Sometimes I have to put text on a path

Saturday, May 19, 2012

Molecular visualization Off-Line and On-Line : spiderGL, a JavaScript 3D Graphics library which relies on WebGL for realtime rendering



1/ Web application, a shader authoring tool:
code generation
(input just a mesh, file= .obj)

Try it online or download the zipped archive (an HTTP server is needed):

2/ Visualization Methods for Molecular Studies on the Web Platform

Standard representation of molecular surface properties using color ramps and field lines (leftmost), the same properties drawn using complex shading techniques (center) and the electrical interaction of two proteins (rightmost), rendered on a Web Page by using SpiderGL and WebGL.

Molecular visualization Off-Line and On-Line

The solution of the 3D structure of myoglobin in 1958 by Kendrew [Kendrew et al. 1958] marked the beginning of the new era of protein structural biology. Since then, a large number of protein structures have been solved and today the Protein Data Bank counts over 60.000 entries [Berman et al. 2003]. With the availability of all these data and the advance of computer graphics technologies, many research groups have developed tools for the manipulation and visualization of 3D structures such as VMD [Humphreyet al. 1996], SPDBViewer [Guex and Peitsch 1997], Chimera [Pettersen et al. 2004] and PyMOL [Delano 2002]. Beside working on the atomic structure, most programs can nowadays also calculate surface features such as electrostatic potential (using, for example, tools like APBS [Baker et al. 2001] or DelPhi [Rocchia et al. 2002]) and hydropathy [Kyte and Doolittle 1982].

In addition to the many standalone visualization tools, there are also web viewers especially designed for molecular structures, such as Jmol [jmo 2002] and MDL Chime, which represent a simple way
to visualize molecules directly on browser. MDL Chime, used by the Protein Explorer website was gradually phased out in favor of Jmol, which is nowadays the most used plugin for molecular visualization, used by websites such as Proteopedia and RCSB PDB Protein Data Bank.
Following the advance of techniques for the generation of CG movies, in the last few years many different groups focused on the creation of animated movies depicting biological molecules and
cellular processes. The movies range from the simple representations of the mechanical functioning of a single protein, to complex events involving many subjects. These works are important scientific efforts and add to their educational value the bonus of rising interest in the general public to approach biology. Some of these examples are collected on websites [McGill 2010; SCIVIS 2005].

3D Content on Web

The Virtual Markup Modeling Language (VRML) [Raggett 1994] (then replaced by X3D [Don Brutzmann 2007]) was proposed as a text based format for specifying 3D scenes in terms of geometry and material properties and for the definition of basic user interaction. The format itself was a standard, but the rendering in the web browser was relaying on specific plugins. The Java Applets are probably the most used method to add dynamic content, not necessarily 3D, in the web browsers. The
philosophy of Java applets is that the URL to the applet and its data are put in the HTML page and then executed by the Java Virtual Machine, a third part component. The implementation of JVM
on all the operating systems made Java applets ubiquitous and the introduction of binding to OpenGL such as JOGL [JOG ] added control on the 3D graphics hardware. A similar idea lies behind the
ActiveX [Microsoft Corporation 1996] technology, developed by Microsoft from 1996. Unlike Java Applets, ActiveX controls are not bytecode but dynamic linked Windows libraries which share
the same memory space as the calling process (i.e. the browser), and so much faster to execute. These technologies enable the incorporation of 3D graphics in a web page but they all do it by handling
a special element of the page itself with a third party component.

WebGL [Group 2009b] is an API specification produced by the Khronos group [Group 2009a] and, as the name suggests, defines the JavaScript analogous of the OpenGL API for C++. WebGL
closely matches OpenGLjES 2.0 and, extremely important, uses GLSL as the language for shader programs, which means that the shader core of existent applications can be reused for their
JavaScript/WebGL version. Since WebGL is a specification, it is up to the web browsers developer to implement it. At the time of this writing, WebGL is supported in the nightly build versions of the most used web browsers (Firefox, Chrome, Safari), and a number of JavaScript libraries are being developed to provide higher level functionalities to create 3D graphics applications. For example WebGLU [DeLillo 2009], which is the WebGL correspondent of GLU [OpenGL ARB ], provides wrappings for placing the camera in the scene or for creating simple geometric primitives, other libraries such as GLGE [Brunt 2010] or SceneJS [Kay 2009] uses WebGL for implementing a scene graph based rendering and animation engines.

Implementation spiderGL

Looking at a webpage with dynamic SpiderGL content, it is possible to see that all of the page logic is defined in the scripting part of the HEAD section, while on the BODY section there is just the page
structure and the interface elements that will be used for user interaction (like buttons, text areas and other controls). Among these elements, the most important is an html canvas object, that is the place where the WebGL layer does the on-screen rendering. ("< " are transformed : "[")

[canvas id="SGL_CANVAS" style="border: 1px solid gray"  width="900" height="600"][/canvas]

This canvas is registered as the output area at the end of the scripting; a specific function connects the various events of the canvas to a script object.

v a r  glMolViewer = new SpiderGLMolViewer ( ) ;
sglRegisterCanvas("SGL_CANVAS" , glMolViewer , 3 0 . 0 ) ;

The glMolViewer object is the main actor for the scene setup and rendering of our molecular visualization. The structure of this object employs the event handling subsystem provided by SpiderGL, which is inspired from the one used by the GLUT library [Kilgard ]. Each event coming from the canvas triggers a specific function with a given name and parameters; SpiderGL exploits the JavaScript language feature to give the possibility to dynamically add or remove listeners and redirect events. In this simple example, the only listener is the main object itself. (...)

This development process is straightforward for someone with an experience in graphical programming, while may prove to be difficult for users with a different background, like biology, physics or chemistry. This kind of setup is for sure more difficult to master with respect to setup of other existing platforms, like Jmol which, true to their nature, provide much simpler (but restrictive) access to their scene graph, with specific functions to import data and a series of predefined rendering modes. However, the gain in terms of flexibility and expressive power vastly compensate the initial steeper learning curve. Moreover, the learning of this technology is made easier by the possibility of initially use the higher level structures and functions implemented by SpiderGL to easily setup a basic visualization scheme and then start playing with lower level functions to obtain more complex effects. It is also important to note that most of the available JavaScript utility/UI libraries on the net may be used in conjunction with SpiderGL, adding more ready-made components to assemble a powerful, interactive, webpage.

3/ landscape refelction/refraction on a cup:

This example uses how to use cube maps and spherical harmonics to render objects with a natural light effect. GOOD.


SpiderGL: A JavaScript 3D Graphics Library for Next-Generation WWW

a web front-end that automates the processing of MRI and Diffusion MRI

The Brain Surface and Tractography Viewer was developed at Children’s Hospital Boston in the Fetal-Neonatal Neuroimaging and Development Science Center as part of a web front-end that automates the processing of MRI and Diffusion MRI. This application allows researchers to very rapidly explore processed MRI data in real-time within the web browser using WebGL. The application renders cortical surface reconstructions and fiber tracts generated by FreeSurfer and the Diffusion Toolkit, two automated brain imaging tools developed at the MGH Martinos Center for Biomedical Imaging. The user can view the gray-white surface and pial surface along with various curvature measures. Further, the fiber tracts are registered to the cortical surface and can be viewed inside the brain surfaces.

WebGL, JavaScript, jQuery

Adjust your photos in your browser in realtime with ten different image filters.
Adjust your photos in your browser in realtime with ten different image filters. This uses WebGL for speed, is entirely client-side, and is open source on GitHub. It was coded from scratch in 24 hours for HackNY, a hackathon in NYC, where it won second place.

magnetic therapy/stimulation and hemoglobin-red blood cell-capillaries; the Magnetic permeability and the magnetic reluctivity and the magnetic susceptibility ; Latex and maxwell's equations; magnetism, magnet, electromagnet, Static and Stationary Magnetic Fields

 In this figure µ (usually µr) is the "dimensionless" number µ/(µ0).
The term of "permeability" was coined in September, 1885 by Oliver Heaviside. 

Rem: 1)all equations are in png with latex in the alt (just right clic on the image to get the code).
2) all the figure contain its URL (auto-bibliography; or sometimes i put the URL below the figure).

This post is a short comment about µ which is the magnetic permeability (and also a compliation of wikipedia and others sites)
It is not easy to define µ and to understand this quantity.
en.Wikipedia :
and in the case of vacuum:
Try with other langages.wikipedia  (each x.wikipedia are different encyclopedia and  depand on wikipedians ;)

Permeability is the measure of the ability of a material to support the formation of a magnetic field within itself.
The reciprocal of magnetic permeability is magnetic reluctivity.

Graphical illustration of  the equation B=µH. Simplified comparison of permeabilities for: ferromagnetsf), paramagnetsp), free space(μ0) and diamagnetsd). This µf is not scaled (in fact it is near of the B-axis).

The auxiliary magnetic field H represents how a magnetic field B influences the organization of magnetic dipoles in a given medium, including dipole migration and magnetic dipole reorientation. Its relation to permeability is
\mathbf{B}=\mu \mathbf{H}
where μ is a scalar if the medium is isotropic or a second rank tensor for an anisotropic medium.
In this post we will assume that µ is a scalar, B and H will be on the same axis (just a comment: in the case of some new special metamaterials we can get a negative µ).

In terms of relative permeability, the magnetic susceptibility is:
χm = μr − 1.
χm, a "dimensionless" quantity, is sometimes called volumetric or bulk susceptibility, to distinguish it from χp (magnetic mass or specific susceptibility) and χM (molar or molar mass susceptibility).

The magnetization could be modeled as: M = χm H

Permeability a constant?
In general, permeability is not a constant (but near of a constant for most of materials), as it can vary with the position in the medium, the frequency of the field applied, humidity, temperature... Permeability as a function of electromagnetic frequency can take on real or complex values.

Table of 'microscopic' equations

Formulation in terms of total charge and current
Name Differential form Integral form
Gauss's law \nabla \cdot \mathbf{E} = \frac {\rho} {\varepsilon_0} \int\!\!\!\!\!\!\!\!\;\!\;\!\subset\;\!\;\!\!\;\!\!\!\!\!\!\!\int_{\partial V}\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\;\;\;\;\!\!\supset \mathbf E\;\cdot\mathrm{d}\mathbf A = \frac{Q(V)}{\varepsilon_0}
Gauss's law for magnetism \nabla \cdot \mathbf{B} = 0 \int\!\!\!\!\!\!\!\!\;\!\;\!\subset\;\!\;\!\!\;\!\!\!\!\!\!\!\int_{\partial V}\!\!\!\!\!\!\!\!\!\!\!\!\!\!\!\;\;\;\;\!\!\supset \mathbf B\;\cdot\mathrm{d}\mathbf A = 0
Maxwell–Faraday equation
(Faraday's law of induction)
\nabla \times \mathbf{E} = -\frac{\partial \mathbf{B}} {\partial t} \oint_{\partial S} \mathbf{E} \cdot \mathrm{d}\mathbf{l}  = - \frac {\partial \Phi_S{(\mathbf B)}}{\partial t}
Ampère's circuital law
(with Maxwell's correction)
\nabla \times \mathbf{B} = \mu_0\mathbf{J} + \mu_0 \varepsilon_0 \frac{\partial \mathbf{E}} {\partial t}\ \oint_{\partial S} \mathbf{B} \cdot \mathrm{d}\mathbf{l} = \mu_0 I_S + \mu_0 \varepsilon_0 \frac {\partial \Phi_S{(\mathbf E)}}{\partial t}


µ0 only appears in the Maxwell-Ampère's circuital law. If you use H (not B), it is hidden in H then this equation with B is better ;)

Good luck with units:
permeability is the inductance per unit length. In SI units, permeability is measured in henries per metre (H·m−1 = J/(A2·m) = N A−2). H has dimensions current per unit length and is measured in units of amperes per metre (A m−1). The product μH thus has dimensions inductance times current per unit area (H·A/m2). But inductance is magnetic flux per unit current, so the product has dimensions magnetic flux per unit area. This is just the magnetic field B, which is measured in webers (volt-seconds) per square-metre (V·s/m2), or teslas (T).

B the magnetic induction
the Laplace force (a macroscopic force on the wire, when a wire carrying an electrical current is placed in a magnetic field):
 d \vec F  = I\cdot d \vec l \wedge \vec B \;

or F=qE then Volt=Newton/(C)
then tesla=Volt/(m/s)

Idl (or J.dV with J Ampere/m2 and dV m3) plays the same role of the electric charge "q" (or densityOfCharge*dV : (C/m3)*m3).

\mathrm{1\, T = 1\,\frac{V\cdot s}{m^2} = 1\,\frac{N}{A\cdot m} = 1\,\frac{Wb}{m^2} = 1\,\frac{kg}{C\cdot s} = 1\,\frac{kg}{A\cdot s^2} = 1\,\frac{N\cdot s}{C\cdot m}}
Because the tesla is so large in regards to everyday usage, common engineering practice is to report the strength of magnets in Gauss. 10 G = 1 mT (millitesla).

B perpendicular to F and to dl

H Magnetic field strength
A magnetic dipole is "a closed circulation of electric current" (Maxwell-Ampère's circuital law). The dipole moment has dimensions current times area, units ampere square-metre (A·m2), and magnitude equal to the current around the loop times the area of the loop. H is related to the magnetic dipole density. The H field at a distance from a dipole has magnitude proportional to the dipole moment divided by distance cubed which has dimensions current per unit length.Then without "dimensionless tricks" H is a quantity with many space effects : (A.m2)/m3. H has also a time effect (A= Coulomb/s).

Ampère is a very bad unit to understand something (but it is a very good units in regard to 1Newton and electrotechnics).

Now we will see the magnitude.
I separate this aspect clearly because it is the most important.
If we dont consider magnets and/or strong stationnary or transient electric currents, all the materials are, in apparence, not "interactive" with magnetic fields.

They are grouped by orders of magnitud:
   0.1 pT  - brain activity, human brain magnetic field:

      1 pT  - cardiac activity:
    20 µT  - strength of magnetic tape near tape head
    31 µT  - strength of Earth's magnetic field at 0° latitude (on the equator)
    58 µT  - strength of Earth's magnetic field at 50° latitude
    0.5 mT  - the suggested exposure limit for cardiac pacemakers
                    by American Conference of Governmental Industrial Hygienists (ACGIH)
    5 mT - the strength of a typical refrigerator magnet
    0.15 T - Sunspots. They are temporary phenomena on the photosphere of the Sun that appear visibly as dark spots compared to surrounding regions. They are caused by intense magnetic activity, which inhibits convection by an effect comparable to the eddy current brake, forming areas of reduced surface temperature.
    1.25 T - Magnetic field intensity at the surface of a neodymium magnet; strength of a modern neodymium-iron-boron (Nd2Fe14B) rare earth magnet. A coin-sized neodymium magnet can lift more than 9 kg, can pinch skin.
    1 T to 2.4 T - coil gap of a typical loudspeaker magnet
    1.5 T to 3 T - strength of medical magnetic resonance imaging systems in practice,
          experimentally up to 17 T
     5 T - The strongest fields encountered from permanent magnets are from Halbach spheres.
  45 T - strongest continuous magnetic field yet produced in a laboratory (Florida State University's National High Magnetic Field Laboratory USA, dec 1999; 34 tons).

   91.4 T - strongest (pulsed) magnetic field yet obtained non-destructively in a laboratory (Forschungszentrum Dresden-Rossendorf.

   2.8 kT - strongest (pulsed) magnetic field ever obtained (with explosives) in a laboratory (VNIIEF in Sarov, Russia, 1998). DOI:


Magnetic levitation
   16 T - strength used to levitate a frog
The levitation trick works because giant magnetic fields slightly distort the orbits of electrons in the frog's atoms. The resulting electric current generates a magnetic field in the opposite direction to that of the magnet. A field of 16 teslas created an attractive force strong enough to make the frog float until it made its escape.
The team has also levitated plants, grasshoppers and fish. "If you have a magnet that is big enough, you could levitate a human," says Peter Main, one of the researchers.
He adds that the frog did not seem to suffer any ill effects: "It went back to its fellow frogs looking perfectly happy." 

A live frog levitates inside a 32 mm diameter vertical bore of a Bitter solenoid in a magnetic field of about 16 teslas at the High Field Magnet Laboratory of the Radboud University in Nijmegen the Netherlands:
Water possesses diamagnetic properties likewise, although less vivid, which makes the levitation of living beings, containing a large quantity of water, possible. So far the Henri Heim frog levitation experiment within the electromagnetic pair (1997) and the Jung Ming Lu mouse levitation experiment within the electric magnet (2009) have been a success (despite the former assumption of mammals being unable to levitate due to the differing ration of the liquid to the general body mass). 

"The Frog That Learned to Fly". Radboud University Nijmegen.  For Geim's account of diamagnetic levitation. "Everyone's MagnetismPDF (688 KB). Physics Today. September 1998. pp. 36–39. For the experiment with Berry, see Berry, M. V.; Geim, Andre. (1997). "Of flying frogs and levitrons" PDF (228 KB). European Journal of Physics 18: 307–313.
Earnshaw's theorem proves that using only static ferromagnetism it is impossible to stably levitate against gravity, but servomechanisms, the use of diamagnetic materials, superconduction, or systems involving eddy currents permit this to occur.
All materials have diamagnetic properties, but the effect is very weak, and is usually overcome by the object's paramagnetic or ferromagnetic properties, which act in the opposite manner. Any material in which the diamagnetic component is strongest will be repelled by a magnet.
Earnshaw's theorem does not apply to diamagnets. These behave in the opposite manner to normal magnets owing to their relative permeability of μr < 1 (i.e. negative magnetic susceptibility).

Diamagnetic levitation can be used to levitate very light pieces of pyrolytic graphite or bismuth above a moderately strong permanent magnet. As water is predominantly diamagnetic, this technique has been used to levitate water droplets and even live animals, such as a grasshopper, frog and a mouse. However, the magnetic fields required for this are very high, typically in the range of 16 teslas, and therefore create significant problems if ferromagnetic materials are nearby.
The minimum criterion for diamagnetic levitation is
 B \frac{dB}{dz} = \mu_0 \, \rho \, \frac{g}{\chi}
Assuming ideal conditions along the z-direction of solenoid magnet:

Induced currents

These schemes work due to repulsion due to Lenz's law. When a conductor is presented with a time-varying magnetic field electrical currents in the conductor are set up which create a magnetic field that causes a repulsive effect.

Relative motion between conductors and magnets

If one moves a base made of a very good electrical conductor such as copper, aluminium or silver close to a magnet, an (eddy) current will be induced in the conductor that will oppose the changes in the field and create an opposite field that will repel the magnet (Lenz's law). At a sufficiently high rate of movement, a suspended magnet will levitate on the metal, or vice versa with suspended metal. Litz wire made of wire thinner than the skin depth for the frequencies seen by the metal works much more efficiently than solid conductors.
An especially technologically-interesting case of this comes when one uses a Halbach array instead of a single pole permanent magnet, as this almost doubles the field strength, which in turn almost doubles the strength of the eddy currents. The net effect is to more than triple the lift force. Using two opposed Halbach arrays increases the field even further.
Halbach arrays are also well-suited to magnetic levitation and stabilisation of gyroscopes and electric motor and generator spindles.

Oscillating electromagnetic fields

A conductor can be levitated above an electromagnet (or vice versa) with an alternating current flowing through it. This causes any regular conductor to behave like a diamagnet, due to the eddy currents generated in the conductor. Since the eddy currents create their own fields which oppose the magnetic field, the conductive object is repelled from the electromagnet, and most of the field lines of the magnetic field will no longer penetrate the conductive object.
This effect requires non-ferromagnetic but highly conductive materials like aluminium or copper, as the ferromagnetic ones are also strongly attracted to the electromagnet (although at high frequencies the field can still be expelled) and tend to have a higher resistivity giving lower eddy currents. Again, litz wire gives the best results.
The effect can be used for stunts such as levitating a telephone book by concealing an aluminium plate within it.
At high frequencies (a few tens of kilohertz or so) and kilowatt powers small quantities of metals can be levitated and melted using levitation melting without the risk of the metal being contaminated by the crucible.

Just some comments about magnetic therapy []:
Magnets produce energy in the form of magnetic fields. Two main types of magnets exist: static or permanent magnets, in which the magnetic field is generated by the spin of electrons within the material itself, and electromagnets, in which a magnetic field is generated when an electric current is applied. Most magnets that are marketed to consumers for health purposes are static magnets of various strengths, typically between 30 and 300 mT. Magnets have been incorporated into arm and leg wraps, mattress pads, necklaces, shoe inserts and bracelets.

The worldwide magnet therapy industry
The worldwide magnet therapy industry totals sales of over a billion dollars per year [], including $300 million dollars per year in the United States alone [].

The ideas of "air du temps":
Even in the magnetic fields used in clinical magnetic resonance imaging, which are many times stronger of 300mT magnet ((i) 0.2 to 9.4 teslas static B and (ii) MegaHertz B), "none" of the claimed effects are observed [].

The TMS and rTMS is based on transient pulses of 1Teslas/(10-50microseconds) with 5000-8000Ampères/(10-50microseconds) in a coil. In this case some effects are clearly measured on the skin and "sometimes" on the surface of the cortex (e.g. motor cortex). The main effects seem to come from induced electric fields (the Maxwell–Faraday equation expresses that a time variation of B create an electric field: it is the induction).

There are many applications of induction (with high levels of B and E) and we need the transduction of eddy currents (courants de Foucault) and of Ohmic losses in special metals ("for induction") to increase the temperature...

There are a lot of controversies about magnet therapy:

Ref:  CMAJ September 25, 2007 vol. 177 no. 7 doi: 10.1503/cmaj.061344

Hemoglobin, red blood cell and capillaries
Although hemoglobin, the blood protein that carries oxygen, is weakly  diamagnetic in the oxygenated
and weakly paramagnetic in the deoxygenated state (diamagnetic -> is repulsed by magnetic fields), the magnets used in magnetic therapy seems to be be many orders of magnitude too weak to have any measurable in vivo effect on blood flow.
At 500-600mT (static field), an effect on red blood cells microcirculation (a 40% decrease of RBC velocity  at 600mT @1.5mm in the tissue) was measured:
[Brix, G. et al. Static magnetic fields affect capillary flow of red blood cells in striated skin muscle. Microcirculation 15, 15-26 (2008)]
It has been demonstrated that both normal [10, 11, 14, 35] and sickled [21] human erythrocytes are
aligned by SMF(statif magnetic fields) in cell suspensions. A highly significant orientation was also reported for sickled erythrocytes flowing through a 0.38T field in an in vitro flow apparatus [4]. In a series of experiments [10, 11, 35], Higashi and coworkers found that normal intact RBCs orient with their disk planes parallel to the magnetic field direction. Alignment was detectable at a flux density of 1T and almost 100% of the cells were oriented when exposed to 4T. Since orientation was not influenced by the spin state of hemoglobin (which is diamagnetic in the oxygenated
and paramagnetic in the deoxygenated state), it has been concluded that normal RBCs are oriented primarily due to the anisotropic diamagnetism of cell membrane components. On the other hand, estimations performed for normal RBCs by Schenck [25] indicate that the anisotropic diamagnetic susceptibility of single RBCs is probably too small to orient RBCs flowing in large vessels. These estimations, however, did not take into account that RBCs move in an oriented and deformed state through capillaries, which may change their anisotropic susceptibility (...)
In the case of dynamic RBC clustering, the SMF-induced torque, which increases with the number of anisotropic RBCs coupled, can be much larger than for single RBCs [25]. To obtain a deeper understanding of the observed effect of SMFs on microvascular blood flow, the existing computer models describing dynamic clustering of RBCs in capillaries should be extended to include the physical interaction of the different blood components with an external SMF.
As a first step in this direction, Haik et al. developed a simplified mathematical model, which couples orientation effects of RBCs with the shear stress by introducing a magnetically induced viscosity of blood that adds to the kinetic viscosity. In agreement with their theoretical considerations, the authors experimentally observed an increased viscosity of human blood flowing in a thin plastic tube when exposed to magnetic flux densities between 3 and 10 T as compared to measurements performed in the absence of a SMF [9; Haik Y, Pai V, Chen CJ. (2001). Apparent viscosity of human blood in a high static magnetic field. J Magn Magn Mater 225:180–186.]
Further work will be required to identify potential synergistic or alternative mechanisms by which SMFs are able to affect capillary RBC flow. For example, alterations of the endothelial glycocalyx or of the surface properties of RBCs may play an important role. It is widely recognized that the glycocalyx, a translucent layer with fixed negative charges, has manifold physiological functions. Crucial among these is its role as a hydrodynamic exclusion layer preventing the interaction of proteins in the RBCs and endothelial cell membranes; in modulating leukocyte attachment and rolling; and as a transducer of mechanical forces to the intracellular cytoskeleton in the initiation of intracellular signaling [31] (see also [16,29]). (...)
Muscle capillaries are mainly oriented in parallel and intersected perpendicularly by the magnetic field.(...)
Patients undergoing MR procedures at higher magnetic field strengths occasionally report on mild nausea and headache, which may possibly be related to an altered blood flow pattern [14; Kuchel PW, Coy A, Stilbs P. (1997). NMR “diffusion- diffraction’’ of water revealing alignment of erythrocytes in a magnetic field and their dimensions and membrane transport characteristics. Magn Reson Med 37:637–643].

---[Haik,2001; Apparent viscosity of human blood in a high static magnetic field;]
Studying the effect of magnetic field on the blood is of interest to many researchers. Pauling and Coryell [1; 1936] were first to report the diamagnetic susceptibility of oxyhemoglobin and the paramagnetic susceptibility of deoxyhemoglobin. The value for the effective magnetic moments of the Fe2+ complex in hemoglobin of red blood cells is derived from their measurements. Higashi et al. [2] studied the orientation of normal erythrocytes in a strong static magnetic field with a maximum field strength of 8 T. The erythrocytes were found to orient with their disc plane parallel to the magnetic field direction. Yamagishi [3] reported a similar behavior of red blood cells at 4 T. Further, Yamagishi [3] found that platelets orient with the applied magnetic field at 3 T. We and others [3] have observed that fibrinogen, one of the plasma proteins, is polymerized and aligns with the applied field already at 4 T. Shalygin and coworkers [4] studied the behavior of erythrocytes in a high-gradient magnetic field. They reported that the susceptibility of the diamagnetic erythrocytes (oxygenated blood in artery) was found to be −(0.13–0.65)×10−8 cgs emu/cm3 Oe. For the paramagnetic (deoxygenated blood in vein) it was (13–33)×10−8 cgs emu/cm3 Oe. Similar results were reported by Haik and coworkers [5]. Motta et al. [6] reported orientation of the human hemoglobin when subjected to high magnetic field. Nakano et al. [7] reported that the torque needed to rotate an erythrocyte was very small when the magnetic field was rotating almost parallel to the heme planes in the unit cell, while it was very large when the magnetic field was oriented perpendicular to the heme planes. This demonstrates that the orientation of blood cells when subjected to a magnetic field is due to the magnetic torque. In this orientation, blood cells and the surrounding plasma fluid will interact and, combined with the magnetic force, increase the apparent viscosity of the blood.

--- [Cano,2006;Computer simulation of magnetic properties of human blood; Chemical Physics Letters 432 (2006) 548–552]
Shalygin et al. [6] studied the behaviour of erythrocytes under strong magnetic field gradients. These authors reported a susceptibility for diamagnetic erythrocytes of -(0.13–0.65)x10-8 cgs emu/cm3 Oe and (13–33)x10-8 cgs emu/cm3 Oe for paramagnetic erythrocytes.
From the point of view of the modelling of biological systems it is important to determine which are the basic molecular features that are necessary for a proper modelling. Over the years, primitive models have been very useful in the modelling of complex fluids by computer simulations [9]. In this Letter, we address the description of the magnetic susceptibility of blood using a primitive model comprised of a dipolar hard-spheres fluid (DHS) in the presence of a external field. We study two variations of this model, depending on the physical values used to reproduce the magnetic behaviour of human blood, either red blood cells or reduced hemoglobin molecules.

Following Ref. [8], we are going to consider the susceptibility per ml of substance. The magnetic susceptibility for whole blood, v, is given by

where χp and χd are the paramagnetic and diamagnetic susceptibility contributions, and mp and md are their fractions, respectively. The paramagnetic contribution arises from the deoxyhemoglobin, whereas the diamagnetic term is basically given by the susceptibility of water molecules, since 60% of blood solution is water [8]. Then, vd ~ 0.6 and χd = 0.6 χwater = -5.4x10-6. The susceptibility of whole human blood is χ = 3.5x10-6 [12]. Using these results in Eq. (7), an estimated value for χp is obtained,
χp =  2:2x10-5  (8)
This value agrees with reported data of χp, that has been determined within the range
-6.07x10-6 ≤ χp ≤ 2.2x10-5 [8,12–17]. Since
χp =nRC χRC  (9)
where nRC is the number of red cells contained within 1 ml of blood, nRC = 5x10^9 [18], and χRC is the magnetic susceptibility of a red blood cell, the magnetic susceptibility of a red blood cell is obtained using Eqs. (8) and (9),
χRC ~ 5x10-15
According to Eq. (5), the magnetization M of a RBC due to the effect of an external magnetic field H is given by
M =χRC
Assuming that the magnetization M is basically given by the dipolar moment of the cell, µRC
where VRC is the volume occupied by a RBC,
VRC = 9.0 x10-11 ml [18], then Eqs. (10)–(12) enable us to have a estimated value of µRC


The relation between life and bio-magnet exists:
Science 23 December 2011: Vol. 334 no. 6063 pp. 1720-1723; DOI: 10.1126/science.1212596
A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria
a comment in french:

Download: the Latex Source , the full Postscript or PDF notes , Randy's Mathematica examples [1,2,3,4], just the figures, the homework assignment, or the solutions.

Ref: for latex and Equation numbering

list of software (molecular graphics,molecular mechanics modeling,quantum chemistry), van der waals radius; and many water effects

molecules and  chromophores, dyes, absorbers, absorption spectrum (macroscopic) and nanoworld...


List of molecular graphics:

List of software for molecular mechanics modeling:

List of quantum chemistry and solid-state physics software:

GPU accelerated molecular modelling software:


JOELib — Java version of OpenBabel/OELib

Structure download:
lucifer yellow:

Electron Density Server:
"ex-ample": deoxyhemoglobin

MolviZ.Org: Molecular Visualization Resources with rich collection of molecules:

Molecule editor;
Free Standalone programs (multiplatform & MacOSX), just "small programs for dummies":
2/ MacMolPlt : A modern graphics program for plotting 3-D molecular structures and normal modes (vibrations):
3/Ball view (MACOSX Darwin: auto with CPack (
4/ Crystallographic Object-Oriented Toolkit: Coot: near of Alwyn Jones' OQuantaXtalViewCCP4mg
5/CueMol2 aims to visualize the crystallographic models of macromolecules. Currently supported files are molecular coordinates (PDB format), electron density (CCP4, CNS , and BRIX formats), MSMS surface data, and APBS electrostatic potential map. Powered by Mozilla XULRunner, the application framework of Firefox and Thunderbird (and other mozilla-based application as well).
6/Gabedit (release:October, 2009) is a Graphical User Interface to GAMESS (US) , GAUSSIAN, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, Orca and Q-Chem computational chemistry packages.
7/Molden (dec 2010):
10/SPARTAN (demo):; Molecular mechanics calculations and quantum chemical calculations; spectral properties; VERY GOOD.
13/; correction of pdb file.

Online editors/viewers with many one-click web services:
2D: in pure Javascript,
Ref: J Cheminform. 2011 Sep 20;3(1):32. PubChem3D: a new resource for scientists.
or stand alone PubChem 3D Viewer

Web-based systems are based on 3 strategies
  1. VRML
  2. java (JMol needs java machine).
  3. WebGL : Javascript, HTML5. It doesn't need Java or plugins.
WebGL (Web Graphics Library) is a JavaScript API for rendering interactive 3D graphics within any compatible web browser. WebGL programs consist of control code written in JavaScript and shader code that is executed on a computer's Graphics Processing Unit (GPU). Notable early applications of WebGL include Google Maps and Google Body or Zygote BodyOn October 13, 2011 the Google Body site was shut down. Then on January 9, 2012 Zygote Body was launched and core code base (with the Google Cow model as a demo) was made available as an open source project called:

GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like Jmol, but MUCH faster, GLmol is a 3D molecular viewer based on WebGL and Javascript.

Surface calculation and visualization (in development; available in special version):
  • van der Waals surface
  • Molecular surface
  • Solvent accessible surface
  • Solvent excluded surface
Surface representation is a convenient way to visualize protein-protein and protein-ligand interactions. However, surface calculation of macromolecules is computationally and memory intensive. Furthermore, calculated mesh is very complex, often exceeding 500000 polygons. Therefore its implementation in Javascript/WebGL was considered to be very difficult.
 EDTSurf algorithm published by Dong Xu and Yang Zhang in 2009 (EDTSurf: Quick and accurate construction of macromolecular surfaces; D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS ONE 4(12): e8140) is very efficient and runs with practical speed (even after I ported it to Javascript). I integrated it with GLmol, my WebGL-based molecular viewer, and release it here. 
Example: Solvent excluded surface of horse deoxyhaemoglobin (PDBID: 2DHB)
Computation time and Memory usage
In modern computers with Intel Core i5/i7 processor, grid size up to 180x180x180 can be calculated in acceptable time (5-10sec). Although Firefox 8 was about 3 times slower than Chrome, with Firefox 9, the difference is getting smaller. Current problem is its memory usage. It uses about 500MB RAM for computation. The original version written in C++ doesn't use so much memory. Now I am working to reduce memory usage in my Javascript version. Basically, if GLmol runs on your PC, this demo should work. For better performance, I recommend Google Chrome with sufficient memory (>1GB for browser). You can try alpha version from the following link. Please note that this is ALPHA version and there remains many issues. WARNING! This program consumes lots of memory (500-700MB). Your browser and computer might GET VERY SLOW and EVEN CRASH if memory is insufficient!
Demo version
To limit CPU & memory usage, calculation grid size is restricted to 180x180x180. Therefore, if you calculate a large surface, output quality will be compromised.

To learn how to embed GLmol into your page, please examine source code of :        (1)
The following model is horse deoxyhaemoglobin(Adapted from PDB 2DHB).
The Iron atom (colored ocher) is coordinated by five nitrogen atoms (colored blue); four from a heme and one from a histidine residue in the protein. When oxidized, an oxygen molecule binds at the opposite side of the histidine as another axial ligand.
You can embed multiple instances of GLmol in a page. Molecular representations can be customized by Javascript. For the details, please examine the source code of this page (1). If it is not clear, don't hesitate to ask (biochem_fan at
Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Angstrom units resolution.Bolton, W.,  Perutz, M.F.,  Journal: (1970) Nature 228: 551-552

WebGL Other libraries:
just for the fun:
Technology: WebGL, ChemDoodle Web Components, jQuery, glMatrix, XHR2

Visualization Methods for Molecular Studies on the Web Platform
see also:

The ChemDoodle Web Components, which display 3D molecular models and other chemical structures in web pages, have hit version 4.4.0; this new and improvedProtein Data Bank model demo is particularly nice, as is this new demo for crystallography.

Many frameworks:

List of molecular graphics systems with Java applet :
Jmol: Java applet or stand-alone application. It does not require 3D acceleration plugins.
Jmol supports many molecular file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML).
extension for mediawiki: The tag can be used to display in 3d a molecule file that has been previously uploaded into Wikipedia. Some examples of its usage are available in the Jmol wiki:
MDL Chime is a free plugin used by web browsers (windows) to display the 3D structures of molecules. It is based on the RasMol code. Stable release: 2.6 SP7 / July 31, 2007; 5 years ago. Chime largely has been superseded by Jmol. A feature of Chime which is not yet reproduced with Jmol is the calculation of electrostatic or hydrophobic potential for use in coloring molecular surfaces. Instead, Jmol relies on this data being provided by other calculation packages.
Molekel: stable 5.4 / August 2009; 2 years ago. 36MB Mac OS X Intel (built on Mac OS X 10.4.11; require X11 due to a dependency in one of the libraries). Complete control over the generation of molecular surfaces (bounding box and resolution); Visualization of the following surfaces: orbitals; Isosurface from electron density data; Isosurface from Gaussian cube grid data;Solvent-accessible surface (SAS); Solvent excluded surface (SES); Van del Waals radii; Animation of molecular surfaces; Animation of vibrational modes;Export animation; Plane widget to visualize a scalar field: the plane can be freely moved in 3d space and the points on the plane surface will be colored according to the value of the scalar field: a cursor can be moved on the plane surface to show the exact value of the field at a specific point in space; Fully Doxygen-commented source code. You can also build: and

Sirius; Interactive calculation of hydrogen bonding, steric clashes, Ramachandran plots
SRS3D Viewer:
WebMol (very old).
Proteopedia; Java applet integrated into web front-end.
Chemistry Development Kit: The CDK was created by Steinbeck, Willighagen and Gezelter, the developers of Jmol and JChemPaint (2D). The CDK itself is a library, instead of a user program. However, it has been integrated into various environments to make its functionality available, the R (programming language),CDK-Taverna (a Taverna workbench plugin), Bioclipse, and Cinfony. Additionally, CDK extensions exist for KNIME and Excel (excel-cdk). Chemoinformatics: substructure search using exact structures and SMARTS-like queries, QSAR descriptor calculation, Kuhn et al (2010). "CDK-Taverna: an open workflow environment for cheminformatics". BMC Bioinformatics 11: 159. doi:10.1186/1471-2105-11-159.

Extensible Computational Chemistry Environment (ECCE) The Extensible Computational Chemistry Environment provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies.
-importing results from NWChem, GAMESS-UK, AMICA, Gaussian 94, Gaussian 98, and Gaussian 03 calculations
-Remote submission of calculations to UNIX and Linux workstations, Linux clusters, and supercomputers. Supported queue management systems include PBS, LSF, NQE/NQS, LoadLeveler and Maui Scheduler.

First, "virtual molecules" are only an image.  How to visualize virtual molecules-macromolecules-nanostructures?

Physical models and computer models:
MD = Molecular Dynamics; MM = Molecular modelling and molecular orbital visualization; Optical = Optical microscopy; SMI = Small molecule interactions;

Stand-alone systems: around 30 software
Web-based systems: 4-10 systems

The most important representation is the "space-filling" representation



≠ spherical single atom
For a molecule, volume enclosed by the "van der Waals surface".
The van der Waals volume of a molecule is always smaller than the sum of the van der Waals volumes of the constituent atoms: the atoms can be said to "overlap" when they form chemical bonds.


(Ref theory homogenization:

The van der Waals volume of an atom or molecule is determined by experimental measurements on gases from 
  1. the van der Waals constant b, 
  2. the polarizability α or 
  3. the molar refractivity A
In all 3 cases, measurements are made on macroscopic samples and it is normal to express the results as molar quantities. To find the van der Waals volume of a single atom or molecule, it is necessary to divide by the Avogadro constant NA.

the van der Waals constant b, 

The van der Waals equation of state is the simplest and best-known modification of the ideal gas law :
where n is the amount of substance of the gas in question and a and b are adjustable parameters; a is a correction for intermolecular forces and b corrects for finite atomic or molecular sizes; the value of b equals the volume of one mole of the atoms or molecules.

The van der Waals equation also has a "microscopic interpretation": molecules interact with one another. The interaction is strongly repulsive at very short distance, becomes mildly attractive at intermediate range, and vanishes at long distance.

Thus, a fraction of the total space becomes unavailable to each molecule as it executes random motion. In the equation of state, this volume of exclusion (nb) should be subtracted from the volume of the container (V), thus: (V - nb). The other term a(n/V)^2 that is introduced in the van der Waals equation, describes a weak attractive force among molecules (known as the van der Waals force), which increases when n increases or V decreases and molecules become more crowded together.

For helium (monoatomic gas) b = 23.7 cm3/mol.
-> rw= 0.211nm
This method may be extended to diatomic gases by approximating the molecule as a rod with rounded ends where the diameter is 2rw and the internuclear distance is d. The algebra is more complicated, but the relation:
can be solved by the normal methods for cubic functions.

O2: d=0.1208nm; b=31.83cm3/mol  (Values of d and b from Weast (1981))
Therefore the van der Waals volume of a single molecule: Vw=0.05286nm^3;
which corresponds to rw = 0.206nm.

The molar refractivity A

The molar refractivity A of a gas is related to its refractive index n by the Lorentz–Lorenz equation:
The refractive index of helium n = 1.000 0350 at 0 °C and 101.325 kPa which corresponds to a molar refractivity A = 5.23×10–7 m3/mol. Dividing by the Avogadro constant gives Vw= 8.685×10–31 m3 = 0.0008685 nm3, corresponding to rw= 0.059nm.

The polarizability

The polarizability α of a gas is related to its electric susceptibility χe by the relation

and the electric susceptibility may be calculated from tabulated values of the relative permittivity εr using the relation χe = εr–1. The electric susceptibility of helium χe = 7×10–5 at 0 °C and 101.325 kPa, which corresponds to a polarizability α = 2.307×10–41 Cm2/V. The polarizability is related the van der Waals volume by the relation

so the van der Waals volume of helium Vw=2.073×10–31 m3 = 0.0002073nm3 by this method, corresponding to rw=0.037nm.
The term "atomic polarizability" is preferred as polarizability is a precisely defined (and measurable) physical quantity, whereas "van der Waals volume" can have any number of definitions depending on the method of measurement.

Helium rw=0.140nm=140pm

For example, the van der Waals volumes and surfaces of amino acids are given in The Amino Acid Repository:

At the other extreme scale (nanometre/picometre; "microscopic theory"), the Lennard-Jones potential (also referred to  12-6 potential) is a model that "approximates" the interaction between a pair of atoms (neutral) or molecules [Lennard-Jones,1924;]. 
Ex-ample: Argon r0=0.335nm and E0 =0.01eV , the Lennard-Jones potential  is a potential energy:
r=r0 @ Ep=0.


1/r^12    = approximation of The Pauli exclusion principle (no 2 identical fermions (particles with half-integer spin) may occupy the same quantum state simultaneously; a more rigorous statement is that the total wave function for two identical fermions is anti-symmetric with respect to exchange of the particles;
1/r^6      = approximation of The van der Waals force (or van der Waals interaction)
The van der Waals force is the sum of the attractive or repulsive forces between molecules (or between parts of the same molecule) other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral molecules.
It includes 3 forces (
-force between two permanent dipoles (Keesom force)
-force between a permanent dipole and a corresponding induced dipole (Debye force)
-force between two instantaneously induced dipoles (London dispersion force)

where ε is the "depth of the potential well", σ is the finite distance at which the inter-particle potential is zero, r is the distance between the particles, and  is the distance at which the potential reaches its minimum. At rm, the potential function has the value −ε. The distances are related as rm=2^(1/6)σ~1.225σ.
Whereas the functional form of the attractive term has a clear physical justification, the repulsive term has no theoretical justification. It is used because it approximates the Pauli repulsion well, and is more convenient due to the relative computational efficiency of calculating r^12 as the square of r^6 [].
The L-J potential is particularly accurate for noble gas atoms (helium (He), neon (Ne), argon (Ar), krypton (Kr), xenon (Xe), and radon (Rn)) and is a good approximation at long and short distances for neutral atoms and molecules.

The Stockmayer potential [Stockmayer W. H.  J. Chem. Phys., 1941] or the 12-6-3 potential (a mathematical model for representing the interactions between pairs of atoms or molecules) consists of the Lennard-Jones potential with an embedded point dipole [], [wikipedia-russian], [], [googleBooks-H20-NH3], [liquid water:]:

Assuming that the molecules interact as alined dipoles of maximum attraction, values for sigma, epsilon, and delta were determined for various polar molecules by a least squares fit of experimental viscosity data. Satisfactory results were obtained for slightly polar molecules, but not for more highly polar molecules (polar gases) such as NH3 or H2O [].
The Stockmayer term takes into account the increased repulsion between dipoles of similar orientation:

 When the orientation of the dipole is switched to opposite orientation, the plot shows the added attraction between the molecules.

Rem: the main quantity is = a potential well is the region surrounding a local minimum of potential energy. Energy captured in a potential well is "unable" to convert to another type of energy.

Bridge from macroscopic to microscopic physics: the Boltzmann constant, k (entropy), is a bridge between macroscopic and microscopic physics, since temperature (T) makes sense only in the macroscopic world, while the quantity kT gives a quantity of energy which is on the order of the average energy of a given atom in a substance with a temperature T. k=8.617×10−5 eV/K then 0.013eV, at room temperature.

In the case of bulk liquid water at room temperature, there are many models and many data:
The molecules of H20 are constantly moving in relation to each other, and the hydrogen bonds (highly directional hydrogen-bond network structure) are continually breaking and reforming at timescales faster than 250 femtoseconds [].
A water molecule can form a maximum of 4 hydrogen bonds because it can accept 2 and donate 2 hydrogen atoms. Other molecules (hydrogen fluoride, ammonia, methanol) form hydrogen bonds but they do not show anomalous behavior of thermodynamic, kinetic or structural properties like those observed in water. The answer to the apparent difference between water and other hydrogen bonding liquids lies in the fact that apart from water none of the hydrogen bonding molecules can form 4 hydrogen bonds, either due to an inability to donate/accept hydrogens or due to steric effects in bulky residues. In water, local tetrahedral order due to the 4 hydrogen bonds gives rise to an open structure and a 3-dimensional bonding network, resulting in the anomalous decrease of density when cooled below 4 °C.
Although hydrogen bonding is a relatively weak attraction compared to the covalent bonds within the water molecule itself, it is responsible for a number of water's physical properties. One such property is its relatively high melting and boiling point temperatures; more energy is required to break the hydrogen bonds between molecules. The extra bonding between water molecules also gives liquid water a large specific heat capacity. This high heat capacity makes water a good heat storage medium (coolant) and heat shield.

5-site model and 3-site model (Flexible SPC water)

In molecular dynamics simulations the flexible simple point charge water model (or Flexible SPC water; a re-parametrization of the 3-site SPC water model) gives the correct density and dielectric permittivity of water [Praprotnik,2004;]. Flexible SPC is implemented in the MDynaMix, Abalone programs... The SPC model assumes an ideal tetrahedral shape (HOH angle of 109.47°) instead of the observed angle of 104.5°.

Remark: Atomic units (a.u.) form a system of natural units which is especially convenient for nm or pm calculations. There are 2 different kinds of atomic units, which one might name Hartree atomic units and Rydberg atomic units, which differ in the choice of the unit of mass and charge.
Some particle has a mass m which is 2.4 times the mass of electron---2.4 a.u.

electron density and cloud

The Electron Localization Function ELF η(r) for a chemical system is a scalar field in 3D space.
Concerning the interpretation of the absolute values of ELF in the original paper [BECKE1990] the following hint was given: "... the upper limit ELF = 1 corresponding to perfect localization and the value ELF=½ corresponding to electron-gas-like pair probability". Two remarks can be made:
1.) Concerning the upper limit it may be justified that the authors interpret this value "corresponding to perfect localization" as they have given before their definition of "localization". However, in order to avoid confusion, e.g. with the much older physical concept of localized and itinerant electrons used in modern solid state electronic structure theory, the analysis of ELF should usually be performed in terms "high/low values of η" instead of "high/low electron localization". A simple example may serve as a demonstration: a single-determinant (Hartree-Fock or Kohn-Sham) solution for a H2 molecule gives one doubly occupied &sigma bonding orbital. The &eta(r) distribution is equal to 1.0 everywhere in space. Thus, in the sense of the above definition, each electron is "perfectly localized" at every point in space. Concluding this remark there certainly is a relation (to be found in the future) between the physical concept of localized and itinerant electrons and ELF but it seems to be a subtle one and the terms should not be intermixed.
2.) For the value η = ½ the authors give the absolutly correct interpretation. Any further interpretation of the &eta = ½ and lower values has to be justified strictly. Clearly, points or regions with &eta(r) = 0.5 for a chemical system do not imply "perfectly delocalized electrons".

For many years the size of atoms/molecules has been approximated by physical models in which the volumes of plastic balls describe where much of the electron density is to be found often sized to van der Waals radii. That is, the surface of these models is meant to represent a specific level of density of the electron cloud.

It is now relatively common to see images of surfaces that have been colored to show quantities such as electrostatic potential. Common surfaces in molecular visualization include solvent-accessible ("Lee-Richards") surfaces, solvent-excluded ("Connolly") surfaces, and isosurfaces. Opaque isosurfaces do not allow the atoms to be seen and identified and it is not easy to deduce them. Because of this, isosurfaces are often drawn with a degree of transparency.

In the last decade almost all of this technology has become commoditized. In 1992, Roger Sayle released his RasMol program into the public domain. MG continues to see innovation that balances technology and art, and currently zero-cost or open source programs such as PyMOL and Jmol have very wide use and acceptance. Recently the wide spread diffusion of advanced graphics hardware, has improved the rendering capabilities of the visualization tools. The capabilities of current shading languages allow the inclusion of advanced graphic effects (like ambient occlusion, cast shadows and non-photorealistic rendering techniques) in the interactive visualization of molecules. These graphic effects, beside being eye candy, can improve the comprehension of the three dimensional shapes of the molecules. An example of the effects that can be achieved exploiting recent graphics hardware can be seen in the simple open source visualization system QuteMol.
Forster-distance-calculator: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants.

Nowadays fitting of the molecular structure to the electron density map is largely automated by algorithms with computer graphics a guide to the process. An example is the XtalView XFit program (~100000 lines of C and Fortran).

---------------web services: visualizing molecular dynamics (from pdb file)
Molecules are "bouillaunantes" (@ T much greater than 0°K)
-motions that occur in proteins and other macromolecules:
-with Flexible SPC water model: PC &linux:

-This site provides tools for online normal mode calculation, even for large proteins and including all atoms, and algorithms that use normal modes for structural refinement or optimization:


For nano:

NanoEngineer-1 and QuteMol (viewer with many "realistics"):

Electronic absorption spectra (one or multiphoton) and solvents

Which software can I use to calculate the effects of solvents on the electronic absorption spectra properties of molecules?
I mean spectra properties like transition energies, oscillator strength, transition moments and polarizabilities etc...
Gaussian 09 using the keyword: Solvent=(). In the users book you will find which solvents are available for calculating.
NWChem ( It is open source (100MB) and these types of calculations can be done either with continuum models or QM/MM. This is a tricky business. The continuum solvation model won't work if hydrogen bonds play a role in your case. Alternatively, you can represent the solvent explicitly. This needs a molecular simulation and afterwards you will average your result over several snapshots of your solute/solvent system. The latter computations would be done in a QM/MM fashion.
You see, it's getting hairy. But there has been some recent progress in this. Yet, the method - called polarizable embedding (PE) - is still in a developer's state. It is implemented in DALTON (for DFT and coupled cluster). Contact the authors of that method for a collaborative investigation.
Excited States in Solution through Polarizable Embedding; J. Chem. Theory Comput., 2010, 6 (12), pp 3721–3734; DOI: 10.1021/ct1003803:
See also: Advances in Quantum Chemistry, Volume 61, chap 3, (40pages) 2011.
THE JOURNAL OF CHEMICAL PHYSICS 134, 104108 (2011), The polarizable embedding coupled cluster PE-CC method, Kristian Sneskov,Tobias Schwabe,Jacob Kongsted,Ove Christiansen:
GPU and NWchem:
The calculation of excitation energies, one- and two-photon absorption properties, polarizabilities and
hyperpolarizabilities all coupled to a polarizable MM environment. Previously, one of us reported the
polarizable embedding density functional theory (PE-DFT) approach describing in the process the polarizable embedding Hartree–Fock (PE-HF) method. This is essential for this work since the reference orbitals are those from a PE-HF calculation.

They investigated the absorption spectrum of aqueous N-methyl acetamide (NMA; important building block of all proteins) with a specific focus on polarization effects. The formamide and NMA systems each consists of 120 conformations generated in a calibrated MD simulation containing roughly 250 water molecules. Previously, this has been shown to be sufficient to incorporate the bulk properties of water. All Photoactive yellow protein (PYP)  calculations are based on the x-ray structure of PYP  (PDB accession code 1nwz) with a reported accuracy of 0.82 Å.

The PE-CC strategy and calculations described in this paper have been implemented and carried out in a local version of the DALTON quantum chemistry program.
Dalton is an ab initio quantum chemistry software program, capable of calculating various molecular properties using the Hartree–Fock, MP2, MCSCF and coupled cluster theories. Version 2.0 of DALTON added support for density functional theory DFT calculations. DALTON by the Centre for Theoretical and Computational Chemistry. CTCC was founded by the Norwegian Research Council in 2007 and the duration of the project is 10 years. One main focus is on method development in electronic structure theory.

---basics with mathematica:


Nanostructures modeling at classical and quantum levels.

polymers, nanotubes, proteins, nucleic acids, quantum dots..., nanophotonics, nanofluidics...
a list of free computer programs: (Flexible SPC water model, Implicit water model; Quantum chemistry with aid of CP2K and PC GAMESS/Firefly; Linux and XP) (CoNTub v2.0 (Released May-13-2011)) (demo version; Nanotube Modeler is a program for generating xyz-coordinates of nano geometries (Nanotubes, Nanocones, Graphene sheets, Nano-holes, Viruses).JCrystal is a computer program for creating, editing, displaying and deploying crystal shapes. It also includes the JCrystalApplet for exporting interactive webpages.) (Web-Accessible Nanotube Structure Generator and  TubeGen utility (stand alone)) is a science and engineering gateway

For nanoparticules Silver, Gold, Nickel-Silver (surface plasmon resonance band)
A theoretical study of structural, electronic and optical properties of complexes, clusters and nanostructures:
Optical response of silver nanoclusters complexed with aromatic thiol molecules: a time-dependent density functional study; M Harb et al 2011 J. Phys. B: At. Mol. Opt. Phys. 44 035101 doi:10.1088/0953-4075/44/3/035101

Molecular Modeling Basics 

---> from  Jan H. Jensen
A big part of the motivation for my blog came from writing a book called Molecular Modeling Basics that was published in May, 2010 by CRC Press ( While writing the applications sections it was frustrating to turn the beautifully colored figures into black-and-white versions in order to keep the cost of the book reasonable.

Molecular Modeling in Chemical Education.

He creates Jmol applications for educational use, like this one, which animates rotational and vibrational energy states in water:
for water : Electrostatic potential maps
the strengths of interaction between methane, methane-water, and water dimer is due to their differences in polarity, which can be visualized using molecular electrostatic potentials (MEPs):
with  interactive Jmol versions with java:

When molecules (CH4 and H20) attract:

The molecular dimers shown in Figure 4.14 have very different interaction energies: -0.5, -1.0, -0.6, and -5.1 kcal/mol, respectively; which are reasonably well reproduced at the M06/6-31+G(2d,p)// M06/6-31G(d) level of theory: -0.4, -0.5, 0.0, and -4.9 kcal/mol.
The source of this difference in intermolecular attraction can be easily visualized with electrostatic potential maps (Figure 4.15). Methane is non-polar and the main source of attraction in the methane dimer is dispersive forces (which are hard to visualize). Water is polar, and the methane–water interaction (where the water is the H-donor) is a bit stronger than the methane dimer. This is due to an electrostatic interaction - more specifically polarization, but more about this in a future post.
0.002 au isodensity surface with superimposed molecular electrostatic potential for (a) methane dimer, (b) water–methane dimer where water acts as an H-bond donor, (c) water–methane dimer where methane acts as an H-bond donor, and (d) water dimer. The maximum potential value is 0.05 au and the level of theory is M06/6-31+G(2d,p)//M06/6-31G(d).

Instructions on how to make interactive electrostatic potential maps with Jmol can be found hereFinally, I introduce a new feature (pop-up windows) to the blog because I can't figure out how to include Jmol buttons (which gives more control to the viewer) into blog posts. This feature also gives you access to the underlying GAMESS files as I have discussed here.


0.002 au isodensity surface with superimposed electrostatic potential of (a) Li+, (b) Na+, and (c) K+ ion. The maximum potential value is 0.8 au, and the level of theory is B3LYP/6-31G(d).

Why does the ionization energy decrease on from Li to Na to K? That's the same as asking why the electron affinities decrease on going from Li+ to Na+ to K+.

This Figure shows the ions colored by how positive they are at the surface (i.e. the electrostatic potential superimposed on the 0.002 isodensity surface). The darker the
color the more positive the ion, and it is clear that the Li+ ion is “more positive” than Na+, which is more positive than K+. Thus, more energy should be released when adding an electron to Li+ compared to Na+, and hence more energy is needed to remove an electron from Li
compared to Na (and similarly for K).

The reason why Li+ is “more positive” than Na+ or, more accurately, why the potential on the 0.002 au isodensity surface is more positive for Li+ than for Na+, is that the former is a smaller ion than the latter, so the surface is closer to the +1 charge at the center of the ion.

When making these figures it is very important to get the relative sizes of the ions correct, but this can be difficult since each image can be zoomed to an arbitrary size. He shows how to control this in MacMolPlt using the Manual Windows Parameter window.

"Ex-amples" with HF and "monopole, dipole, quadrupole":

Contour plot of the RHF/6-31G(d) electrostatic potential and 0.002 au isodensity surface of (a) CH3COO-, (b) HF, and (c) F2. The maximum/minimum contour values are, respectively, 0.5/0.025; 0.1/0.005; and 0.005/0.00025 au respectively. Blue corresponds to a negative potential. In each case the outer-most contour looks like the corresponding contour in the electrostatic potential due to a charge, dipole, and quadrupole, respectively.
Rotating molecules in PowerPoint
2 ways of doing this that are relatively easy.
One is to create an animated gif file using the Polyview3D web server, and inserting the file as a movie in Powerpoint. With polyview3D many choices (pymol or rasmol)
 Another option is to set the molecule spinning in, for example, Avogadro and then simply record part of the screen using a screencasting program (for example  Screencast-o-matic is free, and can make mp4 files, which can be included in Powerpoint).