (2) predicting their movement using Newton's equation of motion.

Butter & OilWithout models, it is very difficult to understand what happens at the molecular level. However, that does not mean that what goes on at the molecular level is unimportant. On the contrary

Molecular Workbench Learning Environment

Molecular WorkbenchSAM activities are presented in the Molecular Workbench (MW), a free, open source learning environment that integrates molecular dynamics, lesson authoring, student interaction and content delivery. Using the MW modeling environment, students gain an understanding of what is happening at the atomic scale. This, in turn, can help them understand multiple macroscopic phenomena across the sciences.

“Molecular Workbench.. allows [students]... to generate ideas for experiments, design them, change the parameters as they are carried out, analyze the data that can be shown in graphical and pictorial formats, draw conclusions and share this information with their teachers and fellow students.“

 

The SAM activities were field tested in multiple classes in five diverse schools. Project research was designed primarily to provide feedback to ensure that our materials, assessments, and teacher supports were effective. A number of data sources were employed, including:

  • A Molecular Concept Inventory (MCI) developed in each of the three disciplines (physics, chemistry, and biology) to measure student gains in atomic-scale reasoning. The MCIs were administered before using any activity in the discipline and again after using at least four activities.
  • Embedded assessments in each activity, consisting of questions distributed throughout the activity and a page of questions at the end.
  • Teacher Surveys completed by each teacher immediately after using an activity.
  • Classroom observations conducted in two sites that were within driving distance.
  • A poll, conducted by the external evaluator, of field test teachers on their satisfaction with the materials, approach, and technology.

In year two, formative feedback received from these sources resulted in substantial changes in the materials and the MCI assessment with the result that the final materials resulted in student gains in understanding atomic-scale phenomena, teachers liked the materials, and most teachers would continue to use them.

In year three, 17 of 24 classes selected at random had significant learning gains at the p <.05 level. Gains in all ten of the chemistry classes were significant at the p <.05 level and seven at the p <.001 level. Three of the five physics classes had significant gains at p <.05.

In a subsequent test of revised materials by a different project at CC with 40 Rhode Islands teachers grouped by discipline, all groups had gains at the p <.002 level with moderate effect sizes in chemistry and biology.

A fourth year of project research was subsequently funded by NSF (via "RAPID" funding), targeting student learning in the capstone course (biology) of the three-year course sequence. As of Fall 2010, results from this research are being analyzed.

Prior Results

The Science of Atoms and Molecules project draws on work done with prior grants. In-class research on the effectiveness of Molecular Workbench-based activities is part of each grant. This report will focus on the results from the Molecular Logic grant, which ended in January 2006, and on the Molecular Literacy grant, which has completed its development phase, is in its field-testing phase, and will enter its dissemi-nation phase early next year.

Molecular Logic: Bringing the Power of Molecular Logic to High School Biology

The overall goal of the Molecular Logic (MOLO) project was to supplement high school biology curricula with model-based activities for teaching the physics, chemistry, and molecular biology underpinning biological phenomena. The Molecular Logic project created a set of ten-plus "Molecular Stepping Stones," each an activity focused on one of the basic physical-chemical principles underlying biological processes. These activities were piloted and field-tested in 66 classrooms (16 urban classrooms, 32 suburban, and 18 rural classrooms) and revised. Approximately 1300 students used the materials as part of the study.

Research on Stepping Stones:

During the formative and summative field tests, a pre-test was administered at the beginning of the academic year and a post-test was administered at the end. The items in the assessment were designed to focus on reasoning about the interactions of molecules in relationship to the biological phenomena explored. All test items were short-answer questions for which a rubric was created; Molecular Workbench staff scored test items. Two members scored a subset of tests in order to evaluate inter-rater reliability, which was r=87%.

Below are paired t-test scores for a selection of ten of the classes from the 2004 and 2005 field tests. These classes were chosen to reflect a cross-section of upper- and lower-level classes, as well as a distribution of classes from urban, suburban, and rural locations. For additional data, see http://molo.concord.org/research/.

Pre-Post Learning Gains Test Scores

ClassMeanDiff DFt-valuep-value
113.4711611.68<.0001
2 12.3421810.511<.0001
34.667184.106.0034
41.036133.366.0051
59.7921110.48<.0001
66.5166.842<.0001
76.188153.807.0017
83.962123.749.0028
9 9.526187.397<.0001
1010.38229.268<.0001

Overall, these students show a significant increase in learning. For the above classes, an analysis of variance (ANOVA) was computed in order to determine whether there were any statistically significant differences on the total post-test score based on class level. The analysis revealed that the higher classes performed significantly better (Mean diff 12.5, DF=116, t value=10.638, P value =<.0001) than the lower level students. However, there are no differences in gain scores based on the level. This implies that students make similar gains in learning, but students in upper level classes tend to start with a higher conceptual understanding.

Molecular Reasoning:

To determine further the role of the models on student conceptual understanding, a set of randomly selected pre- and post-tests from upper- and lower-level classes were analyzed for the inclusion of the vocabulary of intermolecular interactions in their reasoning about biological phenomena. Because the Stepping Stone activities were done as supplementary materials to a full-year biology course, the impact of approximately ten activities on student learning (and, by default, their answers to the post-test questions) could most directly be measured by the inclusion of inter-particle interactions. For example, in answering the first question of the assessment –“The instructions on the fertilizer (KCl, a salt like NaCl) for your plant requests that you add water with the fertilizer. Explain what happens to the fertilizer from the moment you add the water to the point when the nutrients enter a root cell.“

Final Evaluation

Excerpted from the Final Evaluation in January 2010:
EXTERNAL EVALUATOR’S REPORT TO THE CONCORD CONSORTIUM AND THE NATIONAL SCIENCE FOUNDATION ON THE SCIENCE OF ATOMS AND MOLECULES: ENABLING THE NEW SECONDARY SCIENCE CURRICULUM PROJECT
January 31, 2010

Goal and Objectives for the SAM project

The goal of the SAM project has been adhered to quite faithfully over the three years of its life. As stated in its proposal this goal is as follows:
“The goal of this project is to provide the materials and professional development resources that schools need to implement high-quality secondary science curricula with a unifying theme of atoms and molecules. Students will acquire a progressive understanding of the centrality of atomic-scale phenomena and their implications. Materials will be presented in a form suitable for all students. The project will also offer the support and professional development that teachers need to use the materials and integrate them effectively into their courses.“ 1

Summary

Overall, this reviewer believes the SAM Project to be a most worthwhile endeavor. As can be seen from the narrative above, the project has made substantial progress since its inception. It has met and, in many cases, exceeded the objectives set forth in its proposal to the National Science Foundation. As mentioned above, the management at Concord is well- organized, creative, technically proficient, research oriented and, importantly, responsive and sensitive to the needs and concerns of participating teachers and students. As can be seen from the evolution of the content of the activities Concord staff has listened to the experiences of participating teachers and to the suggestions of its advisory committee and has made changes that have improved the applicability of the materials. This has worked for most, but not all, of the activities. Several of the activities, as noted above, were felt by some teachers to be either too difficult or lay beyond what was offered in the classroom. However, as can be seen from the questionnaire above - as well as from this reviewer’s discussion with teachers and students – in large part the activities were appropriate and helped learning.

Read the full SAM Final Evaluation Report.

Future Opportunities

The SAM project is central to our efforts to support reform of the secondary science curriculum. We envision a vastly improved approach to science teaching that will delve deeper, connect more concepts, and be far more motivating. The National Science Foundation funding that allowed us to develop and test the 24 SAM activities is just the beginning. We have incorporated SAM materials into other projects at the Concord Consortium and we invite others to use and expand them. The software is open source and the materials are freely available for educational use under a Digital Commons license.

Extensions of SAM work into other projects

RI-TEST. Thanks to funding from the NSF, the RI-ITEST project provides extensive professional development to over 100 Rhode Island science teachers on the use of SAM. That project, under the direction of Daniel Damelin, added a teacher portal that provides formative feedback to teachers who use SAM. When you register for SAM, you are using a RI-ITEST portal.

Innovative Technology in Science Inquiry Scale Up (ITSI-SU). The models and activities developed by SAM are available in short segments that can be easily edited and shared thanks to NSF funding of the ITSI-SU project. This project provides professional development at sites around the country on the use of models and probeware in science education in grades 4-12. Interested teachers should email itsisu@concord.org.

Rhode Island Technology Enhanced Science (RITES). The Concord Consortium is a partner on RITES, a Math-Science Partnership grant to the University of Rhode Island, funded by NSF. Many SAM models and simulations have been incorporated into the RITES Investigations software.

Molecular Workbench. The Molecular Workbench can be used to make molecular dynamics models and to author activities. All SAM activities are authored in MW as well as collections of activities from earlier projects. You can use MW to make your own activities and to share them with the MW community.

The staff of The Concord Consortium will continue to support the software and activities developed for the Science of Atoms and Molecules project. We also would be happy to collaborate on research projects to further refine the educational materials.

What is a SAM activity?

Each of the 24 SAM activities (listed and linked in the table below) is a package of short, connected lessons that include interactive simulations. The activities are usually 8-10 pages in length and designed to be used during the course of two class periods. Each activity page contains one or two simulations for observation and experimentation, explanatory text and graphics, instructions for using the simulation, and embedded questions for assessment. Both formative and summative assessments are embedded right in each activity. Multiple choice questions allow students to check their answers; open response questions ask students to explain their reasoning. Summative assessment is also provided in the form of a Summary page with 6-8 questions.

Overview and Descriptions

To open a full description of an activity with a link to launch it, click on the activity's title in the table below. Before starting the SAM activities in the classroom, an introduction helps students (and teachers) understand how to use SAM activities and their models and simulations. Make sure to check out the Introduction to Molecular Modeling Activity.

Click on an activity name to learn more about it and access a Launch Activity link.

  Physics Chemistry Biology
Introduction Introduction to Molecular Modeling
Motion and Energy Atoms and Energy Phase Change Diffusion, Osmosis, and Active Transport
Heat and Temperature Gas Laws Cellular Respiration
Charge Electrostatics Intermolecular Attractions Four Levels of Protein Structure
Electric Current Molecular Geometry Protein Partnering and Function
Solubility
Atoms and Molecules Atomic Structure Chemical Bonds Introduction to Macromolecules
Lipids and Carbohydrates
Newton's Laws at the Atomic Scale Chemical Reactions and Stoichiometry Nucleic Acids and Proteins
DNA to Proteins
Light Atoms, Excited States and Photons   Harvesting Light for Photosynthesis
Spectroscopy

Introduction to Modeling in SAM

Introduction to Modeling in SAMExplore the concept of molecular modeling and the specific types of models used in SAM activities, along with their controls; starting at a simple level, complexity is added one layer at a time. Students grasp the most important parts of the models and understand how a computer model can be a good representation of what happens in the real world.

Launch the Activity

Learning Goals

Students will be able to:

  • Run a SAM computer model
  • Use the simulation controls of basic SAM models
  • Take a snapshot of a model, annotate it, and use it to answer a question
  • Do an experiment with a SAM simulation
  • Rotate and change the display of a 3D molecule

Atoms and Energy

Atoms and EnergyExplore the First Law of Thermodynamics with molecular-level simulations of kinetic and potential energy.

Launch the Activity

Learning Goals

Students will be able to:

  • Differentiate between kinetic and potential energy
  • Explain how kinetic energy can be converted to potential energy and vice versa
  • Analyze energy graphs and the motion of objects in a system to learn about the Law of Conservation of Energy
  • Apply the First Law of Thermmodynamics when heating or cooling a system
  • Differentiate between energy transfer in an open system and energy conversion
Links to Related Activities
Physics
Chemistry
Biology

Phase Change

Phase ChangeDiscover how phase changes happen and what happens during the latent heat periods of phase change graphs at the atomic level by using simulation measurements of atomic-level kinetic and potential energy.

Launch the Activity

Learning Goals

Students will be able to:

  • Give example of phase changes that occur every day and how they affect the world around us
  • Describe what the phases of matter (solid, liquid, and gas) look like at the atomic level
  • Explain how the forces of attraction are what keep atoms in a particular phase at a specific temperature
  • Explain how the input of energy into a system affects the state of matter
  • Describe how both latent heat and evaporative cooling play a role in changes of phase
Links to Related Activities
Physics
Chemistry
Biology

Diffusion, Osmosis, and Active Transport

Diffusion, Osmosis, and Active TransportControl the concentrations of ions and other molecules, track individual molecules as they diffuse, discover why cell membranes are selectively permeable, explore the effect of surface area, and see how active transport works to move ions against a concentration gradient.

Launch the Activity

Learning Goals

Students will be able to:

  • Compare diffusion and osmosis
  • Explain how concentration differences affect the overall flow of molecules
  • Describe the dynamic nature of equilibrium
  • Apply the principles of diffusion to red blood cells in a real biological system
  • Explain how increased surface area increases the rate of diffusion
  • Explore active transport by experimenting with the relationship between ion concentration and ATP concentration, and observing the formation of electrical energy
Links to Related Activities
Physics
Chemistry
Biology

Heat and Temperature

Heat and TemperatureManipulate simulations to discover temperature as a measure of kinetic energy of atoms and heat as the transfer of energy from hot systems to colder system.

Launch the Activity

Learning Goals

Students will be able to:

  • Distinguish between heat and temperature at the atomic level
  • Determine temperature is related to both the speed and the mass of atoms
  • Explain that temperature is a measure of the average kinetic energy of atoms and molecules in a system
  • Experiment with the amount of energy and the size of a system and its relationship to a rise in temperature
  • Compare thermal radiation and heat conduction
Links to Related Activities
Physics
Chemistry
Biology
  • Molecular Recognition

Gas Laws

Gas LawsExplore the interrelationships of pressure, temperature, and volume with atomic models of Boyle's Law, Charles's Law, Gay-Lussac's Law, and Avogadro's Law.

Launch the Activity

Learning Goals

Students will be able to:

  • Describe gas pressure as it relates to collisions of molecules on a surface of an object
  • Explore the relationship between pressure, volume, temperature, and number of particles as shown in the Ideal Gas Law (PV = nRT)
  • Describe the relationship between pressure and volume in a gas (Boyle's law)
  • Describe the effect of varying the temperature on the volume of a gas (Charles's law)
  • Describe the relationship between temperature and pressure in a gas (Gay? Lussac's law)
  • Explain the relationship between the number of particles and volume of a gas as demonstrated by Avogadro's law
  • Create a model demonstrating why the soda can collapsed and explain the model using the gas laws
Links to Related Activities
Physics
Chemistry
Biology

Cellular Respiration

Cellular RespirationExplore glycolysis and the Krebs cycle reactions from a molecular point of view and discover how the electron transport chain works in the mitochondria to produce ATP for the cell.

Launch the Activity

Learning Goals

Students will be able to:

  • Explain how ATP is used as the cellular energy source
  • Identify electron-accepting molecules NAD and FAD and explain their role in the Electron Transport Chain
  • Recognize glycolysis and the Krebs cycle as the process of breaking down glucose into carbon dioxide and water
  • Understand that cellular respiration is an aerobic process
  • State the overall reaction of cellular respiration
  • Explain the role of enzymes in glycolysis and Krebs cycle
  • Explain how ATP is made by ATP synthase in the mitochondria
Links to Related Activities
Physics
Chemistry
Biology

Electrostatics

ElectrostaticsDiscover how atoms can be charged and manipulate charge and distance to examine Coulomb's Law.

Launch the Activity

Learning Goals

Students will be able to:

  • Explain how a neutral atom can become a charged particle, an ion
  • Define Coulomb forces as a result of like charges repelling each other and unlike charges attracting
  • Determine that the force generated between atoms is dependent on the amount of charge they carry and the distance between them
  • Explore the mathematical relationship described in Coulomb equations
  • Explain polarization in terms of charge redistribution
  • Give an example of how screening is at work in a biological system, such as a cell
Links to Related Activities
Physics
Chemistry
Biology

Intermolecular Attractions

Intermolecular AttractionsExplore how London dispersion attraction and dipole-dipole interactions explain the different boiling points of materials and apply that reasoning to DNA, antibodies, and gecko feet.

Launch the Activity

Learning Goals

Students will be able to:

  • Describe the difference between the kinds of molecules attracted via London Dispersion attractions and dipole-dipole attractions
  • Indicate which type of intermolecular attraction is generally stronger
  • Describe two factors that affect the strength of intermolecular attractions
  • Determine which substance would have the highest boiling point based upon its molecular structure
  • Explain why oil and water don't mix
Links to Related Activities
Physics
Chemistry
Biology

Four Levels of Protein Structure

Four Levels of Protein StructureUsing interactive models, explore how the charge, shape, and polarity of amino acids affect the four levels of protein structure through polar and nonpolar interactions, hydrogen bonding, disulfide bonds, and salt bridges.

Launch the Activity

Learning Goals

Students will be able to:

  • Recognize that a protein's three-dimensional shape allows it to perform a specific task
  • Identify the primary structure of a protein as a linear sequence of amino acids
  • Identify the unique side chains of amino acids that give them their properties
  • Explore how amino acids interact with water and how that affects the way proteins fold
  • Differentiate among the common secondary structures of a protein and identify the importance of hydrogen bonding in stabilizing these structures
  • Identify tertiary structure as the final folding pattern of a protein and infer that mistakes in folding are responsible for many human diseases
  • Explain that quaternary structure occurs when a protein is composed of more than one protein chain (subunit), and that the subunits come together to achieve the protein's function
Links to Related Activities
Physics
Chemistry
Biology

Electric Current

Electric CurrentExplore the relationships between voltage, current, and resistance that make up Ohm's Law using molecular models of circuits.

Launch the Activity

Learning Goals

Students will be able to:

  • Explain how voltage is the driving force behind electron movement
  • Define electric current as the number of electrons flowing through a wire over a given period of time
  • Explain how conductivity and resistivity relate to electric current
  • Infer the relationships between current, voltage, and resistance as described in Ohm's Law (I = V / R)
  • Explain how electricity can be converted to other forms of energy
Links to Related Activities
Physics
Biology

Molecular Geometry

Molecular GeometryUse models of electron arrangement around atoms to discover how molecules form linear, trigonal planar, and trigonal pyramidal shapes.

Launch the Activity

Learning Goals

Students will be able to:

  • Explain that the three-dimensional shape of a molecule is dependent on interactions of electrons, including repulsion to other electrons and attraction to nuclei
  • Recognize linear, trigonal planar, and tetrahedral molecule shapes based on areas of electron density
  • Explain how both shared and unshared electrons (as represented in Lewis dot diagrams) influence a molecule's geometry and use this knowledge to predict the 3D shape of a molecule
  • Differentiate between electron geometry and molecular shape
  • Apply their understanding of small molecule geometry to larger molecules such as fatty acids
Links to Related Activities
Physics
Chemistry
Biology

Solubility

SolubilityExplore molecular views of solvents and solutes to explain how substances dissolve, the differing solubilities of particular solutes in polar and nonpolar solvents, and the effects of temperature on dissolution rates and saturation.

Launch the Activity

Learning Goals

Students will be able to:

  • Create a solution using a model and identify examples of solutions
  • Reason that, for dissolving to occur, the attractions between molecules of a solute and water molecules must be stronger than the solute's intermolecular attractions
  • Discuss how temperature affects the rate of solutes dissolving in solvents and the molecular reasons for saturation
Links to Related Activities
Physics
Chemistry
Biology

Protein Partnering and Function (formerly Molecular Recognition)

Protein Partnering and FunctionBuild "partnerships" between a protein and small molecules, explore the effects of surface charge, polarity and shape on partnering, and learn the importance of a "good fit" between molecules.

Launch the Activity

Learning Goals

Students will be able to:

  • Identify the amino acids on the surface of a protein as responsible for the characteristics of the surface
  • Predict the relative strengths of molecular interactions based on the degree of charge and surface complementarity ("good fit")
  • Predict the characteristics of a ligand ("partner molecule") based on its binding site
  • Make a connection between the surface characteristics of a protein and the protein's function
Links to Related Activities
Physics
Chemistry
Biology

Atomic Structure

Atomic StructureExplore ion formation, isotopes, and electron orbital placement using interactive models of atomic structure.

Launch the Activity

Learning Goals

Students will be able to:

  • Explore the probabilistic electron orbital model to help explain where electrons are most likely to be found
  • Explain that all atoms have similar structure, differing only in the number of protons, neutrons, and electrons
  • Build models of atoms and ions and identify patterns in numbers of protons and neutrons in stable nuclei and ions
  • Describe simple patterns in the periodic table
Links to Related Activities
Physics
Chemistry
Biology

Chemical Bonds

Chemical BondsExplore how differing electronegativities lead to ionic, polar covalent, and nonpolar covalent bonds between atoms.

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Learning Goals

Students will be able to:

  • Explain how negatively charged electrons may interact with other charged particles (opposite charges attract and like charges repel)
  • Explore how a covalent bond is formed between two atoms
  • Explain the term electronegativity and how it plays a role in the formation of chemical bonds: polar covalent, non-polar covalent, and ionic
  • Determine how a dipole is related to the electronegativity of a molecule
  • Predict atomic bonding patterns based on an understanding of electronegativity
Links to Related Activities
Physics
Chemistry
Biology

Introduction to Macromolecules

Introduction to MacromoleculesCompare molecular sizes and shapes with the everyday world, and create polymers from monomer components in this broad introduction to macromolecules.

Launch the Activity

Learning Goals

Students will be able to:

  • Identify the four types of macromolecules and provide examples of their roles in living beings
  • Order relevant cellular objects by size (for example, cell, nucleus, macromolecule,molecule, atom)
  • List four or five of the six elements that make up the macromolecules of living things
  • Identify characteristics common to biological macromolecules: that they can have hundreds or thousands of atoms, that they are made of six or fewer elements, that many are polymers made of closely related or identical units called monomers
Links to Related Activities
Biology

Lipids and Carbohydrates

Lipids and CarbohydratesDiscover how polar bonds and weak intermolecular interactions affect the properties of lipids and carbohydrates, and learn about some of the functions of lipids and carbohydrates in living organisms.

Launch the Activity

Learning Goals

Students will be able to:

  • Define lipids as molecules that do not dissolve in water
  • Recognize what makes lipids non-polar and carbohydrates polar, and determine how polarity affects the solubility of the molecule
  • Explore the structure and function of various polysaccharides
Links to Related Activities
Physics
Chemistry
Biology

Newton's Laws at the Atomic Scale

Newton's Laws at the Atomic ScaleExplore how Newton's Three Laws of Motion at the atomic level explain how mass spectrometry and rockets work.

Launch the Activity

Learning Goals

Students will be able to:

  • Describe how Newton's laws are relevant and in action at the atomic level
  • Observe how Brownian motion seems to contradict Newton's first law and deduce how interactions of individual atoms can approximate Brownian motion
  • Use models to experimentally derive Newton's second law (F=ma) and determine why some atoms move faster than others when equal forces are applied
  • Explain how attraction between atoms (either neutral or oppositely charged) relates to Newton's third law
  • Analyze a real-world example showing Newton's third law
Links to Related Activities
Physics
Chemistry
Biology

Chemical Reactions and Stoichiometry

Chemical Reactions and StoichiometryControl the concentrations of molecules and temperatures of reactions to explore reaction rate dynamically, and change the ratios of chemicals and observe the effects to learn how to balance chemical equations.

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Learning Goals

Students will be able to:

  • Recognize that chemical reactions happen when bonds form and bonds break
  • Analyze how concentration and temperature affect reaction rate
  • Write a chemical reaction, balance the equation, and explain what is happening in words
  • Define the limiting reactant in a chemical equation
  • Classify chemical reactions as: synthesis, decomposition, or single displacement
Links to Related Activities
Physics
Chemistry
Biology

Nucleic Acids and Proteins

Nucleic Acids and ProteinsCreate your own images of DNA using a 3D viewer, explore base pairing, and use interactive models of amino acids, protein chains, and water to understand how proteins fold.

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Learning Goals

Students will be able to:

  • Identify examples of proteins and their functions
  • Identify the monomer components of nucleic acids and proteins
  • Recognize how the side chains of amino acids vary in terms of polarity and determine how this polarity affects the surface, relationship with water, and consequent shape and function of the protein
  • Connect the information carried in DNA to the sequence of its nucleotides
  • Recognize how changes in amino acid sequence cause changes in the folding of the protein
Links to Related Activities
Physics
Chemistry
Biology

DNA to Proteins

DNA to ProteinsTranscribe DNA into RNA, translate RNA into proteins, and make mutations using interactive models. Learn about the interrelationships between DNA, RNA, and proteins.

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Learning Goals

Students will be able to:

  • Describe how DNA, consisting of four bases, can store the genetic code for proteins, which are made from a sequence of twenty different types of amino acids
  • Describe the processes of translation and transcription
  • Manipulate the DNA code and predict how it will change the sequence of mRNA and potentially a protein
  • Explain the effects of various types of mutations, including substitutions, insertions and deletions, on the resulting transcription and translation of a gene
  • Demonstrate how substituting one nucleotide for another often makes no significant change in the shape of a protein, unless it occurs at a critical location
Links to Related Activities
Physics
Chemistry
Biology

Atoms, Excited States and Photons

Atoms, Excited States and PhotonsInvestigate how atoms can be excited to give off radiation (photons) with models of electron energy diagrams.

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Learning Goals

Students will be able to:

  • Determine that atoms have different energy levels and store energy when they go from a ground state to an excited state
  • Discover that different atoms require different amounts of energy to be excited
  • Explain that excited atoms give up energy in collisions
  • Explore the way atoms absorb and emit light of particular colors in the form of photons ("wave packets of energy")
  • Determine that atoms interact with photons if the photons' energy is equal to the difference between the atom's excited and ground states
Links to Related Activities
Physics
Biology

Harvesting Light for Photosynthesis

Harvesting Light for PhotosynthesisDiscover how chlorophyll and other pigments absorb photons and how plants use solar energy to make carbohydrates.

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Learning Goals

Students will be able to:

  • Interpret a model of photons emitted by sunlight
  • Describe how different colored leaves absorb, reflect, and transmit different photons due to the presence or absence of a variety of pigments
  • Correlate the energy of a photon to the change in energy levels of electrons in molecules
  • Observe the structure of a chlorophyll molecule and explain how it can transfer energy to other molecules
Links to Related Activities
Physics
Biology

Spectroscopy

SpectroscopyExplore why excited atoms emit different wavelengths of radiation through a simulation of electron energy levels and learn how to identify atoms based on their unique atomic spectra.

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Learning Goals

Students will be able to:

  • Determine that the frequency of a photon is determined by the difference of energy levels between the states of an excited electron
  • Add energy and excite atoms
  • Analyze photon emissions and identify atoms that emit them
  • Determine that atoms can absorb photons of specific frequencies
  • Explore emissions spectra, and identify atoms by their spectrum
Links to Related Activities
Physics
Biology

Activity Spotlight

Electric Current

Electric Current

Explore the relationships between voltage, current, and resistance that make up Ohm's Law using molecular models of circuits.

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Guided Tour

Click on the short video at right to sit back and watch the main features of a SAM activity unfold. There are 24 SAM activities altogether - 8 in physics, 7 in chemistry, and 9 in biology. Most SAM activities are best taught over two class periods. So for each discipline (physics, chemistry, and biology) SAM offers activities for 14-18 class periods. This is approximately 10% of available instructional time -- large enough to have an impact on learning but small enough to fit into existing courses. The activities range in length from 5 to 15 short pages. Each activity includes a range of built-in assessments, some that help students monitor their own progress, and some that allow teachers to assess understanding.

Teachers can track student progress on the activities with a free reporting system. To access reporting, register at our portal site. Students can also monitor their own progress via a student reporting interface.

Starting at the Student's Level

The first page of each SAM activity is motivational, grounding the lesson in a phenomenon students can identify with, or raising a big question that will be explored in the activity.

Interactive SAM ModelInteractive Models

Each activity contains multiple models for students to manipulate, encountering and learning from the dynamics of physical, chemical, and biological systems. The models (including Molecular Workbench and Flash) have been authored to give students specific controls that enhance learning. Instructional steps and challenges accompany the model on the page. Activities also provide background text and graphics for making connections between representations in models.

SAM activities also feature rotatable, zoomable 3D models of molecules, with regions targeted for exploration. Jmol is used for these interactive molecules, which range from small organics to large biomolecules such as lipids, proteins, and DNA.

SAM Assessment Questionclick to enlargeActivity Assessment Questions

Nearly every activity page includes multiple choice, open-response, and/or image-based assessments. Some multiple-choice questions allow students to check their answers and receive feedback (shown above).

SAM Snapshotclick to enlargeIlluminating Student Thinking

Image-based assessments elucidate student thinking about models and data. Students take “snapshots“ of a simulation, annotate to demonstrate their understanding, and choose one to submit as an answer to the question.

SAM Hintclick to enlargeHints Support Student Success

Difficult concepts can be made more approachable with buttons that trigger hints to appear as pop-ups. Hints can be accessed from assessments, model instructions, and elsewhere in an activity, providing content-specific support.

Summary Questions

The last page of the activity has a set of summary questions that may be printed out independently and used for assessment. Homework Questions are in the Teacher Guides.

Reports for Tracking Progress

As students progress through an activity, their answers to all assessment questions are saved automatically, including the snapshots used to answer questions. Student work can then be accessed by teachers in report format and printed for grading or other feedback to students. Students can access reports on their own work and/or save them for a portfolio. Reports are stored in their personal spaces within Molecular Workbench software. To save student data and gain access through reporting, it is necessary to obtain a unique user name and password through our free registration. Register for the SAM Activities.

Teacher Guides

SAM Teacher GuideA Teacher Guide supports the teaching of each SAM activity.

View a sample teacher guide.

To download the full versions of the teacher guides, register as a teacher. Registration is free and has several advantages over using the activities without registering.

The teacher guides contain nine sections to assist teachers in preparing, teaching, evaluating, and reinforcing student understanding:

  • Activity Overview
  • Learning Objectives
  • Student Misconceptions
  • Models to Highlight
  • Discussion Questions
  • Connections to Other SAM Activities
  • Answer Guide
  • Homework Assignment
  • Homework Answers

Technical Requirements

Full access to all of the SAM materials requires computers running Windows, OS X, or Linux, with the following software installed: Java 1.4+, Flash 9+, and a PDF reader. If you experience technical difficulties running the activities, contact Frieda Reichsman - freichsman@concord.org.

Introduction to Modeling in SAM

Model SAM ActivityExplore the concept of molecular modeling and the specific types of models used in SAM activities, along with their controls; starting at a simple level, complexity is added one layer at a time. Students grasp the most important parts of the models and understand how a computer model can be a good representation of what happens in the real world.

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Learning Goals

Students will be able to:

  • Run a SAM computer model
  • Use the simulation controls of basic SAM models
  • Take a snapshot of a model, annotate it, and use it to answer a question
  • Do an experiment with a SAM simulation
  • Rotate and change the display of a 3D molecule

Links for teachers

Teachers Guides

A Teacher Guide supports the teaching of each SAM activity.

View a sample teacher guide.

To download the full versions of the teacher guides, register as a teacher. Registration is free.

The teacher guides contain nine sections to assist teachers in preparing, teaching, evaluating, and reinforcing student understanding:

  • Activity Overview
  • Learning Objectives
  • Student Misconceptions
  • Models to Highlight
  • Discussion Questions
  • Connections to Other SAM Activities
  • Answer Guide
  • Homework Assignment
  • Homework Answers

Technical Requirements

Full access to all of the SAM materials requires computers running Windows, OS X, or Linux, with the following software installed: Java 1.4+, Flash 9+, and a PDF reader. If you experience technical difficulties running the activities, contact Frieda Reichsman - freichsman@concord.org.

Why Register?

Register for the SAM Activities

Get the full benefit of the SAM activities by registering— the advantages are listed below. Watch the video to see the registration process.

Why register?

  • Your students' work will be saved as they progress through the activities. Stop the activity at any time, and students can return to finish in a subsequent class period, or for homework.
  • You'll be able to assign activities to your class and manage them online. Only the activities you assign to a class will be available to students in that class. Assign as many or as few activities as you wish.
  • You can access student reports for individuals or groups, and for the class as a whole. Get reports of a subset of the questions in the activity, or the entire set of assessments. Multiple choice questions are auto-scored for you as part of the report.
  • You'll be able to get the Teacher Guide for each activity with learning goals, model highlights, answer keys, and homework sheets.

For full details on how to register and access the reporting features, download the SAM Portal Guide. Or, proceed to the Activity Portal.

Making Connections between SAM Activities

We can trace the flow of ideas between the SAM activities in physics, chemistry, and biology in a number of different ways.

For every SAM activity, there is a subset of related activities that support and provide lead-ins to the activity. In turn, each activity can support another subset of SAM activities. By exploring these connections, you can inform your teaching and can help your students by drawing out the relationships between the concepts and even between the sciences. Each teacher might draw the connecting lines between activities a little differently.

Viewing all the connections between the activities simultaneously is overwhelming, so we created an interactive graphic to be able to visualize the connections to and from one activity at a time. These connections are the ones we see most clearly - you may see other connections that can support and illuminate atoms and molecules for your students.

SAM Activity Map

hold mouse over box to isolate concepts - click mouse button to lock activity highlight

Activity Map

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